IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Cell (0092-8674) 2013 imex curation Nardini M., Gnesutta N., Donati G., Gatta R., Forni C., Fossati A., Vonrhein C., Moras D., Romier C., Bolognesi M., Mantovani R. martino.bolognesi@unimi.it, mantor@unimi.it 26-Jun-2013: Contacted by IntAct-Help. Only protein-protein interactions human-hct116 Human colon carcinoma HCT116 cells hct116 Human colon carcinoma line HCT116 ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Nardini M., Gnesutta N., Donati G., Gatta R., Forni C., Fossati A., Vonrhein C., Moras D., Romier C., Bolognesi M., Mantovani R. Histone 2 and 3 interactions could not be captured as these could not be ascribed to a single gene product. martino.bolognesi@unimi.it, mantor@unimi.it Accepted 2013-JUN-20 by PPORRAS 26-Jun-2013: Contacted by IntAct-Help. Cell (0092-8674) 2013 Only protein-protein interactions imex curation Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Cell (0092-8674) 2013 imex curation Nardini M., Gnesutta N., Donati G., Gatta R., Forni C., Fossati A., Vonrhein C., Moras D., Romier C., Bolognesi M., Mantovani R. martino.bolognesi@unimi.it, mantor@unimi.it 26-Jun-2013: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Nardini M., Gnesutta N., Donati G., Gatta R., Forni C., Fossati A., Vonrhein C., Moras D., Romier C., Bolognesi M., Mantovani R. martino.bolognesi@unimi.it, mantor@unimi.it Accepted 2013-JUN-20 by PPORRAS 26-Jun-2013: Contacted by IntAct-Help. Cell (0092-8674) 2013 Only protein-protein interactions imex curation Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Cell (0092-8674) 2013 imex curation Nardini M., Gnesutta N., Donati G., Gatta R., Forni C., Fossati A., Vonrhein C., Moras D., Romier C., Bolognesi M., Mantovani R. martino.bolognesi@unimi.it, mantor@unimi.it 26-Jun-2013: Contacted by IntAct-Help. Only protein-protein interactions human-hct116 Human colon carcinoma HCT116 cells hct116 Human colon carcinoma line HCT116 ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Nardini M., Gnesutta N., Donati G., Gatta R., Forni C., Fossati A., Vonrhein C., Moras D., Romier C., Bolognesi M., Mantovani R. Two round of immunoprecipitation were undertaken in this re-ChIP experiment. Histone 2 and 3 interactions could not be captured as these could not be ascribed to a single gene product. martino.bolognesi@unimi.it, mantor@unimi.it Accepted 2013-JUN-20 by PPORRAS 26-Jun-2013: Contacted by IntAct-Help. Cell (0092-8674) 2013 Only protein-protein interactions imex curation pcna_human_gene Proliferating cell nuclear antigen gene gene gene human Homo sapiens Human son_human_gene Protein SON gene gene gene human Homo sapiens Human cks2_human_gene Cyclin-dependent kinases regulatory subunit 2 gene gene gene human Homo sapiens Human cdk1_human_gene Cyclin-dependent kinase 1 gene gene gene human Homo sapiens Human ccnb1_human_gene G2/mitotic-specific cyclin-B1 gene gene gene human Homo sapiens Human nfya_human Nuclear transcription factor Y subunit alpha NFYA Nuclear transcription factor Y subunit A CAAT box DNA-binding protein subunit A protein protein human Homo sapiens Human MEQYTANSNSSTEQIVVQAGQIQQQQQGGVTAVQLQTEAQVASASGQQVQTLQVVQGQPLMVQVSGGQLITSTGQPIMVQAVPGGQGQTIMQVPVSGTQGLQQIQLVPPGQIQIQGGQAVQVQGQQGQTQQIIIQQPQTAVTAGQTQTQQQIAVQGQQVAQTAEGQTIVYQPVNADGTILQQVTVPVSGMITIPAASLAGAQIVQTGANTNTTSSGQGTVTVTLPVAGNVVNSGGMVMMVPGAGSVPAIQRIPLPGAEMLEEEPLYVNAKQYHRILKRRQARAKLEAEGKIPKERRKYLHESRHRHAMARKRGEGGRFFSPKEKDSPHMQDPNQADEEAMTQIIRVS D00BE17041EB1A9E nfyb_human Nuclear transcription factor Y subunit beta NFYB HAP3 Nuclear transcription factor Y subunit B CAAT box DNA-binding protein subunit B protein protein human Homo sapiens Human MTMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFREAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLITTDGQQQNVMVYTTSYQQISGVQQIQFS 1ADFA0E45F3CF972 abc3b_human_gene DNA dC->dU-editing enzyme APOBEC-3B gene gene gene human Homo sapiens Human pdia4_human_gene Protein disulfide-isomerase A4 gene gene human Homo sapiens Human ccnb2_human_gene G2/mitotic-specific cyclin-B2 gene gene gene human Homo sapiens Human hsp13_human_gene Heat shock 70 kDa protein 13 gene gene gene human Homo sapiens Human nfyc_human Nuclear transcription factor Y subunit gamma NFYC Nuclear transcription factor Y subunit C CAAT box DNA-binding protein subunit C Transactivator HSM-1/2 protein protein human Homo sapiens Human MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQGQRNASQGKPRRCLKETLQITQTEVQQGQQQFSQFTDGQRNSVQQARVSELTGEAEPREVKATGNSTPCTSSLPTTHPPSHRAGASCVCCSQPQQSSTSPPPSDALQWVVVEVSGTPNQLETHRELHAPLPGMTSLSPLHPSQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQAPQVTGD B17B2C7F622653B9 nfya-nfyb 2 15 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 10 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) 9 unspecified role unspecified role neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) physical association physical association Figs 1, 2B, Supp. Fig. 2; Supp. Table 1 3.1A Rworking = 0.19 Rfree = 0.25 nfyb-ccnb2 1 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 13 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-ccnb1 1 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-pcna 1 4 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-cdk1 1 7 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-pdia4 1 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 12 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-cks2 1 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 6 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-abc3b 1 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 11 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-hsp13 1 14 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 6B Lys138Arg mutation of NFYB prevented the the deposition of H3 methylations on the CCAAT promoters but had no effect on the binding of NFYB. nfyb-cdk1-1 3 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 7 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 7A NF-YB is ubiquitinated in vivo on active promoters nfyb-ccnb2-1 3 10 unspecified role unspecified role bait bait region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 13 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 7A NF-YB is ubiquitinated in vivo on active promoters nfyb-son 3 5 unspecified role unspecified role prey prey ccaat promoter region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 10 unspecified role unspecified role bait bait region ubiquitinylated lysine ubiquitinylated lysine undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined association association Fig. 7A NF-YB is ubiquitinated in vivo on active promoters