#ID(s) interactor A ID(s) interactor B Alt. ID(s) interactor A Alt. ID(s) interactor B Alias(es) interactor A Alias(es) interactor B Interaction detection method(s) Publication 1st author(s) Publication Identifier(s) Taxid interactor A Taxid interactor B Interaction type(s) Source database(s) Interaction identifier(s) Confidence value(s) Expansion method(s) Biological role(s) interactor A Biological role(s) interactor B Experimental role(s) interactor A Experimental role(s) interactor B Type(s) interactor A Type(s) interactor B Xref(s) interactor A Xref(s) interactor B Interaction Xref(s) Annotation(s) interactor A Annotation(s) interactor B Interaction annotation(s) Host organism(s) Interaction parameter(s) Creation date Update date Checksum(s) interactor A Checksum(s) interactor B Interaction Checksum(s) Negative Feature(s) interactor A Feature(s) interactor B Stoichiometry(s) interactor A Stoichiometry(s) interactor B Identification method participant A Identification method participant B uniprotkb:O95983 uniprotkb:Q16576 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-352227|ensembl:ENSP00000369427|intact:EBI-3505029|uniprotkb:Q5JP00 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:rbbp7_human(display_long)|uniprotkb:RBBP7(gene name)|psi-mi:RBBP7(display_short)|uniprotkb:RBAP46(gene name synonym)|uniprotkb:Retinoblastoma-binding protein 7(gene name synonym)|uniprotkb:Retinoblastoma-binding protein p46(gene name synonym)|uniprotkb:Histone acetyltransferase type B subunit 2(gene name synonym)|uniprotkb:Nucleosome-remodeling factor subunit RBAP46(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_002884.1|ensembl:ENST00000380087(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0003723"(RNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006260"(DNA replication)|go:"GO:0006325"(chromatin organization)|go:"GO:0016581"(NuRD complex)|go:"GO:0030308"(negative regulation of cell growth)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042393"(histone binding)|go:"GO:0048545"(response to steroid hormone)|go:"GO:0070370"(cellular heat acclimation)|interpro:IPR001680(WD40 repeat)|interpro:IPR015943(WD40/YVTN repeat-like)|interpro:IPR019775|interpro:IPR020472|interpro:IPR022052|interpro:IPR036322|mint:Q16576|rcsb pdb:3CFS|rcsb pdb:3CFV|rcsb pdb:7M3X|reactome:R-HSA-212300|reactome:R-HSA-2559580|reactome:R-HSA-3214815|reactome:R-HSA-3214841|reactome:R-HSA-3214847|reactome:R-HSA-3214858|reactome:R-HSA-427389|reactome:R-HSA-5617472|reactome:R-HSA-606279|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-8951664|reactome:R-HSA-8953750|reactome:R-HSA-9609690|reactome:R-HSA-9679191|reactome:R-HSA-9710421|ensembl:ENSG00000102054(gene)|refseq:NP_001185648.1|dip:DIP-436N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:qANLG0ui7jm3Uy4+IRnxR8Kir7c9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q09028 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-620823|uniprotkb:B4DRH0|ensembl:ENSP00000362592|uniprotkb:P31149|uniprotkb:Q53H02|uniprotkb:Q96BV9|uniprotkb:D3DPQ3|uniprotkb:B2R6G9 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:rbbp4_human(display_long)|uniprotkb:Retinoblastoma-binding protein 4(gene name synonym)|uniprotkb:Retinoblastoma-binding protein p48(gene name synonym)|uniprotkb:Chromatin assembly factor 1 subunit C(gene name synonym)|uniprotkb:Chromatin assembly factor I p48 subunit(gene name synonym)|uniprotkb:Nucleosome-remodeling factor subunit RBAP48(gene name synonym)|uniprotkb:RBBP4(gene name)|psi-mi:RBBP4(display_short)|uniprotkb:RBAP48(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSG00000162521(gene)|ensembl:ENST00000373493(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000785"(chromatin)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006260"(DNA replication)|go:"GO:0006335"(DNA replication-dependent chromatin assembly)|go:"GO:0006336"(DNA replication-independent chromatin assembly)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0007049"(cell cycle)|go:"GO:0008285"(negative regulation of cell population proliferation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0016589"(NURF complex)|go:"GO:0031497"(chromatin assembly)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033186"(CAF-1 complex)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042393"(histone binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|interpro:IPR001680(WD40 repeat)|interpro:IPR015943(WD40/YVTN repeat-like)|interpro:IPR019775|interpro:IPR020472|interpro:IPR022052|mint:Q09028|rcsb pdb:2XU7|rcsb pdb:3GFC|rcsb pdb:4PBY|rcsb pdb:4PBZ|rcsb pdb:4PC0|rcsb pdb:4R7A|rcsb pdb:5FXY|rcsb pdb:5VTB|rcsb pdb:5WAI|rcsb pdb:5WAK|rcsb pdb:5XWR|rcsb pdb:5XXQ|rcsb pdb:5Y1U|rcsb pdb:6BW3|rcsb pdb:6BW4|rcsb pdb:6C23|rcsb pdb:6C24|rcsb pdb:6G16|rcsb pdb:6NQ3|rcsb pdb:6WKR|rcsb pdb:6ZRC|rcsb pdb:6ZRD|rcsb pdb:7AOA|rcsb pdb:7KSO|rcsb pdb:7KSR|rcsb pdb:7KTP|rcsb pdb:7M40|reactome:R-HSA-1362277|reactome:R-HSA-1362300|reactome:R-HSA-1538133|reactome:R-HSA-156711|reactome:R-HSA-212300|reactome:R-HSA-2559580|reactome:R-HSA-3214815|reactome:R-HSA-3214841|reactome:R-HSA-427389|reactome:R-HSA-5617472|reactome:R-HSA-606279|reactome:R-HSA-6804758|reactome:R-HSA-69202|reactome:R-HSA-69205|reactome:R-HSA-69656|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-8953750|reactome:R-HSA-9609690|reactome:R-HSA-9679191|reactome:R-HSA-9710421|interpro:IPR036322|refseq:NP_001128727.1|refseq:NP_001128728.1|refseq:NP_005601.1|dip:DIP-33495N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:CbyJMIjpW1A4sZijP0IGRYc8o4I9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q8TDI0 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-1042816|uniprotkb:O75032|uniprotkb:Q5TG89|uniprotkb:Q9UFR9|uniprotkb:Q7LGH2|intact:EBI-28978813|ensembl:ENSP00000262450 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:chd5_human(display_long)|uniprotkb:CHD5(gene name)|psi-mi:CHD5(display_short)|uniprotkb:KIAA0444(gene name synonym)|uniprotkb:ATP-dependent helicase CHD5(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSP00000262450|refseq:NP_056372.1|ensembl:ENSG00000116254(gene)|ensembl:ENST00000262450(transcript)|go:"GO:0000792"(heterochromatin)|go:"GO:0003677"(DNA binding)|go:"GO:0003678"(DNA helicase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0008285"(negative regulation of cell population proliferation)|go:"GO:0016020"(membrane)|go:"GO:0016581"(NuRD complex)|go:"GO:0016607"(nuclear speck)|go:"GO:0021895"(cerebral cortex neuron differentiation)|go:"GO:0035093"(spermatogenesis, exchange of chromosomal proteins)|go:"GO:0043967"(histone H4 acetylation)|go:"GO:0046872"(metal ion binding)|go:"GO:0061628"(H3K27me3 modified histone binding)|go:"GO:0070615"|go:"GO:0098532"(histone H3-K27 trimethylation)|go:"GO:1901798"(positive regulation of signal transduction by p53 class mediator)|interpro:IPR000330(SNF2-related)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|interpro:IPR000953(Chromo domain)|interpro:IPR001650(DNA/RNA helicase, C-terminal)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002464(DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site)|interpro:IPR009462(Protein of unknown function DUF1086)|interpro:IPR009463(Protein of unknown function DUF1087)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR012957(CHD, C-terminal 2)|interpro:IPR012958(CHD, N-terminal)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR014001(DEAD-like helicase, N-terminal)|interpro:IPR016197(Chromo domain-like)|interpro:IPR019786|interpro:IPR019787|interpro:IPR023780|interpro:IPR027417|interpro:IPR028727|interpro:IPR038718|mint:Q8TDI0|rcsb pdb:6GUU go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:LHBjWFoo0asvv1GpRsGBz1gN9gM9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:P52292 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-349938|uniprotkb:Q9BRU5|ensembl:ENSP00000504685|intact:EBI-28977049|ensembl:ENSP00000332455|ensembl:ENSP00000438483|ensembl:ENSP00000462331|ensembl:ENSP00000463602|ensembl:ENSP00000504655|uniprotkb:B9EJD6|uniprotkb:Q53YE3|intact:EBI-9377406|uniprotkb:Q6NVW7 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:ima1_human(display_long)|uniprotkb:KPNA2(gene name)|psi-mi:KPNA2(display_short)|uniprotkb:RCH1(gene name synonym)|uniprotkb:SRP1(gene name synonym)|uniprotkb:Karyopherin subunit alpha-2(gene name synonym)|uniprotkb:SRP1-alpha(gene name synonym)|uniprotkb:RAG cohort protein 1(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_002257.1|refseq:NP_001307540.1|ensembl:ENST00000330459(transcript)|ensembl:ENST00000537025(transcript)|ensembl:ENST00000579754(transcript)|ensembl:ENST00000584026(transcript)|ensembl:ENST00000677086(transcript)|ensembl:ENST00000679078(transcript)|go:"GO:0000018"(regulation of DNA recombination)|go:"GO:0000139"(Golgi membrane)|go:"GO:0003723"(RNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005789"(endoplasmic reticulum membrane)|go:"GO:0005829"(cytosol)|go:"GO:0006259"(DNA metabolic process)|go:"GO:0006607"(NLS-bearing protein import into nucleus)|go:"GO:0008139"(nuclear localization sequence binding)|go:"GO:0016020"(membrane)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043657"(host cell)|go:"GO:0061608"(nuclear import signal receptor activity)|go:"GO:0075506"(entry of viral genome into host nucleus through nuclear pore complex via importin)|go:"GO:0098892"(extrinsic component of postsynaptic specialization membrane)|go:"GO:0098978"(glutamatergic synapse)|go:"GO:0099527"(postsynapse to nucleus signaling pathway)|go:"GO:1903902"(positive regulation of viral life cycle)|interpro:IPR000225(Armadillo)|interpro:IPR002652(Importin-alpha-like, importin-beta-binding region)|interpro:IPR011989(Armadillo-like helical)|interpro:IPR016024(Armadillo-type fold)|interpro:IPR024931|interpro:IPR032413|interpro:IPR036975|mint:P52292|rcsb pdb:1EFX|rcsb pdb:1QGK|rcsb pdb:1QGR|rcsb pdb:3FEX|ensembl:ENSG00000182481(gene)|rcsb pdb:3FEY|rcsb pdb:3WPT|rcsb pdb:4E4V|rcsb pdb:4WV6|rcsb pdb:5H43|rcsb pdb:7N8J|reactome:R-HSA-111932|reactome:R-HSA-1169408|reactome:R-HSA-168276|reactome:R-HSA-442729|reactome:R-HSA-5693548|reactome:R-HSA-9018519|ensembl:ENSP00000332455|ensembl:ENSP00000438483|ensembl:ENSP00000462331|ensembl:ENSP00000463602|ensembl:ENSP00000504655|ensembl:ENSP00000504685|dip:DIP-6205N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:DFtAbvPxkzWJO/fRLPGxA6pEEJQ9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q13330 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-714236|uniprotkb:Q8NFI8|uniprotkb:Q96GI8|uniprotkb:A5PLK4|intact:EBI-28976623|ensembl:ENSP00000333633|uniprotkb:Q86SW2 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:mta1_human(display_long)|uniprotkb:MTA1(gene name)|psi-mi:MTA1(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_001190187.1|refseq:NP_004680.2|ensembl:ENSP00000333633|ensembl:ENST00000405646|ensembl:ENSP00000384180|ensembl:ENST00000438610|ensembl:ENSP00000393438|ensembl:ENSG00000182979(gene)|ensembl:ENST00000331320(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|reactome:R-HSA-427389|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|reactome:R-HSA-3232118|go:"GO:0005635"(nuclear envelope)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0006302"(double-strand break repair)|go:"GO:0007165"(signal transduction)|go:"GO:0008270"(zinc ion binding)|go:"GO:0010212"(response to ionizing radiation)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0040029"(regulation of gene expression, epigenetic)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043153"(entrainment of circadian clock by photoperiod)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0005634"(nucleus)|go:"GO:0043231"(intracellular membrane-bounded organelle)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:1902499"(positive regulation of protein autoubiquitination)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR017930|interpro:IPR035170|interpro:IPR040138|mint:Q13330|rcsb pdb:4BKX|rcsb pdb:4PBY|rcsb pdb:4PBZ|rcsb pdb:4PC0|rcsb pdb:5FXY|rcsb pdb:5ICN|rcsb pdb:6G16|rcsb pdb:6ZRC|rcsb pdb:6ZRD|rcsb pdb:7AO8|go:"GO:0045475"(locomotor rhythm)|rcsb pdb:7AO9|rcsb pdb:7AOA|reactome:R-HSA-3214815|dip:DIP-41751N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:nDDSb5B6YCbq5/6qvgtnUWtP23M9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q14839 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-372916|uniprotkb:Q8IXZ5|intact:EBI-28978241|ensembl:ENSP00000440542 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:chd4_human(display_long)|uniprotkb:CHD4(gene name)|psi-mi:CHD4(display_short)|uniprotkb:ATP-dependent helicase CHD4(gene name synonym)|uniprotkb:Mi-2 autoantigen 218 kDa protein(gene name synonym)|uniprotkb:Mi2-beta(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSP00000440542|ensembl:ENST00000645095|ensembl:ENSP00000496634|refseq:NP_001264.2|refseq:XP_006719021.1|refseq:NP_001284482.1|ensembl:ENSG00000111642(gene)|ensembl:ENST00000544040(transcript)|go:"GO:0000785"(chromatin)|go:"GO:0001221"(transcription coregulator binding)|go:"GO:0003677"(DNA binding)|go:"GO:0003678"(DNA helicase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005813"(centrosome)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016020"(membrane)|go:"GO:0016581"(NuRD complex)|go:"GO:0032991"(protein-containing complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070615"|go:"GO:0090575"(RNA polymerase II transcription regulator complex)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|interpro:IPR000330(SNF2-related)|interpro:IPR000953(Chromo domain)|interpro:IPR001650(DNA/RNA helicase, C-terminal)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002464(DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site)|interpro:IPR009462(Protein of unknown function DUF1086)|interpro:IPR009463(Protein of unknown function DUF1087)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR012957(CHD, C-terminal 2)|interpro:IPR012958(CHD, N-terminal)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR014001(DEAD-like helicase, N-terminal)|interpro:IPR016197(Chromo domain-like)|interpro:IPR019786|interpro:IPR019787|interpro:IPR023780|interpro:IPR027417|interpro:IPR038718|mint:Q14839|rcsb pdb:1MM2|rcsb pdb:1MM3|rcsb pdb:2EE1|rcsb pdb:2L5U|rcsb pdb:2L75|rcsb pdb:2N5N|rcsb pdb:4O9I|rcsb pdb:6BGG|rcsb pdb:6Q3M|rcsb pdb:6RYR|rcsb pdb:6RYU|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9031628|reactome:R-HSA-9679191|dip:DIP-31183N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:E9eHT/41SIFRiz54J81hvPQeHIE9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:O94776 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-1783035|uniprotkb:Q68DB1|uniprotkb:Q9UQB5|ensembl:ENSP00000278823 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:mta2_human(display_long)|uniprotkb:MTA2(gene name)|psi-mi:MTA2(display_short)|uniprotkb:MTA1L1(gene name synonym)|uniprotkb:PID(gene name synonym)|uniprotkb:Metastasis-associated 1-like 1(gene name synonym)|uniprotkb:p53 target protein in deacetylase complex(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_004730.2|refseq:NP_001317221.1|dip:DIP-46519N|ensembl:ENSG00000149480(gene)|ensembl:ENST00000278823(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005667"(transcription regulator complex)|go:"GO:0006306"(DNA methylation)|go:"GO:0006333"(chromatin assembly or disassembly)|go:"GO:0008270"(zinc ion binding)|go:"GO:0010762"(regulation of fibroblast migration)|go:"GO:0016020"(membrane)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0032991"(protein-containing complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR035170|interpro:IPR037964|interpro:IPR040138|interpro:IPR043151|mint:O94776|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:D4wOsdMJYhY/ltvcnnuMHqNrFkc9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q92769 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-301821|uniprotkb:Q5SRI8|uniprotkb:Q5SZ86|uniprotkb:Q8NEH4|uniprotkb:B4DL58|ensembl:ENSP00000430432|uniprotkb:E1P561|uniprotkb:B3KRS5 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:hdac2_human(display_long)|uniprotkb:HDAC2(gene name)|psi-mi:HDAC2(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0008134"(transcription factor binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0009913"(epidermal cell differentiation)|go:"GO:0010718"(positive regulation of epithelial to mesenchymal transition)|go:"GO:0010977"(negative regulation of neuron projection development)|go:"GO:0016358"(dendrite development)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0019213"(deacetylase activity)|go:"GO:0019899"(enzyme binding)|go:"GO:0031000"(response to caffeine)|go:"GO:0031072"(heat shock protein binding)|go:"GO:0032041"("NAD-dependent histone deacetylase activity (H3-K14 specific)")|go:"GO:0032496"(response to lipopolysaccharide)|go:"GO:0032732"(positive regulation of interleukin-1 production)|go:"GO:0032760"(positive regulation of tumor necrosis factor production)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0032967"(positive regulation of collagen biosynthetic process)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033558"(protein deacetylase activity)|go:"GO:0034605"(cellular response to heat)|go:"GO:0035094"(response to nicotine)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042220"(response to cocaine)|go:"GO:0042475"(odontogenesis of dentin-containing tooth)|go:"GO:0042493"|go:"GO:0042531"(positive regulation of tyrosine phosphorylation of STAT protein)|go:"GO:0042733"(embryonic digit morphogenesis)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0043066"(negative regulation of apoptotic process)|go:"GO:0043392"(negative regulation of DNA binding)|go:"GO:0043433"(negative regulation of DNA-binding transcription factor activity)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045347"(negative regulation of MHC class II biosynthetic process)|go:"GO:0045862"(positive regulation of proteolysis)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0048149"(behavioral response to ethanol)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0051059"(NF-kappaB binding)|go:"GO:0055093"(response to hyperoxia)|go:"GO:0060789"(hair follicle placode formation)|go:"GO:0061000"(negative regulation of dendritic spine development)|go:"GO:0061029"(eyelid development in camera-type eye)|go:"GO:0061198"(fungiform papilla formation)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070301"(cellular response to hydrogen peroxide)|go:"GO:0070829"(obsolete heterochromatin maintenance)|go:"GO:0070932"(histone H3 deacetylation)|go:"GO:0070933"(histone H4 deacetylation)|go:"GO:0071300"(cellular response to retinoic acid)|go:"GO:0071560"(cellular response to transforming growth factor beta stimulus)|go:"GO:1902437"(positive regulation of male mating behavior)|go:"GO:1903351"(cellular response to dopamine)|go:"GO:1990841"(promoter-specific chromatin binding)|go:"GO:2000273"(positive regulation of signaling receptor activity)|go:"GO:2000757"(negative regulation of peptidyl-lysine acetylation)|interpro:IPR000286(Histone deacetylase superfamily)|interpro:IPR003084(Histone deacetylase)|interpro:IPR023696|interpro:IPR023801|interpro:IPR037138|mint:Q92769|rcsb pdb:3MAX|rcsb pdb:4LXZ|rcsb pdb:4LY1|rcsb pdb:5IWG|rcsb pdb:5IX0|rcsb pdb:6G3O|rcsb pdb:6WBW|go:"GO:0048714"(positive regulation of oligodendrocyte differentiation)|ensembl:ENSG00000196591(gene)|ensembl:ENST00000519065(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0001975"(response to amphetamine)|go:"GO:0003300"(cardiac muscle hypertrophy)|go:"GO:0003682"(chromatin binding)|go:"GO:0003723"(RNA binding)|rcsb pdb:6WHN|rcsb pdb:6WHO|rcsb pdb:6WHQ|rcsb pdb:6WHZ|rcsb pdb:6WI3|rcsb pdb:6XDM|rcsb pdb:6XEB|rcsb pdb:6XEC|rcsb pdb:7KBG|rcsb pdb:7KBH|rcsb pdb:7LTG|rcsb pdb:7LTK|rcsb pdb:7LTL|reactome:R-HSA-193670|reactome:R-HSA-2122947|reactome:R-HSA-2644606|reactome:R-HSA-2894862|reactome:R-HSA-3214815|reactome:R-HSA-350054|reactome:R-HSA-427389|reactome:R-HSA-427413|reactome:R-HSA-4551638|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9022692|reactome:R-HSA-9022699|reactome:R-HSA-9615017|reactome:R-HSA-9619665|reactome:R-HSA-9679191|reactome:R-HSA-983231|rcsb pdb:6WBZ|refseq:NP_001518.3|dip:DIP-24220N|refseq:XP_011534090.1|refseq:XP_016866288.1 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:K4PpGz9E9/TrQZsgvrJuc+uYCn89606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q9HCE3 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-9691987|uniprotkb:Q4G0V6|uniprotkb:Q7L7Z7|uniprotkb:Q96QR7|uniprotkb:Q9NVJ6|intact:EBI-28972886|ensembl:ENSP00000338217|ensembl:ENSP00000465709|ensembl:ENSP00000466007|ensembl:ENSP00000468238|ensembl:ENSP00000468532 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:zn532_human(display_long)|uniprotkb:ZNF532(gene name)|psi-mi:ZNF532(display_short)|uniprotkb:KIAA1629(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSP00000338217|ensembl:ENSP00000466007|ensembl:ENSP00000468532|ensembl:ENSP00000465709|ensembl:ENSP00000468238|refseq:NP_001305655.1|refseq:NP_001305656.1|refseq:NP_001305657.1|refseq:XP_016881301.1|refseq:XP_016881302.1|refseq:XP_016881303.1|refseq:XP_016881304.1|refseq:XP_016881305.1|refseq:XP_016881306.1|refseq:XP_016881307.1|refseq:NP_060651.2|ensembl:ENSG00000074657(gene)|ensembl:ENST00000336078(transcript)|ensembl:ENST00000589288(transcript)|ensembl:ENST00000591083(transcript)|ensembl:ENST00000591230(transcript)|ensembl:ENST00000591808(transcript)|go:"GO:0003677"(DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0046872"(metal ion binding)|interpro:IPR013087(Zinc finger, C2H2-type/integrase, DNA-binding)|interpro:IPR036236|interpro:IPR041697 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:cML0j1IoxCUTQDtyZ/XyeEbtsCM9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q12873 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-523590|uniprotkb:Q9Y4I0|intact:EBI-28978117|ensembl:ENSP00000332628|uniprotkb:D3DTQ9|uniprotkb:E9PG89 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:chd3_human(display_long)|uniprotkb:ATP-dependent helicase CHD3(gene name synonym)|uniprotkb:Mi-2 autoantigen 240 kDa protein(gene name synonym)|uniprotkb:Mi2-alpha(gene name synonym)|uniprotkb:Zinc finger helicase(gene name synonym)|uniprotkb:CHD3(gene name)|psi-mi:CHD3(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 interpro:IPR023780|interpro:IPR027417|interpro:IPR036910|interpro:IPR038718|mint:Q12873|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-4551638|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|ensembl:ENSG00000170004(gene)|ensembl:ENST00000330494(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000976"(transcription cis-regulatory region binding)|go:"GO:0003677"(DNA binding)|go:"GO:0003678"(DNA helicase activity)|go:"GO:0003723"(RNA binding)|go:"GO:0004386"(helicase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005730"(nucleolus)|go:"GO:0005737"(cytoplasm)|go:"GO:0005813"(centrosome)|go:"GO:0006333"(chromatin assembly or disassembly)|go:"GO:0006355"(regulation of transcription, DNA-templated)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0007051"(spindle organization)|go:"GO:0007098"(centrosome cycle)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016581"(NuRD complex)|go:"GO:0016605"(PML body)|go:"GO:0034451"(centriolar satellite)|go:"GO:0036121"(double-stranded DNA helicase activity)|go:"GO:0043044"|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR012957(CHD, C-terminal 2)|interpro:IPR012958(CHD, N-terminal)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR014001(DEAD-like helicase, N-terminal)|interpro:IPR016197(Chromo domain-like)|interpro:IPR019786|go:"GO:0070615"|interpro:IPR019787|interpro:IPR023779|go:"GO:0140603"(obsolete ATP hydrolysis activity)|interpro:IPR000330(SNF2-related)|interpro:IPR000953(Chromo domain)|interpro:IPR001650(DNA/RNA helicase, C-terminal)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002464(DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site)|interpro:IPR009462(Protein of unknown function DUF1086)|interpro:IPR009463(Protein of unknown function DUF1087)|ensembl:ENSP00000332628|ensembl:ENST00000358181|ensembl:ENSP00000350907|ensembl:ENST00000380358|ensembl:ENSP00000369716|refseq:NP_001005271.2|refseq:NP_001005273.1|refseq:NP_005843.2|dip:DIP-32496N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:UjefFUXiV28qhOP9BoIUansxl+k9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:O14519 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q8N1G0 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-1210558|uniprotkb:Q68DQ8|uniprotkb:Q9H937|uniprotkb:Q9P2A7|uniprotkb:D3DV17|ensembl:ENSP00000319829|ensembl:ENSP00000336620 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:zn687_human(display_long)|uniprotkb:ZNF687(gene name)|psi-mi:ZNF687(display_short)|uniprotkb:KIAA1441(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_001291692.1|refseq:NP_065883.1|refseq:NP_001291693.1|refseq:XP_011508114.1|refseq:XP_011508115.1|ensembl:ENSG00000143373(gene)|ensembl:ENST00000324048(transcript)|ensembl:ENST00000336715(transcript)|go:"GO:0003677"(DNA binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0046872"(metal ion binding)|interpro:IPR013087(Zinc finger, C2H2-type/integrase, DNA-binding)|interpro:IPR036236|interpro:IPR041697|mint:Q8N1G0 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:NR6q/E7oFHWVxeOkmRTyG6HKTvQ9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q9BTC8 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-2461787|uniprotkb:Q9NSP2|uniprotkb:Q9ULF4|ensembl:ENSP00000385823 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:mta3_human(display_long)|uniprotkb:MTA3(gene name)|psi-mi:MTA3(display_short)|uniprotkb:KIAA1266(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_001269684.1|refseq:NP_001269685.1|refseq:NP_065795.1|refseq:NP_001317371.1|dip:DIP-47460N|ensembl:ENST00000405094(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0008270"(zinc ion binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0010971"(positive regulation of G2/M transition of mitotic cell cycle)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043231"(intracellular membrane-bounded organelle)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0044877"(protein-containing complex binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR017930|interpro:IPR035170|interpro:IPR040138|interpro:IPR043151|mint:Q9BTC8|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|ensembl:ENSG00000057935(gene) go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:wxPsfH6FguY8n4PFwaj1iJNTWPc9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q92610 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-1210420|uniprotkb:Q2M1T2|uniprotkb:Q504Y9|ensembl:ENSP00000299927|ensembl:ENSP00000452877 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:zn592_human(display_long)|uniprotkb:ZNF592(gene name)|psi-mi:ZNF592(display_short)|uniprotkb:KIAA0211(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:XP_011520548.1|refseq:XP_011520549.1|refseq:XP_005255053.1|refseq:NP_055445.2|refseq:XP_016878223.1|ensembl:ENSG00000166716(gene)|ensembl:ENST00000299927(transcript)|ensembl:ENST00000560079(transcript)|go:"GO:0003677"(DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0046872"(metal ion binding)|interpro:IPR013087(Zinc finger, C2H2-type/integrase, DNA-binding)|interpro:IPR036236|interpro:IPR041697 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:eElXHEWfzjVaiLf6Ns2u5SBqhKs9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q86YP4 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-726224|uniprotkb:Q7L3J2|uniprotkb:Q96F28|uniprotkb:Q9NPU2|uniprotkb:Q9NXS1|uniprotkb:B5MC40|ensembl:ENSP00000351552|ensembl:ENSP00000353463 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:p66a_human(display_long)|uniprotkb:GATA zinc finger domain-containing protein 2A(gene name synonym)|uniprotkb:GATAD2A(gene name)|psi-mi:GATAD2A(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_060130.3|refseq:NP_001287875.1|refseq:XP_011526407.1|ensembl:ENSG00000167491(gene)|ensembl:ENST00000358713(transcript)|ensembl:ENST00000360315(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0006306"(DNA methylation)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016581"(NuRD complex)|go:"GO:0016607"(nuclear speck)|go:"GO:0030674"(protein-macromolecule adaptor activity)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR032346|interpro:IPR040386|mint:Q86YP4|rcsb pdb:2L2L|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|dip:DIP-36053N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:s2G27yMihH9d7ny/v1GZ7aeTpDQ9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q9UJQ4 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-9692025|uniprotkb:A2A2D8|uniprotkb:Q540H3|uniprotkb:Q6Y8G6|ensembl:ENSP00000217086 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:sall4_human(display_long)|uniprotkb:SALL4(gene name)|psi-mi:SALL4(display_short)|uniprotkb:ZNF797(gene name synonym)|uniprotkb:Zinc finger protein 797(gene name synonym)|uniprotkb:Zinc finger protein SALL4(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_001304960.1|refseq:NP_065169.1|ensembl:ENST00000217086(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000792"(heterochromatin)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0000981"(DNA-binding transcription factor activity, RNA polymerase II-specific)|go:"GO:0001833"(inner cell mass cell proliferation)|go:"GO:0001843"(neural tube closure)|go:"GO:0003281"(ventricular septum development)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0019827"(stem cell population maintenance)|go:"GO:0030326"(embryonic limb morphogenesis)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043231"(intracellular membrane-bounded organelle)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0046872"(metal ion binding)|interpro:IPR013087(Zinc finger, C2H2-type/integrase, DNA-binding)|interpro:IPR036236|rcsb pdb:5XWR|rcsb pdb:6UML|rcsb pdb:7BQU|rcsb pdb:7BQV|reactome:R-HSA-2892247|reactome:R-HSA-452723|reactome:R-HSA-8943724|ensembl:ENSG00000101115(gene) go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:0YCBo+3W7AsmZQM2JxbG5PoLwkU9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q8WXI9 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-923440|uniprotkb:Q5VUR2|uniprotkb:Q7LG68|uniprotkb:Q9ULS0|uniprotkb:D3DUZ2|ensembl:ENSP00000357644|ensembl:ENSP00000458280|ensembl:ENSP00000489184 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:p66b_human(display_long)|uniprotkb:GATAD2B(gene name)|psi-mi:GATAD2B(display_short)|uniprotkb:KIAA1150(gene name synonym)|uniprotkb:p66/p68(gene name synonym)|uniprotkb:GATA zinc finger domain-containing protein 2B(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_065750.1|refseq:XP_005245421.1|dip:DIP-36054N|ensembl:ENSG00000143614(gene)|ensembl:ENSG00000261992(gene)|ensembl:ENST00000368655(transcript)|ensembl:ENST00000576342(transcript)|ensembl:ENST00000634544(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0005654"(nucleoplasm)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016581"(NuRD complex)|go:"GO:0016607"(nuclear speck)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0043565"(sequence-specific DNA binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR013088(Zinc finger, NHR/GATA-type)|interpro:IPR032346|interpro:IPR040386|mint:Q8WXI9|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:pLKkMcJBBWdyMTf+2axWzvZLKP09606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q9ULU4 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-765834|uniprotkb:Q13517|uniprotkb:Q4JJ94|uniprotkb:Q4JJ95|uniprotkb:Q5TH09|uniprotkb:Q6MZM1|uniprotkb:Q8WXC5|uniprotkb:Q9H1F3|uniprotkb:Q9H1F4|uniprotkb:Q9H1F5|uniprotkb:Q9H1L8|uniprotkb:Q9H1L9|uniprotkb:Q9H2G5|uniprotkb:Q9NYN3|uniprotkb:Q9UIX6|uniprotkb:Q2HXV7|uniprotkb:E1P5U5|uniprotkb:B7Z680|uniprotkb:Q2HXV2|uniprotkb:Q2HXV8|uniprotkb:Q2HXW0|uniprotkb:Q2HXW1|uniprotkb:Q2HXW2|uniprotkb:Q2HXV4|uniprotkb:Q2HXV9|uniprotkb:B3KVL2|uniprotkb:B7Z2A8|uniprotkb:B7Z3E0|uniprotkb:B7ZM62|uniprotkb:F5H0X3|uniprotkb:H7C0U2|uniprotkb:J3KPU3|uniprotkb:Q2HXV1|uniprotkb:Q2HXV3|uniprotkb:Q5TH11|ensembl:ENSP00000312237 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:pkcb1_human(display_long)|uniprotkb:Rack7(gene name synonym)|uniprotkb:Cutaneous T-cell lymphoma-associated antigen se14-3(gene name synonym)|uniprotkb:Zinc finger MYND domain-containing protein 8(gene name synonym)|uniprotkb:ZMYND8(gene name)|psi-mi:ZMYND8(display_short)|uniprotkb:KIAA1125(gene name synonym)|uniprotkb:RACK7(gene name synonym)|uniprotkb:PRKCBP1(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_036540.3|refseq:NP_898868.1|refseq:NP_898869.1|refseq:XP_011527053.1|refseq:NP_001268711.1|refseq:NP_001268706.1|refseq:NP_001268710.1|ensembl:ENST00000262975|ensembl:ENSP00000262975|ensembl:ENSP00000312237|ensembl:ENST00000352431|ensembl:ENSP00000335537|ensembl:ENST00000355972|ensembl:ENSP00000348246|ensembl:ENST00000360911|ensembl:ENSP00000354166|ensembl:ENST00000372023|ensembl:ENSP00000361093|ensembl:ENST00000396281|ensembl:ENSP00000379577|refseq:NP_001268702.1|refseq:NP_001268703.1|refseq:NP_001268704.1|refseq:NP_001268705.1|refseq:NP_001268707.1|refseq:NP_001268712.1|refseq:XP_005260417.1|refseq:XP_005260423.1|ensembl:ENST00000446994|ensembl:ENSP00000396725|ensembl:ENST00000458360|ensembl:ENSP00000392964|ensembl:ENST00000461685|ensembl:ENSP00000418210|ensembl:ENST00000471951|ensembl:ENSP00000420095|ensembl:ENST00000536340|ensembl:ENSP00000439800|ensembl:ENST00000540497|ensembl:ENSP00000443086|refseq:NP_001268713.1|refseq:XP_005260413.1|refseq:NP_001268700.1|refseq:NP_001268701.1|refseq:XP_006723825.1|refseq:XP_016883250.1|refseq:XP_016883256.1|refseq:XP_016883257.1|go:"GO:0005737"(cytoplasm)|go:"GO:0005794"(Golgi apparatus)|go:"GO:0008270"(zinc ion binding)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0030336"(negative regulation of cell migration)|go:"GO:0035064"(methylated histone binding)|go:"GO:0043197"(dendritic spine)|go:"GO:0043198"(dendritic shaft)|go:"GO:0047485"(protein N-terminus binding)|go:"GO:0051491"(positive regulation of filopodium assembly)|go:"GO:0060999"(positive regulation of dendritic spine development)|go:"GO:0070577"(lysine-acetylated histone binding)|go:"GO:0098815"(modulation of excitatory postsynaptic potential)|go:"GO:0140297"(DNA-binding transcription factor binding)|go:"GO:1902897"(regulation of postsynaptic density protein 95 clustering)|go:"GO:1902952"(positive regulation of dendritic spine maintenance)|interpro:IPR000313(PWWP)|interpro:IPR001487(Bromodomain)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002893(Zinc finger, MYND-type)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR019786|interpro:IPR019787|interpro:IPR021931|interpro:IPR035505|interpro:IPR036427|interpro:IPR037967|interpro:IPR044075|mint:Q9ULU4|rcsb pdb:4COS|rcsb pdb:5B73|rcsb pdb:5MQ4|go:"GO:0005654"(nucleoplasm)|rcsb pdb:5Y1Z|ensembl:ENSG00000101040(gene)|ensembl:ENST00000311275(transcript)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0005634"(nucleus) go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:z46jFcDnmKauE75GMeApPZmfdDM9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q13547 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-301834|uniprotkb:Q92534|ensembl:ENSP00000362649 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:hdac1_human(display_long)|uniprotkb:HDAC1(gene name)|psi-mi:HDAC1(display_short)|uniprotkb:RPD3L1(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSG00000116478(gene)|ensembl:ENST00000373548(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0000979"(RNA polymerase II core promoter sequence-specific DNA binding)|go:"GO:0001046"(core promoter sequence-specific DNA binding)|go:"GO:0001975"(response to amphetamine)|go:"GO:0002039"(p53 binding)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006325"(chromatin organization)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0006476"(protein deacetylation)|go:"GO:0007492"(endoderm development)|go:"GO:0008134"(transcription factor binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0008285"(negative regulation of cell population proliferation)|go:"GO:0009913"(epidermal cell differentiation)|go:"GO:0010629"(negative regulation of gene expression)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0019899"(enzyme binding)|go:"GO:0021766"(hippocampus development)|go:"GO:0030182"(neuron differentiation)|go:"GO:0031000"(response to caffeine)|go:"GO:0032041"("NAD-dependent histone deacetylase activity (H3-K14 specific)")|go:"GO:0032496"(response to lipopolysaccharide)|go:"GO:0032732"(positive regulation of interleukin-1 production)|go:"GO:0032760"(positive regulation of tumor necrosis factor production)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033558"(protein deacetylase activity)|go:"GO:0034599"(cellular response to oxidative stress)|go:"GO:0035851"(Krueppel-associated box domain binding)|go:"GO:0042475"(odontogenesis of dentin-containing tooth)|go:"GO:0042493"|go:"GO:0042531"(positive regulation of tyrosine phosphorylation of STAT protein)|go:"GO:0042733"(embryonic digit morphogenesis)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043005"(neuron projection)|go:"GO:0043025"(neuronal cell body)|go:"GO:0043044"|go:"GO:0019213"(deacetylase activity)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070888"(E-box binding)|go:"GO:0070932"(histone H3 deacetylation)|go:"GO:0070933"(histone H4 deacetylation)|go:"GO:0071356"(cellular response to tumor necrosis factor)|go:"GO:0090090"(negative regulation of canonical Wnt signaling pathway)|go:"GO:0140297"(DNA-binding transcription factor binding)|go:"GO:1900221"(regulation of amyloid-beta clearance)|go:"GO:1990841"(promoter-specific chromatin binding)|go:"GO:2000273"(positive regulation of signaling receptor activity)|go:"GO:2000343"("positive regulation of chemokine (C-X-C motif) ligand 2 production")|go:"GO:2000676"(positive regulation of type B pancreatic cell apoptotic process)|go:"GO:2000757"(negative regulation of peptidyl-lysine acetylation)|go:"GO:2001243"(negative regulation of intrinsic apoptotic signaling pathway)|interpro:IPR000286(Histone deacetylase superfamily)|interpro:IPR003084(Histone deacetylase)|interpro:IPR023696|interpro:IPR023801|interpro:IPR037138|mint:Q13547|rcsb pdb:1TYI|rcsb pdb:4BKX|rcsb pdb:5ICN|rcsb pdb:6Z2J|rcsb pdb:6Z2K|rcsb pdb:7AO8|rcsb pdb:7AO9|rcsb pdb:7AOA|reactome:R-HSA-1362277|reactome:R-HSA-1362300|reactome:R-HSA-1538133|reactome:R-HSA-193670|reactome:R-HSA-201722|reactome:R-HSA-2122947|reactome:R-HSA-2173795|reactome:R-HSA-2173796|reactome:R-HSA-2644606|reactome:R-HSA-2894862|reactome:R-HSA-3214815|reactome:R-HSA-350054|reactome:R-HSA-3769402|reactome:R-HSA-427389|reactome:R-HSA-427413|reactome:R-HSA-4551638|reactome:R-HSA-4641265|reactome:R-HSA-6804758|reactome:R-HSA-69205|reactome:R-HSA-73762|reactome:R-HSA-8936459|reactome:R-HSA-8943724|reactome:R-HSA-9018519|reactome:R-HSA-9022538|reactome:R-HSA-9022692|go:"GO:0017053"(transcription repressor complex)|go:"GO:0043066"(negative regulation of apoptotic process)|reactome:R-HSA-9022699|reactome:R-HSA-9022702|reactome:R-HSA-9615017|reactome:R-HSA-9679191|reactome:R-HSA-983231|go:"GO:0043524"(negative regulation of neuron apoptotic process)|go:"GO:0043922"(negative regulation by host of viral transcription)|go:"GO:0044877"(protein-containing complex binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0046676"(negative regulation of insulin secretion)|go:"GO:0047485"(protein N-terminus binding)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0048714"(positive regulation of oligodendrocyte differentiation)|go:"GO:0051059"(NF-kappaB binding)|go:"GO:0052548"(regulation of endopeptidase activity)|go:"GO:0055093"(response to hyperoxia)|go:"GO:0060766"(negative regulation of androgen receptor signaling pathway)|go:"GO:0060789"(hair follicle placode formation)|go:"GO:0061029"(eyelid development in camera-type eye)|go:"GO:0061198"(fungiform papilla formation)|go:"GO:0043124"(negative regulation of I-kappaB kinase/NF-kappaB signaling)|refseq:NP_004955.2|dip:DIP-24184N go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:RP+yIBWH55NgoPTY1nKXqeJL/xY9606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q96KM6 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-1049952|uniprotkb:Q08AK9|uniprotkb:Q9ULM4|ensembl:ENSP00000358904 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:z512b_human(display_long)|uniprotkb:ZNF512B(gene name)|psi-mi:ZNF512B(display_short)|uniprotkb:KIAA1196(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9691985|imex:IM-23066-1 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_065764.1|interpro:IPR013087(Zinc finger, C2H2-type/integrase, DNA-binding)|interpro:IPR036236|mint:Q96KM6|rcsb pdb:2GQJ|reactome:R-HSA-9013424|go:"GO:0046872"(metal ion binding)|ensembl:ENSG00000196700(gene)|ensembl:ENST00000369888(transcript)|go:"GO:0003677"(DNA binding)|go:"GO:0005654"(nucleoplasm)|refseq:XP_011527231.1 go:"GO:0005634"(nucleus) - - figure legend:f1|comment:"To determine the stability of the NuRD complex, several NP-40 and NaCl concentrations were used during the affinity purifications (Fig 1B-D). In each of these pull-downs, known NuRD core subunits were identified. In addition, several previously described NuRD interactors were also detected, including ZMYND8, ZNF592, and SALL4 [8, 14, 17]. Interestingly, we did not pulldown LSD1 in any of our MBD3-GFP purifications. LSD1 has previously been reported as a putative subunit of the NuRD complex [18] but our data on MBD3/NuRD does not agree with this observation. Next, the intensity-based absolute quantification (iBAQ) values were compared between all NuRD subunits and interactors. The iBAQ algorithm normalizes the total mass spec intensity for each protein according to the number of theoretically observable peptides [19]. This allows estimation of the relative abundance of large and small proteins detected in affinity purifications. Since the NuRD complex contains many paralogs that overlap at the peptide level, iBAQ values were summed for all paralogs (Table S1). Comparison of the iBAQ values relative to the GFP-MBD3 bait revealed that most core subunits of NuRD remain tightly bound to each other and to MBD3 despite the presence of high salt (1M NaCl) and NP-40 concentration (0.5%) in the wash steps (Fig 1E). Surprisingly, the core RBBP4 and -7 subunits were very sensitive to NP-40. Increasing the NP-40 concentration from 0.15% to 0.5% led to a decrease in the amount of RBBP4 and -7 associated with the complex (stoichiometry of 5.5 reduced to 4)."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:kdtiH1kX3fw2Si0UVegJb6AS+709606 intact-crc:762BD2C9D783948F|rigid:KsNg29xcbxmr64lcLKhIvsytkwE false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q16576 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-352227|ensembl:ENSP00000369427|intact:EBI-3505029|uniprotkb:Q5JP00 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:rbbp7_human(display_long)|uniprotkb:RBBP7(gene name)|psi-mi:RBBP7(display_short)|uniprotkb:RBAP46(gene name synonym)|uniprotkb:Retinoblastoma-binding protein 7(gene name synonym)|uniprotkb:Retinoblastoma-binding protein p46(gene name synonym)|uniprotkb:Histone acetyltransferase type B subunit 2(gene name synonym)|uniprotkb:Nucleosome-remodeling factor subunit RBAP46(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_002884.1|ensembl:ENST00000380087(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0003723"(RNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006260"(DNA replication)|go:"GO:0006325"(chromatin organization)|go:"GO:0016581"(NuRD complex)|go:"GO:0030308"(negative regulation of cell growth)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042393"(histone binding)|go:"GO:0048545"(response to steroid hormone)|go:"GO:0070370"(cellular heat acclimation)|interpro:IPR001680(WD40 repeat)|interpro:IPR015943(WD40/YVTN repeat-like)|interpro:IPR019775|interpro:IPR020472|interpro:IPR022052|interpro:IPR036322|mint:Q16576|rcsb pdb:3CFS|rcsb pdb:3CFV|rcsb pdb:7M3X|reactome:R-HSA-212300|reactome:R-HSA-2559580|reactome:R-HSA-3214815|reactome:R-HSA-3214841|reactome:R-HSA-3214847|reactome:R-HSA-3214858|reactome:R-HSA-427389|reactome:R-HSA-5617472|reactome:R-HSA-606279|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-8951664|reactome:R-HSA-8953750|reactome:R-HSA-9609690|reactome:R-HSA-9679191|reactome:R-HSA-9710421|ensembl:ENSG00000102054(gene)|refseq:NP_001185648.1|dip:DIP-436N - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:qANLG0ui7jm3Uy4+IRnxR8Kir7c9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q09028 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-620823|uniprotkb:B4DRH0|ensembl:ENSP00000362592|uniprotkb:P31149|uniprotkb:Q53H02|uniprotkb:Q96BV9|uniprotkb:D3DPQ3|uniprotkb:B2R6G9 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:rbbp4_human(display_long)|uniprotkb:Retinoblastoma-binding protein 4(gene name synonym)|uniprotkb:Retinoblastoma-binding protein p48(gene name synonym)|uniprotkb:Chromatin assembly factor 1 subunit C(gene name synonym)|uniprotkb:Chromatin assembly factor I p48 subunit(gene name synonym)|uniprotkb:Nucleosome-remodeling factor subunit RBAP48(gene name synonym)|uniprotkb:RBBP4(gene name)|psi-mi:RBBP4(display_short)|uniprotkb:RBAP48(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 ensembl:ENSG00000162521(gene)|ensembl:ENST00000373493(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000785"(chromatin)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006260"(DNA replication)|go:"GO:0006335"(DNA replication-dependent chromatin assembly)|go:"GO:0006336"(DNA replication-independent chromatin assembly)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0007049"(cell cycle)|go:"GO:0008285"(negative regulation of cell population proliferation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0016589"(NURF complex)|go:"GO:0031497"(chromatin assembly)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033186"(CAF-1 complex)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042393"(histone binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|interpro:IPR001680(WD40 repeat)|interpro:IPR015943(WD40/YVTN repeat-like)|interpro:IPR019775|interpro:IPR020472|interpro:IPR022052|mint:Q09028|rcsb pdb:2XU7|rcsb pdb:3GFC|rcsb pdb:4PBY|rcsb pdb:4PBZ|rcsb pdb:4PC0|rcsb pdb:4R7A|rcsb pdb:5FXY|rcsb pdb:5VTB|rcsb pdb:5WAI|rcsb pdb:5WAK|rcsb pdb:5XWR|rcsb pdb:5XXQ|rcsb pdb:5Y1U|rcsb pdb:6BW3|rcsb pdb:6BW4|rcsb pdb:6C23|rcsb pdb:6C24|rcsb pdb:6G16|rcsb pdb:6NQ3|rcsb pdb:6WKR|rcsb pdb:6ZRC|rcsb pdb:6ZRD|rcsb pdb:7AOA|rcsb pdb:7KSO|rcsb pdb:7KSR|rcsb pdb:7KTP|rcsb pdb:7M40|reactome:R-HSA-1362277|reactome:R-HSA-1362300|reactome:R-HSA-1538133|reactome:R-HSA-156711|reactome:R-HSA-212300|reactome:R-HSA-2559580|reactome:R-HSA-3214815|reactome:R-HSA-3214841|reactome:R-HSA-427389|reactome:R-HSA-5617472|reactome:R-HSA-606279|reactome:R-HSA-6804758|reactome:R-HSA-69202|reactome:R-HSA-69205|reactome:R-HSA-69656|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-8953750|reactome:R-HSA-9609690|reactome:R-HSA-9679191|reactome:R-HSA-9710421|interpro:IPR036322|refseq:NP_001128727.1|refseq:NP_001128728.1|refseq:NP_005601.1|dip:DIP-33495N - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:CbyJMIjpW1A4sZijP0IGRYc8o4I9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q9UBB5 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-923391|uniprotkb:Q9UIS8|uniprotkb:O95242|ensembl:ENSP00000256429 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:mbd2_human(display_long)|uniprotkb:MBD2(gene name)|psi-mi:MBD2(display_short)|uniprotkb:Methyl-CpG-binding protein MBD2(gene name synonym)|uniprotkb:Demethylase(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_003918.1|refseq:NP_056647.1|ensembl:ENSG00000134046(gene)|ensembl:ENST00000256429(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0003682"(chromatin binding)|go:"GO:0003696"(satellite DNA binding)|go:"GO:0003729"(mRNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009612"(response to mechanical stimulus)|go:"GO:0019904"(protein domain specific binding)|go:"GO:0030177"(positive regulation of Wnt signaling pathway)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0034622"|go:"GO:0035197"(siRNA binding)|go:"GO:0035563"(positive regulation of chromatin binding)|go:"GO:0042127"(regulation of cell population proliferation)|go:"GO:0042711"(maternal behavior)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0048568"(embryonic organ development)|go:"GO:0070742"(C2H2 zinc finger domain binding)|go:"GO:0071407"(cellular response to organic cyclic compound)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|mint:Q9UBB5|rcsb pdb:2L2L|rcsb pdb:6C1A|rcsb pdb:6C1T|rcsb pdb:6C1U|rcsb pdb:6C1V|rcsb pdb:6C2F|rcsb pdb:6CNP|rcsb pdb:6CNQ|rcsb pdb:7AO8|rcsb pdb:7AO9|rcsb pdb:7AOA|reactome:R-HSA-427413|reactome:R-HSA-73728 - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:8DO+M6oIpbSfTFPVLADdXaaqzEU9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q8WXI9 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-923440|uniprotkb:Q5VUR2|uniprotkb:Q7LG68|uniprotkb:Q9ULS0|uniprotkb:D3DUZ2|ensembl:ENSP00000357644|ensembl:ENSP00000458280|ensembl:ENSP00000489184 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:p66b_human(display_long)|uniprotkb:GATAD2B(gene name)|psi-mi:GATAD2B(display_short)|uniprotkb:KIAA1150(gene name synonym)|uniprotkb:p66/p68(gene name synonym)|uniprotkb:GATA zinc finger domain-containing protein 2B(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_065750.1|refseq:XP_005245421.1|dip:DIP-36054N|ensembl:ENSG00000143614(gene)|ensembl:ENSG00000261992(gene)|ensembl:ENST00000368655(transcript)|ensembl:ENST00000576342(transcript)|ensembl:ENST00000634544(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0005654"(nucleoplasm)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016581"(NuRD complex)|go:"GO:0016607"(nuclear speck)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0043565"(sequence-specific DNA binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR013088(Zinc finger, NHR/GATA-type)|interpro:IPR032346|interpro:IPR040386|mint:Q8WXI9|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:pLKkMcJBBWdyMTf+2axWzvZLKP09606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q12873 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-523590|uniprotkb:Q9Y4I0|intact:EBI-28978117|ensembl:ENSP00000332628|uniprotkb:D3DTQ9|uniprotkb:E9PG89 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:chd3_human(display_long)|uniprotkb:ATP-dependent helicase CHD3(gene name synonym)|uniprotkb:Mi-2 autoantigen 240 kDa protein(gene name synonym)|uniprotkb:Mi2-alpha(gene name synonym)|uniprotkb:Zinc finger helicase(gene name synonym)|uniprotkb:CHD3(gene name)|psi-mi:CHD3(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 interpro:IPR023780|interpro:IPR027417|interpro:IPR036910|interpro:IPR038718|mint:Q12873|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-4551638|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|ensembl:ENSG00000170004(gene)|ensembl:ENST00000330494(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000976"(transcription cis-regulatory region binding)|go:"GO:0003677"(DNA binding)|go:"GO:0003678"(DNA helicase activity)|go:"GO:0003723"(RNA binding)|go:"GO:0004386"(helicase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005730"(nucleolus)|go:"GO:0005737"(cytoplasm)|go:"GO:0005813"(centrosome)|go:"GO:0006333"(chromatin assembly or disassembly)|go:"GO:0006355"(regulation of transcription, DNA-templated)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0007051"(spindle organization)|go:"GO:0007098"(centrosome cycle)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016581"(NuRD complex)|go:"GO:0016605"(PML body)|go:"GO:0034451"(centriolar satellite)|go:"GO:0036121"(double-stranded DNA helicase activity)|go:"GO:0043044"|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR012957(CHD, C-terminal 2)|interpro:IPR012958(CHD, N-terminal)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR014001(DEAD-like helicase, N-terminal)|interpro:IPR016197(Chromo domain-like)|interpro:IPR019786|go:"GO:0070615"|interpro:IPR019787|interpro:IPR023779|go:"GO:0140603"(obsolete ATP hydrolysis activity)|interpro:IPR000330(SNF2-related)|interpro:IPR000953(Chromo domain)|interpro:IPR001650(DNA/RNA helicase, C-terminal)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002464(DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site)|interpro:IPR009462(Protein of unknown function DUF1086)|interpro:IPR009463(Protein of unknown function DUF1087)|ensembl:ENSP00000332628|ensembl:ENST00000358181|ensembl:ENSP00000350907|ensembl:ENST00000380358|ensembl:ENSP00000369716|refseq:NP_001005271.2|refseq:NP_001005273.1|refseq:NP_005843.2|dip:DIP-32496N - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:UjefFUXiV28qhOP9BoIUansxl+k9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q13330 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-714236|uniprotkb:Q8NFI8|uniprotkb:Q96GI8|uniprotkb:A5PLK4|intact:EBI-28976623|ensembl:ENSP00000333633|uniprotkb:Q86SW2 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:mta1_human(display_long)|uniprotkb:MTA1(gene name)|psi-mi:MTA1(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_001190187.1|refseq:NP_004680.2|ensembl:ENSP00000333633|ensembl:ENST00000405646|ensembl:ENSP00000384180|ensembl:ENST00000438610|ensembl:ENSP00000393438|ensembl:ENSG00000182979(gene)|ensembl:ENST00000331320(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|reactome:R-HSA-427389|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|reactome:R-HSA-3232118|go:"GO:0005635"(nuclear envelope)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0006302"(double-strand break repair)|go:"GO:0007165"(signal transduction)|go:"GO:0008270"(zinc ion binding)|go:"GO:0010212"(response to ionizing radiation)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0040029"(regulation of gene expression, epigenetic)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043153"(entrainment of circadian clock by photoperiod)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0005634"(nucleus)|go:"GO:0043231"(intracellular membrane-bounded organelle)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:1902499"(positive regulation of protein autoubiquitination)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR017930|interpro:IPR035170|interpro:IPR040138|mint:Q13330|rcsb pdb:4BKX|rcsb pdb:4PBY|rcsb pdb:4PBZ|rcsb pdb:4PC0|rcsb pdb:5FXY|rcsb pdb:5ICN|rcsb pdb:6G16|rcsb pdb:6ZRC|rcsb pdb:6ZRD|rcsb pdb:7AO8|go:"GO:0045475"(locomotor rhythm)|rcsb pdb:7AO9|rcsb pdb:7AOA|reactome:R-HSA-3214815|dip:DIP-41751N - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:nDDSb5B6YCbq5/6qvgtnUWtP23M9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q13547 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-301834|uniprotkb:Q92534|ensembl:ENSP00000362649 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:hdac1_human(display_long)|uniprotkb:HDAC1(gene name)|psi-mi:HDAC1(display_short)|uniprotkb:RPD3L1(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 ensembl:ENSG00000116478(gene)|ensembl:ENST00000373548(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0000979"(RNA polymerase II core promoter sequence-specific DNA binding)|go:"GO:0001046"(core promoter sequence-specific DNA binding)|go:"GO:0001975"(response to amphetamine)|go:"GO:0002039"(p53 binding)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006325"(chromatin organization)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0006476"(protein deacetylation)|go:"GO:0007492"(endoderm development)|go:"GO:0008134"(transcription factor binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0008285"(negative regulation of cell population proliferation)|go:"GO:0009913"(epidermal cell differentiation)|go:"GO:0010629"(negative regulation of gene expression)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0019899"(enzyme binding)|go:"GO:0021766"(hippocampus development)|go:"GO:0030182"(neuron differentiation)|go:"GO:0031000"(response to caffeine)|go:"GO:0032041"("NAD-dependent histone deacetylase activity (H3-K14 specific)")|go:"GO:0032496"(response to lipopolysaccharide)|go:"GO:0032732"(positive regulation of interleukin-1 production)|go:"GO:0032760"(positive regulation of tumor necrosis factor production)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033558"(protein deacetylase activity)|go:"GO:0034599"(cellular response to oxidative stress)|go:"GO:0035851"(Krueppel-associated box domain binding)|go:"GO:0042475"(odontogenesis of dentin-containing tooth)|go:"GO:0042493"|go:"GO:0042531"(positive regulation of tyrosine phosphorylation of STAT protein)|go:"GO:0042733"(embryonic digit morphogenesis)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043005"(neuron projection)|go:"GO:0043025"(neuronal cell body)|go:"GO:0043044"|go:"GO:0019213"(deacetylase activity)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070888"(E-box binding)|go:"GO:0070932"(histone H3 deacetylation)|go:"GO:0070933"(histone H4 deacetylation)|go:"GO:0071356"(cellular response to tumor necrosis factor)|go:"GO:0090090"(negative regulation of canonical Wnt signaling pathway)|go:"GO:0140297"(DNA-binding transcription factor binding)|go:"GO:1900221"(regulation of amyloid-beta clearance)|go:"GO:1990841"(promoter-specific chromatin binding)|go:"GO:2000273"(positive regulation of signaling receptor activity)|go:"GO:2000343"("positive regulation of chemokine (C-X-C motif) ligand 2 production")|go:"GO:2000676"(positive regulation of type B pancreatic cell apoptotic process)|go:"GO:2000757"(negative regulation of peptidyl-lysine acetylation)|go:"GO:2001243"(negative regulation of intrinsic apoptotic signaling pathway)|interpro:IPR000286(Histone deacetylase superfamily)|interpro:IPR003084(Histone deacetylase)|interpro:IPR023696|interpro:IPR023801|interpro:IPR037138|mint:Q13547|rcsb pdb:1TYI|rcsb pdb:4BKX|rcsb pdb:5ICN|rcsb pdb:6Z2J|rcsb pdb:6Z2K|rcsb pdb:7AO8|rcsb pdb:7AO9|rcsb pdb:7AOA|reactome:R-HSA-1362277|reactome:R-HSA-1362300|reactome:R-HSA-1538133|reactome:R-HSA-193670|reactome:R-HSA-201722|reactome:R-HSA-2122947|reactome:R-HSA-2173795|reactome:R-HSA-2173796|reactome:R-HSA-2644606|reactome:R-HSA-2894862|reactome:R-HSA-3214815|reactome:R-HSA-350054|reactome:R-HSA-3769402|reactome:R-HSA-427389|reactome:R-HSA-427413|reactome:R-HSA-4551638|reactome:R-HSA-4641265|reactome:R-HSA-6804758|reactome:R-HSA-69205|reactome:R-HSA-73762|reactome:R-HSA-8936459|reactome:R-HSA-8943724|reactome:R-HSA-9018519|reactome:R-HSA-9022538|reactome:R-HSA-9022692|go:"GO:0017053"(transcription repressor complex)|go:"GO:0043066"(negative regulation of apoptotic process)|reactome:R-HSA-9022699|reactome:R-HSA-9022702|reactome:R-HSA-9615017|reactome:R-HSA-9679191|reactome:R-HSA-983231|go:"GO:0043524"(negative regulation of neuron apoptotic process)|go:"GO:0043922"(negative regulation by host of viral transcription)|go:"GO:0044877"(protein-containing complex binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0046676"(negative regulation of insulin secretion)|go:"GO:0047485"(protein N-terminus binding)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0048714"(positive regulation of oligodendrocyte differentiation)|go:"GO:0051059"(NF-kappaB binding)|go:"GO:0052548"(regulation of endopeptidase activity)|go:"GO:0055093"(response to hyperoxia)|go:"GO:0060766"(negative regulation of androgen receptor signaling pathway)|go:"GO:0060789"(hair follicle placode formation)|go:"GO:0061029"(eyelid development in camera-type eye)|go:"GO:0061198"(fungiform papilla formation)|go:"GO:0043124"(negative regulation of I-kappaB kinase/NF-kappaB signaling)|refseq:NP_004955.2|dip:DIP-24184N - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:RP+yIBWH55NgoPTY1nKXqeJL/xY9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:O94776 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-1783035|uniprotkb:Q68DB1|uniprotkb:Q9UQB5|ensembl:ENSP00000278823 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:mta2_human(display_long)|uniprotkb:MTA2(gene name)|psi-mi:MTA2(display_short)|uniprotkb:MTA1L1(gene name synonym)|uniprotkb:PID(gene name synonym)|uniprotkb:Metastasis-associated 1-like 1(gene name synonym)|uniprotkb:p53 target protein in deacetylase complex(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_004730.2|refseq:NP_001317221.1|dip:DIP-46519N|ensembl:ENSG00000149480(gene)|ensembl:ENST00000278823(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005667"(transcription regulator complex)|go:"GO:0006306"(DNA methylation)|go:"GO:0006333"(chromatin assembly or disassembly)|go:"GO:0008270"(zinc ion binding)|go:"GO:0010762"(regulation of fibroblast migration)|go:"GO:0016020"(membrane)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0032991"(protein-containing complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR035170|interpro:IPR037964|interpro:IPR040138|interpro:IPR043151|mint:O94776|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:D4wOsdMJYhY/ltvcnnuMHqNrFkc9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:O14519 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q14839 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-372916|uniprotkb:Q8IXZ5|intact:EBI-28978241|ensembl:ENSP00000440542 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:chd4_human(display_long)|uniprotkb:CHD4(gene name)|psi-mi:CHD4(display_short)|uniprotkb:ATP-dependent helicase CHD4(gene name synonym)|uniprotkb:Mi-2 autoantigen 218 kDa protein(gene name synonym)|uniprotkb:Mi2-beta(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 ensembl:ENSP00000440542|ensembl:ENST00000645095|ensembl:ENSP00000496634|refseq:NP_001264.2|refseq:XP_006719021.1|refseq:NP_001284482.1|ensembl:ENSG00000111642(gene)|ensembl:ENST00000544040(transcript)|go:"GO:0000785"(chromatin)|go:"GO:0001221"(transcription coregulator binding)|go:"GO:0003677"(DNA binding)|go:"GO:0003678"(DNA helicase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005813"(centrosome)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016020"(membrane)|go:"GO:0016581"(NuRD complex)|go:"GO:0032991"(protein-containing complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070615"|go:"GO:0090575"(RNA polymerase II transcription regulator complex)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|interpro:IPR000330(SNF2-related)|interpro:IPR000953(Chromo domain)|interpro:IPR001650(DNA/RNA helicase, C-terminal)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002464(DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site)|interpro:IPR009462(Protein of unknown function DUF1086)|interpro:IPR009463(Protein of unknown function DUF1087)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR012957(CHD, C-terminal 2)|interpro:IPR012958(CHD, N-terminal)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR014001(DEAD-like helicase, N-terminal)|interpro:IPR016197(Chromo domain-like)|interpro:IPR019786|interpro:IPR019787|interpro:IPR023780|interpro:IPR027417|interpro:IPR038718|mint:Q14839|rcsb pdb:1MM2|rcsb pdb:1MM3|rcsb pdb:2EE1|rcsb pdb:2L5U|rcsb pdb:2L75|rcsb pdb:2N5N|rcsb pdb:4O9I|rcsb pdb:6BGG|rcsb pdb:6Q3M|rcsb pdb:6RYR|rcsb pdb:6RYU|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9031628|reactome:R-HSA-9679191|dip:DIP-31183N - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:E9eHT/41SIFRiz54J81hvPQeHIE9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q86YP4 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-726224|uniprotkb:Q7L3J2|uniprotkb:Q96F28|uniprotkb:Q9NPU2|uniprotkb:Q9NXS1|uniprotkb:B5MC40|ensembl:ENSP00000351552|ensembl:ENSP00000353463 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:p66a_human(display_long)|uniprotkb:GATA zinc finger domain-containing protein 2A(gene name synonym)|uniprotkb:GATAD2A(gene name)|psi-mi:GATAD2A(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_060130.3|refseq:NP_001287875.1|refseq:XP_011526407.1|ensembl:ENSG00000167491(gene)|ensembl:ENST00000358713(transcript)|ensembl:ENST00000360315(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0006306"(DNA methylation)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016581"(NuRD complex)|go:"GO:0016607"(nuclear speck)|go:"GO:0030674"(protein-macromolecule adaptor activity)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR032346|interpro:IPR040386|mint:Q86YP4|rcsb pdb:2L2L|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|dip:DIP-36053N - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:s2G27yMihH9d7ny/v1GZ7aeTpDQ9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q92769 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-301821|uniprotkb:Q5SRI8|uniprotkb:Q5SZ86|uniprotkb:Q8NEH4|uniprotkb:B4DL58|ensembl:ENSP00000430432|uniprotkb:E1P561|uniprotkb:B3KRS5 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:hdac2_human(display_long)|uniprotkb:HDAC2(gene name)|psi-mi:HDAC2(display_short) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0008134"(transcription factor binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0009913"(epidermal cell differentiation)|go:"GO:0010718"(positive regulation of epithelial to mesenchymal transition)|go:"GO:0010977"(negative regulation of neuron projection development)|go:"GO:0016358"(dendrite development)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0019213"(deacetylase activity)|go:"GO:0019899"(enzyme binding)|go:"GO:0031000"(response to caffeine)|go:"GO:0031072"(heat shock protein binding)|go:"GO:0032041"("NAD-dependent histone deacetylase activity (H3-K14 specific)")|go:"GO:0032496"(response to lipopolysaccharide)|go:"GO:0032732"(positive regulation of interleukin-1 production)|go:"GO:0032760"(positive regulation of tumor necrosis factor production)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0032967"(positive regulation of collagen biosynthetic process)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033558"(protein deacetylase activity)|go:"GO:0034605"(cellular response to heat)|go:"GO:0035094"(response to nicotine)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042220"(response to cocaine)|go:"GO:0042475"(odontogenesis of dentin-containing tooth)|go:"GO:0042493"|go:"GO:0042531"(positive regulation of tyrosine phosphorylation of STAT protein)|go:"GO:0042733"(embryonic digit morphogenesis)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0043066"(negative regulation of apoptotic process)|go:"GO:0043392"(negative regulation of DNA binding)|go:"GO:0043433"(negative regulation of DNA-binding transcription factor activity)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045347"(negative regulation of MHC class II biosynthetic process)|go:"GO:0045862"(positive regulation of proteolysis)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0048149"(behavioral response to ethanol)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0051059"(NF-kappaB binding)|go:"GO:0055093"(response to hyperoxia)|go:"GO:0060789"(hair follicle placode formation)|go:"GO:0061000"(negative regulation of dendritic spine development)|go:"GO:0061029"(eyelid development in camera-type eye)|go:"GO:0061198"(fungiform papilla formation)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070301"(cellular response to hydrogen peroxide)|go:"GO:0070829"(obsolete heterochromatin maintenance)|go:"GO:0070932"(histone H3 deacetylation)|go:"GO:0070933"(histone H4 deacetylation)|go:"GO:0071300"(cellular response to retinoic acid)|go:"GO:0071560"(cellular response to transforming growth factor beta stimulus)|go:"GO:1902437"(positive regulation of male mating behavior)|go:"GO:1903351"(cellular response to dopamine)|go:"GO:1990841"(promoter-specific chromatin binding)|go:"GO:2000273"(positive regulation of signaling receptor activity)|go:"GO:2000757"(negative regulation of peptidyl-lysine acetylation)|interpro:IPR000286(Histone deacetylase superfamily)|interpro:IPR003084(Histone deacetylase)|interpro:IPR023696|interpro:IPR023801|interpro:IPR037138|mint:Q92769|rcsb pdb:3MAX|rcsb pdb:4LXZ|rcsb pdb:4LY1|rcsb pdb:5IWG|rcsb pdb:5IX0|rcsb pdb:6G3O|rcsb pdb:6WBW|go:"GO:0048714"(positive regulation of oligodendrocyte differentiation)|ensembl:ENSG00000196591(gene)|ensembl:ENST00000519065(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0001975"(response to amphetamine)|go:"GO:0003300"(cardiac muscle hypertrophy)|go:"GO:0003682"(chromatin binding)|go:"GO:0003723"(RNA binding)|rcsb pdb:6WHN|rcsb pdb:6WHO|rcsb pdb:6WHQ|rcsb pdb:6WHZ|rcsb pdb:6WI3|rcsb pdb:6XDM|rcsb pdb:6XEB|rcsb pdb:6XEC|rcsb pdb:7KBG|rcsb pdb:7KBH|rcsb pdb:7LTG|rcsb pdb:7LTK|rcsb pdb:7LTL|reactome:R-HSA-193670|reactome:R-HSA-2122947|reactome:R-HSA-2644606|reactome:R-HSA-2894862|reactome:R-HSA-3214815|reactome:R-HSA-350054|reactome:R-HSA-427389|reactome:R-HSA-427413|reactome:R-HSA-4551638|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9022692|reactome:R-HSA-9022699|reactome:R-HSA-9615017|reactome:R-HSA-9619665|reactome:R-HSA-9679191|reactome:R-HSA-983231|rcsb pdb:6WBZ|refseq:NP_001518.3|dip:DIP-24220N|refseq:XP_011534090.1|refseq:XP_016866288.1 - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:K4PpGz9E9/TrQZsgvrJuc+uYCn89606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:Q9BTC8 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-2461787|uniprotkb:Q9NSP2|uniprotkb:Q9ULF4|ensembl:ENSP00000385823 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:mta3_human(display_long)|uniprotkb:MTA3(gene name)|psi-mi:MTA3(display_short)|uniprotkb:KIAA1266(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_001269684.1|refseq:NP_001269685.1|refseq:NP_065795.1|refseq:NP_001317371.1|dip:DIP-47460N|ensembl:ENST00000405094(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0008270"(zinc ion binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0010971"(positive regulation of G2/M transition of mitotic cell cycle)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043231"(intracellular membrane-bounded organelle)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0044877"(protein-containing complex binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR017930|interpro:IPR035170|interpro:IPR040138|interpro:IPR043151|mint:Q9BTC8|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|ensembl:ENSG00000057935(gene) - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:wxPsfH6FguY8n4PFwaj1iJNTWPc9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O14519 uniprotkb:O95983 intact:EBI-1052532|uniprotkb:F5GYA4|intact:EBI-10988349|ensembl:ENSP00000261692 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 psi-mi:cdka1_human(display_long)|uniprotkb:Putative oral cancer suppressor(gene name synonym)|uniprotkb:Deleted in oral cancer 1(gene name synonym)|uniprotkb:CDK2AP1(gene name)|psi-mi:CDK2AP1(display_short)|uniprotkb:CDKAP1(gene name synonym)|uniprotkb:DOC1(gene name synonym) psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:"MI:0096"(pull down) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692524|imex:IM-23066-2 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_004633.1|refseq:NP_001257362.1|refseq:NP_001257363.1|ensembl:ENSG00000111328(gene)|ensembl:ENST00000261692(transcript)|go:"GO:0001934"(positive regulation of protein phosphorylation)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006261"(DNA-dependent DNA replication)|go:"GO:0007049"(cell cycle)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0070182"(DNA polymerase binding)|interpro:IPR017266(Cyclin-dependent kinase 2-associated protein 2)|mint:O14519|rcsb pdb:2KW6 refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 - - - figure legend:f2|comment:"To further study the potential dynamics of NuRD subunit interactions, a SILAC-based subunit exchange assay was used (Fig 2A) [15]. HeLa cells expressing GFP-CDK2AP-1 were labeled in culture with heavy amino acids (Forward) or light amino acids (Reverse). Similarly, WT HeLa cells were also labeled with light or heavy amino acids. GFP pulldowns were performed immediately after mixing the nuclear extracts (T0) or after overnight incubation (TON). Proteins that are more dynamically associated with NuRD will dissociate from the complex during the overnight incubation step and may be replaced by proteins from the other, differentially labeled extract. This eventually results in a decrease of detected SILAC ratios, where dynamic core subunits and/or interactors will move towards the background cloud in the scatter plot.At T0, all NuRD core subunits are significantly enriched according to boxplot statistics (Fig 2B). However, after overnight incubation, RBBP4 and -7 clearly separate from the other NuRD subunits and migrate towards the background cloud (Fig 2C). To more directly compare the 2 scatter plots, the difference in forward and reverse ratios between the plots was visualized in a graph (Fig 2D). A protein with no change in ratios between experiments would have a value of 0. This graph clearly shows that RBBP4 and -7 are the most dynamic NuRD core subunits. These observations are in agreement with recent structural studies, which suggest that MTA and histone H4 compete for RBBP binding [20]. Furthermore, RBBP4 and -7 are part of many different protein complexes other than NuRD (Sin3 complex, PRC2), which also could explain their observed dynamic behavior [21, 22]."|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:9606(human-hela)|taxid:9606(Homo sapiens epitheloid cervix carcinoma cells) - 2014/08/20 2014/10/16 rogid:ZFfQSqkET3VpjG8UrdHokYRGzj09606 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 intact-crc:9367609A1AE10C80|rigid:m6qzlJBAn0h4gXlEfygbZbjHzW4 false green fluorescent protein tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q13330 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-714236|uniprotkb:Q8NFI8|uniprotkb:Q96GI8|uniprotkb:A5PLK4|intact:EBI-28976623|ensembl:ENSP00000333633|uniprotkb:Q86SW2 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:mta1_human(display_long)|uniprotkb:MTA1(gene name)|psi-mi:MTA1(display_short) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_001190187.1|refseq:NP_004680.2|ensembl:ENSP00000333633|ensembl:ENST00000405646|ensembl:ENSP00000384180|ensembl:ENST00000438610|ensembl:ENSP00000393438|ensembl:ENSG00000182979(gene)|ensembl:ENST00000331320(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|reactome:R-HSA-427389|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|reactome:R-HSA-3232118|go:"GO:0005635"(nuclear envelope)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0005874"(microtubule)|go:"GO:0006302"(double-strand break repair)|go:"GO:0007165"(signal transduction)|go:"GO:0008270"(zinc ion binding)|go:"GO:0010212"(response to ionizing radiation)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0040029"(regulation of gene expression, epigenetic)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043153"(entrainment of circadian clock by photoperiod)|go:"GO:0043161"(proteasome-mediated ubiquitin-dependent protein catabolic process)|go:"GO:0005634"(nucleus)|go:"GO:0043231"(intracellular membrane-bounded organelle)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:1902499"(positive regulation of protein autoubiquitination)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR017930|interpro:IPR035170|interpro:IPR040138|mint:Q13330|rcsb pdb:4BKX|rcsb pdb:4PBY|rcsb pdb:4PBZ|rcsb pdb:4PC0|rcsb pdb:5FXY|rcsb pdb:5ICN|rcsb pdb:6G16|rcsb pdb:6ZRC|rcsb pdb:6ZRD|rcsb pdb:7AO8|go:"GO:0045475"(locomotor rhythm)|rcsb pdb:7AO9|rcsb pdb:7AOA|reactome:R-HSA-3214815|dip:DIP-41751N go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:nDDSb5B6YCbq5/6qvgtnUWtP23M9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q12873 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-523590|uniprotkb:Q9Y4I0|intact:EBI-28978117|ensembl:ENSP00000332628|uniprotkb:D3DTQ9|uniprotkb:E9PG89 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:chd3_human(display_long)|uniprotkb:ATP-dependent helicase CHD3(gene name synonym)|uniprotkb:Mi-2 autoantigen 240 kDa protein(gene name synonym)|uniprotkb:Mi2-alpha(gene name synonym)|uniprotkb:Zinc finger helicase(gene name synonym)|uniprotkb:CHD3(gene name)|psi-mi:CHD3(display_short) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 interpro:IPR023780|interpro:IPR027417|interpro:IPR036910|interpro:IPR038718|mint:Q12873|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-4551638|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|ensembl:ENSG00000170004(gene)|ensembl:ENST00000330494(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000976"(transcription cis-regulatory region binding)|go:"GO:0003677"(DNA binding)|go:"GO:0003678"(DNA helicase activity)|go:"GO:0003723"(RNA binding)|go:"GO:0004386"(helicase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005730"(nucleolus)|go:"GO:0005737"(cytoplasm)|go:"GO:0005813"(centrosome)|go:"GO:0006333"(chromatin assembly or disassembly)|go:"GO:0006355"(regulation of transcription, DNA-templated)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0007051"(spindle organization)|go:"GO:0007098"(centrosome cycle)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016581"(NuRD complex)|go:"GO:0016605"(PML body)|go:"GO:0034451"(centriolar satellite)|go:"GO:0036121"(double-stranded DNA helicase activity)|go:"GO:0043044"|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR012957(CHD, C-terminal 2)|interpro:IPR012958(CHD, N-terminal)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR014001(DEAD-like helicase, N-terminal)|interpro:IPR016197(Chromo domain-like)|interpro:IPR019786|go:"GO:0070615"|interpro:IPR019787|interpro:IPR023779|go:"GO:0140603"(obsolete ATP hydrolysis activity)|interpro:IPR000330(SNF2-related)|interpro:IPR000953(Chromo domain)|interpro:IPR001650(DNA/RNA helicase, C-terminal)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002464(DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site)|interpro:IPR009462(Protein of unknown function DUF1086)|interpro:IPR009463(Protein of unknown function DUF1087)|ensembl:ENSP00000332628|ensembl:ENST00000358181|ensembl:ENSP00000350907|ensembl:ENST00000380358|ensembl:ENSP00000369716|refseq:NP_001005271.2|refseq:NP_001005273.1|refseq:NP_005843.2|dip:DIP-32496N go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:UjefFUXiV28qhOP9BoIUansxl+k9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q14839 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-372916|uniprotkb:Q8IXZ5|intact:EBI-28978241|ensembl:ENSP00000440542 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:chd4_human(display_long)|uniprotkb:CHD4(gene name)|psi-mi:CHD4(display_short)|uniprotkb:ATP-dependent helicase CHD4(gene name synonym)|uniprotkb:Mi-2 autoantigen 218 kDa protein(gene name synonym)|uniprotkb:Mi2-beta(gene name synonym) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSP00000440542|ensembl:ENST00000645095|ensembl:ENSP00000496634|refseq:NP_001264.2|refseq:XP_006719021.1|refseq:NP_001284482.1|ensembl:ENSG00000111642(gene)|ensembl:ENST00000544040(transcript)|go:"GO:0000785"(chromatin)|go:"GO:0001221"(transcription coregulator binding)|go:"GO:0003677"(DNA binding)|go:"GO:0003678"(DNA helicase activity)|go:"GO:0005524"(ATP binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005813"(centrosome)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0008270"(zinc ion binding)|go:"GO:0016020"(membrane)|go:"GO:0016581"(NuRD complex)|go:"GO:0032991"(protein-containing complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070615"|go:"GO:0090575"(RNA polymerase II transcription regulator complex)|go:"GO:0140603"(obsolete ATP hydrolysis activity)|interpro:IPR000330(SNF2-related)|interpro:IPR000953(Chromo domain)|interpro:IPR001650(DNA/RNA helicase, C-terminal)|interpro:IPR001965(Zinc finger, PHD-type)|interpro:IPR002464(DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site)|interpro:IPR009462(Protein of unknown function DUF1086)|interpro:IPR009463(Protein of unknown function DUF1087)|interpro:IPR011011(Zinc finger, FYVE/PHD-type)|interpro:IPR012957(CHD, C-terminal 2)|interpro:IPR012958(CHD, N-terminal)|interpro:IPR013083(Zinc finger, RING/FYVE/PHD-type)|interpro:IPR014001(DEAD-like helicase, N-terminal)|interpro:IPR016197(Chromo domain-like)|interpro:IPR019786|interpro:IPR019787|interpro:IPR023780|interpro:IPR027417|interpro:IPR038718|mint:Q14839|rcsb pdb:1MM2|rcsb pdb:1MM3|rcsb pdb:2EE1|rcsb pdb:2L5U|rcsb pdb:2L75|rcsb pdb:2N5N|rcsb pdb:4O9I|rcsb pdb:6BGG|rcsb pdb:6Q3M|rcsb pdb:6RYR|rcsb pdb:6RYU|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9031628|reactome:R-HSA-9679191|dip:DIP-31183N go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:E9eHT/41SIFRiz54J81hvPQeHIE9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q13547 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-301834|uniprotkb:Q92534|ensembl:ENSP00000362649 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:hdac1_human(display_long)|uniprotkb:HDAC1(gene name)|psi-mi:HDAC1(display_short)|uniprotkb:RPD3L1(gene name synonym) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSG00000116478(gene)|ensembl:ENST00000373548(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0000979"(RNA polymerase II core promoter sequence-specific DNA binding)|go:"GO:0001046"(core promoter sequence-specific DNA binding)|go:"GO:0001975"(response to amphetamine)|go:"GO:0002039"(p53 binding)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006325"(chromatin organization)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0006357"(regulation of transcription by RNA polymerase II)|go:"GO:0006476"(protein deacetylation)|go:"GO:0007492"(endoderm development)|go:"GO:0008134"(transcription factor binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0008285"(negative regulation of cell population proliferation)|go:"GO:0009913"(epidermal cell differentiation)|go:"GO:0010629"(negative regulation of gene expression)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0019899"(enzyme binding)|go:"GO:0021766"(hippocampus development)|go:"GO:0030182"(neuron differentiation)|go:"GO:0031000"(response to caffeine)|go:"GO:0032041"("NAD-dependent histone deacetylase activity (H3-K14 specific)")|go:"GO:0032496"(response to lipopolysaccharide)|go:"GO:0032732"(positive regulation of interleukin-1 production)|go:"GO:0032760"(positive regulation of tumor necrosis factor production)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033558"(protein deacetylase activity)|go:"GO:0034599"(cellular response to oxidative stress)|go:"GO:0035851"(Krueppel-associated box domain binding)|go:"GO:0042475"(odontogenesis of dentin-containing tooth)|go:"GO:0042493"|go:"GO:0042531"(positive regulation of tyrosine phosphorylation of STAT protein)|go:"GO:0042733"(embryonic digit morphogenesis)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043005"(neuron projection)|go:"GO:0043025"(neuronal cell body)|go:"GO:0043044"|go:"GO:0019213"(deacetylase activity)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070888"(E-box binding)|go:"GO:0070932"(histone H3 deacetylation)|go:"GO:0070933"(histone H4 deacetylation)|go:"GO:0071356"(cellular response to tumor necrosis factor)|go:"GO:0090090"(negative regulation of canonical Wnt signaling pathway)|go:"GO:0140297"(DNA-binding transcription factor binding)|go:"GO:1900221"(regulation of amyloid-beta clearance)|go:"GO:1990841"(promoter-specific chromatin binding)|go:"GO:2000273"(positive regulation of signaling receptor activity)|go:"GO:2000343"("positive regulation of chemokine (C-X-C motif) ligand 2 production")|go:"GO:2000676"(positive regulation of type B pancreatic cell apoptotic process)|go:"GO:2000757"(negative regulation of peptidyl-lysine acetylation)|go:"GO:2001243"(negative regulation of intrinsic apoptotic signaling pathway)|interpro:IPR000286(Histone deacetylase superfamily)|interpro:IPR003084(Histone deacetylase)|interpro:IPR023696|interpro:IPR023801|interpro:IPR037138|mint:Q13547|rcsb pdb:1TYI|rcsb pdb:4BKX|rcsb pdb:5ICN|rcsb pdb:6Z2J|rcsb pdb:6Z2K|rcsb pdb:7AO8|rcsb pdb:7AO9|rcsb pdb:7AOA|reactome:R-HSA-1362277|reactome:R-HSA-1362300|reactome:R-HSA-1538133|reactome:R-HSA-193670|reactome:R-HSA-201722|reactome:R-HSA-2122947|reactome:R-HSA-2173795|reactome:R-HSA-2173796|reactome:R-HSA-2644606|reactome:R-HSA-2894862|reactome:R-HSA-3214815|reactome:R-HSA-350054|reactome:R-HSA-3769402|reactome:R-HSA-427389|reactome:R-HSA-427413|reactome:R-HSA-4551638|reactome:R-HSA-4641265|reactome:R-HSA-6804758|reactome:R-HSA-69205|reactome:R-HSA-73762|reactome:R-HSA-8936459|reactome:R-HSA-8943724|reactome:R-HSA-9018519|reactome:R-HSA-9022538|reactome:R-HSA-9022692|go:"GO:0017053"(transcription repressor complex)|go:"GO:0043066"(negative regulation of apoptotic process)|reactome:R-HSA-9022699|reactome:R-HSA-9022702|reactome:R-HSA-9615017|reactome:R-HSA-9679191|reactome:R-HSA-983231|go:"GO:0043524"(negative regulation of neuron apoptotic process)|go:"GO:0043922"(negative regulation by host of viral transcription)|go:"GO:0044877"(protein-containing complex binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0046676"(negative regulation of insulin secretion)|go:"GO:0047485"(protein N-terminus binding)|go:"GO:0048471"(perinuclear region of cytoplasm)|go:"GO:0048714"(positive regulation of oligodendrocyte differentiation)|go:"GO:0051059"(NF-kappaB binding)|go:"GO:0052548"(regulation of endopeptidase activity)|go:"GO:0055093"(response to hyperoxia)|go:"GO:0060766"(negative regulation of androgen receptor signaling pathway)|go:"GO:0060789"(hair follicle placode formation)|go:"GO:0061029"(eyelid development in camera-type eye)|go:"GO:0061198"(fungiform papilla formation)|go:"GO:0043124"(negative regulation of I-kappaB kinase/NF-kappaB signaling)|refseq:NP_004955.2|dip:DIP-24184N go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:RP+yIBWH55NgoPTY1nKXqeJL/xY9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q92769 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-301821|uniprotkb:Q5SRI8|uniprotkb:Q5SZ86|uniprotkb:Q8NEH4|uniprotkb:B4DL58|ensembl:ENSP00000430432|uniprotkb:E1P561|uniprotkb:B3KRS5 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:hdac2_human(display_long)|uniprotkb:HDAC2(gene name)|psi-mi:HDAC2(display_short) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0008134"(transcription factor binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0009913"(epidermal cell differentiation)|go:"GO:0010718"(positive regulation of epithelial to mesenchymal transition)|go:"GO:0010977"(negative regulation of neuron projection development)|go:"GO:0016358"(dendrite development)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0019213"(deacetylase activity)|go:"GO:0019899"(enzyme binding)|go:"GO:0031000"(response to caffeine)|go:"GO:0031072"(heat shock protein binding)|go:"GO:0032041"("NAD-dependent histone deacetylase activity (H3-K14 specific)")|go:"GO:0032496"(response to lipopolysaccharide)|go:"GO:0032732"(positive regulation of interleukin-1 production)|go:"GO:0032760"(positive regulation of tumor necrosis factor production)|go:"GO:0032922"(circadian regulation of gene expression)|go:"GO:0032967"(positive regulation of collagen biosynthetic process)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033558"(protein deacetylase activity)|go:"GO:0034605"(cellular response to heat)|go:"GO:0035094"(response to nicotine)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042220"(response to cocaine)|go:"GO:0042475"(odontogenesis of dentin-containing tooth)|go:"GO:0042493"|go:"GO:0042531"(positive regulation of tyrosine phosphorylation of STAT protein)|go:"GO:0042733"(embryonic digit morphogenesis)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0043066"(negative regulation of apoptotic process)|go:"GO:0043392"(negative regulation of DNA binding)|go:"GO:0043433"(negative regulation of DNA-binding transcription factor activity)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045347"(negative regulation of MHC class II biosynthetic process)|go:"GO:0045862"(positive regulation of proteolysis)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0045893"(positive regulation of transcription, DNA-templated)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0048149"(behavioral response to ethanol)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0051059"(NF-kappaB binding)|go:"GO:0055093"(response to hyperoxia)|go:"GO:0060789"(hair follicle placode formation)|go:"GO:0061000"(negative regulation of dendritic spine development)|go:"GO:0061029"(eyelid development in camera-type eye)|go:"GO:0061198"(fungiform papilla formation)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|go:"GO:0070301"(cellular response to hydrogen peroxide)|go:"GO:0070829"(obsolete heterochromatin maintenance)|go:"GO:0070932"(histone H3 deacetylation)|go:"GO:0070933"(histone H4 deacetylation)|go:"GO:0071300"(cellular response to retinoic acid)|go:"GO:0071560"(cellular response to transforming growth factor beta stimulus)|go:"GO:1902437"(positive regulation of male mating behavior)|go:"GO:1903351"(cellular response to dopamine)|go:"GO:1990841"(promoter-specific chromatin binding)|go:"GO:2000273"(positive regulation of signaling receptor activity)|go:"GO:2000757"(negative regulation of peptidyl-lysine acetylation)|interpro:IPR000286(Histone deacetylase superfamily)|interpro:IPR003084(Histone deacetylase)|interpro:IPR023696|interpro:IPR023801|interpro:IPR037138|mint:Q92769|rcsb pdb:3MAX|rcsb pdb:4LXZ|rcsb pdb:4LY1|rcsb pdb:5IWG|rcsb pdb:5IX0|rcsb pdb:6G3O|rcsb pdb:6WBW|go:"GO:0048714"(positive regulation of oligodendrocyte differentiation)|ensembl:ENSG00000196591(gene)|ensembl:ENST00000519065(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0001975"(response to amphetamine)|go:"GO:0003300"(cardiac muscle hypertrophy)|go:"GO:0003682"(chromatin binding)|go:"GO:0003723"(RNA binding)|rcsb pdb:6WHN|rcsb pdb:6WHO|rcsb pdb:6WHQ|rcsb pdb:6WHZ|rcsb pdb:6WI3|rcsb pdb:6XDM|rcsb pdb:6XEB|rcsb pdb:6XEC|rcsb pdb:7KBG|rcsb pdb:7KBH|rcsb pdb:7LTG|rcsb pdb:7LTK|rcsb pdb:7LTL|reactome:R-HSA-193670|reactome:R-HSA-2122947|reactome:R-HSA-2644606|reactome:R-HSA-2894862|reactome:R-HSA-3214815|reactome:R-HSA-350054|reactome:R-HSA-427389|reactome:R-HSA-427413|reactome:R-HSA-4551638|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9022692|reactome:R-HSA-9022699|reactome:R-HSA-9615017|reactome:R-HSA-9619665|reactome:R-HSA-9679191|reactome:R-HSA-983231|rcsb pdb:6WBZ|refseq:NP_001518.3|dip:DIP-24220N|refseq:XP_011534090.1|refseq:XP_016866288.1 go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:K4PpGz9E9/TrQZsgvrJuc+uYCn89606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q16576 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-352227|ensembl:ENSP00000369427|intact:EBI-3505029|uniprotkb:Q5JP00 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:rbbp7_human(display_long)|uniprotkb:RBBP7(gene name)|psi-mi:RBBP7(display_short)|uniprotkb:RBAP46(gene name synonym)|uniprotkb:Retinoblastoma-binding protein 7(gene name synonym)|uniprotkb:Retinoblastoma-binding protein p46(gene name synonym)|uniprotkb:Histone acetyltransferase type B subunit 2(gene name synonym)|uniprotkb:Nucleosome-remodeling factor subunit RBAP46(gene name synonym) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_002884.1|ensembl:ENST00000380087(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0003723"(RNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006260"(DNA replication)|go:"GO:0006325"(chromatin organization)|go:"GO:0016581"(NuRD complex)|go:"GO:0030308"(negative regulation of cell growth)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042393"(histone binding)|go:"GO:0048545"(response to steroid hormone)|go:"GO:0070370"(cellular heat acclimation)|interpro:IPR001680(WD40 repeat)|interpro:IPR015943(WD40/YVTN repeat-like)|interpro:IPR019775|interpro:IPR020472|interpro:IPR022052|interpro:IPR036322|mint:Q16576|rcsb pdb:3CFS|rcsb pdb:3CFV|rcsb pdb:7M3X|reactome:R-HSA-212300|reactome:R-HSA-2559580|reactome:R-HSA-3214815|reactome:R-HSA-3214841|reactome:R-HSA-3214847|reactome:R-HSA-3214858|reactome:R-HSA-427389|reactome:R-HSA-5617472|reactome:R-HSA-606279|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-8951664|reactome:R-HSA-8953750|reactome:R-HSA-9609690|reactome:R-HSA-9679191|reactome:R-HSA-9710421|ensembl:ENSG00000102054(gene)|refseq:NP_001185648.1|dip:DIP-436N go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:qANLG0ui7jm3Uy4+IRnxR8Kir7c9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q09028 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-620823|uniprotkb:B4DRH0|ensembl:ENSP00000362592|uniprotkb:P31149|uniprotkb:Q53H02|uniprotkb:Q96BV9|uniprotkb:D3DPQ3|uniprotkb:B2R6G9 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:rbbp4_human(display_long)|uniprotkb:Retinoblastoma-binding protein 4(gene name synonym)|uniprotkb:Retinoblastoma-binding protein p48(gene name synonym)|uniprotkb:Chromatin assembly factor 1 subunit C(gene name synonym)|uniprotkb:Chromatin assembly factor I p48 subunit(gene name synonym)|uniprotkb:Nucleosome-remodeling factor subunit RBAP48(gene name synonym)|uniprotkb:RBBP4(gene name)|psi-mi:RBBP4(display_short)|uniprotkb:RBAP48(gene name synonym) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 ensembl:ENSG00000162521(gene)|ensembl:ENST00000373493(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000785"(chromatin)|go:"GO:0000978"(RNA polymerase II cis-regulatory region sequence-specific DNA binding)|go:"GO:0005634"(nucleus)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005829"(cytosol)|go:"GO:0006260"(DNA replication)|go:"GO:0006335"(DNA replication-dependent chromatin assembly)|go:"GO:0006336"(DNA replication-independent chromatin assembly)|go:"GO:0006338"(chromatin remodeling)|go:"GO:0007049"(cell cycle)|go:"GO:0008285"(negative regulation of cell population proliferation)|go:"GO:0016580"(Sin3 complex)|go:"GO:0016581"(NuRD complex)|go:"GO:0016589"(NURF complex)|go:"GO:0031497"(chromatin assembly)|go:"GO:0032991"(protein-containing complex)|go:"GO:0033186"(CAF-1 complex)|go:"GO:0035098"("ESC/E(Z) complex")|go:"GO:0042393"(histone binding)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|interpro:IPR001680(WD40 repeat)|interpro:IPR015943(WD40/YVTN repeat-like)|interpro:IPR019775|interpro:IPR020472|interpro:IPR022052|mint:Q09028|rcsb pdb:2XU7|rcsb pdb:3GFC|rcsb pdb:4PBY|rcsb pdb:4PBZ|rcsb pdb:4PC0|rcsb pdb:4R7A|rcsb pdb:5FXY|rcsb pdb:5VTB|rcsb pdb:5WAI|rcsb pdb:5WAK|rcsb pdb:5XWR|rcsb pdb:5XXQ|rcsb pdb:5Y1U|rcsb pdb:6BW3|rcsb pdb:6BW4|rcsb pdb:6C23|rcsb pdb:6C24|rcsb pdb:6G16|rcsb pdb:6NQ3|rcsb pdb:6WKR|rcsb pdb:6ZRC|rcsb pdb:6ZRD|rcsb pdb:7AOA|rcsb pdb:7KSO|rcsb pdb:7KSR|rcsb pdb:7KTP|rcsb pdb:7M40|reactome:R-HSA-1362277|reactome:R-HSA-1362300|reactome:R-HSA-1538133|reactome:R-HSA-156711|reactome:R-HSA-212300|reactome:R-HSA-2559580|reactome:R-HSA-3214815|reactome:R-HSA-3214841|reactome:R-HSA-427389|reactome:R-HSA-5617472|reactome:R-HSA-606279|reactome:R-HSA-6804758|reactome:R-HSA-69202|reactome:R-HSA-69205|reactome:R-HSA-69656|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-8953750|reactome:R-HSA-9609690|reactome:R-HSA-9679191|reactome:R-HSA-9710421|interpro:IPR036322|refseq:NP_001128727.1|refseq:NP_001128728.1|refseq:NP_005601.1|dip:DIP-33495N go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:CbyJMIjpW1A4sZijP0IGRYc8o4I9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:Q9BTC8 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-2461787|uniprotkb:Q9NSP2|uniprotkb:Q9ULF4|ensembl:ENSP00000385823 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:mta3_human(display_long)|uniprotkb:MTA3(gene name)|psi-mi:MTA3(display_short)|uniprotkb:KIAA1266(gene name synonym) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_001269684.1|refseq:NP_001269685.1|refseq:NP_065795.1|refseq:NP_001317371.1|dip:DIP-47460N|ensembl:ENST00000405094(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0008270"(zinc ion binding)|go:"GO:0008284"(positive regulation of cell population proliferation)|go:"GO:0010971"(positive regulation of G2/M transition of mitotic cell cycle)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043231"(intracellular membrane-bounded organelle)|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0044877"(protein-containing complex binding)|go:"GO:0045892"(negative regulation of transcription, DNA-templated)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR017930|interpro:IPR035170|interpro:IPR040138|interpro:IPR043151|mint:Q9BTC8|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191|ensembl:ENSG00000057935(gene) go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:wxPsfH6FguY8n4PFwaj1iJNTWPc9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry) uniprotkb:O95983 uniprotkb:O94776 intact:EBI-1783068|uniprotkb:Q6PIL9|uniprotkb:Q6PJZ9|uniprotkb:Q86XF4|uniprotkb:A8K4B7|uniprotkb:D6W5Z2|ensembl:ENSP00000412302 intact:EBI-1783035|uniprotkb:Q68DB1|uniprotkb:Q9UQB5|ensembl:ENSP00000278823 psi-mi:mbd3_human(display_long)|uniprotkb:MBD3(gene name)|psi-mi:MBD3(display_short)|uniprotkb:Methyl-CpG-binding protein MBD3(gene name synonym) psi-mi:mta2_human(display_long)|uniprotkb:MTA2(gene name)|psi-mi:MTA2(display_short)|uniprotkb:MTA1L1(gene name synonym)|uniprotkb:PID(gene name synonym)|uniprotkb:Metastasis-associated 1-like 1(gene name synonym)|uniprotkb:p53 target protein in deacetylase complex(gene name synonym) psi-mi:"MI:0030"(cross-linking study) Kloet et al. (2014) imex:IM-23066|pubmed:25123934 taxid:9606(human)|taxid:9606(Homo sapiens) taxid:9606(human)|taxid:9606(Homo sapiens) psi-mi:"MI:0914"(association) psi-mi:"MI:0471"(MINT) intact:EBI-9692565|imex:IM-23066-3 - psi-mi:"MI:1060"(spoke expansion) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0499"(unspecified role) psi-mi:"MI:0496"(bait) psi-mi:"MI:0498"(prey) psi-mi:"MI:0326"(protein) psi-mi:"MI:0326"(protein) refseq:NP_001268382.1|refseq:NP_001268383.1|dip:DIP-46517N|ensembl:ENSG00000071655(gene)|ensembl:ENST00000434436(transcript)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0000792"(heterochromatin)|go:"GO:0001701"(in utero embryonic development)|go:"GO:0003677"(DNA binding)|go:"GO:0003682"(chromatin binding)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005737"(cytoplasm)|go:"GO:0006346"(DNA methylation-dependent heterochromatin assembly)|go:"GO:0007420"(brain development)|go:"GO:0007507"(heart development)|go:"GO:0007568"(aging)|go:"GO:0008327"(methyl-CpG binding)|go:"GO:0009888"(tissue development)|go:"GO:0016573"(histone acetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0031667"(response to nutrient levels)|go:"GO:0032355"(response to estradiol)|go:"GO:0032991"(protein-containing complex)|go:"GO:0043044"|go:"GO:0044030"(regulation of DNA methylation)|go:"GO:0048568"(embryonic organ development)|interpro:IPR001739(Methyl-CpG DNA binding)|interpro:IPR016177(DNA-binding, integrase-type)|interpro:IPR025884|interpro:IPR032343|interpro:IPR037965|mint:O95983|rcsb pdb:2MB7|rcsb pdb:6CC8|rcsb pdb:6CCG|rcsb pdb:6CEU|rcsb pdb:6CEV|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 refseq:NP_004730.2|refseq:NP_001317221.1|dip:DIP-46519N|ensembl:ENSG00000149480(gene)|ensembl:ENST00000278823(transcript)|go:"GO:0000118"(histone deacetylase complex)|go:"GO:0000122"(negative regulation of transcription by RNA polymerase II)|go:"GO:0000785"(chromatin)|go:"GO:0003682"(chromatin binding)|go:"GO:0003713"(transcription coactivator activity)|go:"GO:0003714"(transcription corepressor activity)|go:"GO:0004407"(histone deacetylase activity)|go:"GO:0005654"(nucleoplasm)|go:"GO:0005667"(transcription regulator complex)|go:"GO:0006306"(DNA methylation)|go:"GO:0006333"(chromatin assembly or disassembly)|go:"GO:0008270"(zinc ion binding)|go:"GO:0010762"(regulation of fibroblast migration)|go:"GO:0016020"(membrane)|go:"GO:0016575"(histone deacetylation)|go:"GO:0016581"(NuRD complex)|go:"GO:0032991"(protein-containing complex)|go:"GO:0042826"(histone deacetylase binding)|go:"GO:0043044"|go:"GO:0043565"(sequence-specific DNA binding)|go:"GO:0045944"(positive regulation of transcription by RNA polymerase II)|go:"GO:0061629"(RNA polymerase II-specific DNA-binding transcription factor binding)|interpro:IPR000679(Zinc finger, GATA-type)|interpro:IPR000949(ELM2)|interpro:IPR001005(SANT, DNA-binding)|interpro:IPR001025(Bromo adjacent region)|interpro:IPR009057(Homeodomain-like)|interpro:IPR017884|interpro:IPR035170|interpro:IPR037964|interpro:IPR040138|interpro:IPR043151|mint:O94776|reactome:R-HSA-3214815|reactome:R-HSA-427389|reactome:R-HSA-6804758|reactome:R-HSA-73762|reactome:R-HSA-8943724|reactome:R-HSA-9679191 go:"GO:0005634"(nucleus) - - figure legend:f3|full coverage:Only protein-protein interactions|curation depth:imex curation taxid:-1(in vitro)|taxid:-1(In vitro) - 2014/08/20 2014/10/16 rogid:lm8jh0YVLdljXDhjkTm9B1YSsWA9606 rogid:D4wOsdMJYhY/ltvcnnuMHqNrFkc9606 intact-crc:89F4D361516F2BD0|rigid:dI+chpMTdmRJ0nNIyMdgnXLPfpI false tandem tag:?-? - - - psi-mi:"MI:0427"(Identification by mass spectrometry) psi-mi:"MI:0427"(Identification by mass spectrometry)