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/ Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Cell (0092-8674) 2007 imex curation Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org 01-April-2008: Contacted by JYOTI. davet Only protein-protein interactions 4 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column western blot western blot Immuno blot Immuno blot Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org Accepted 2008-FEB-9 by DAVET. 01-April-2008: Contacted by JYOTI. Cell (0092-8674) 2007 davet Only protein-protein interactions 4 imex curation Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Cell (0092-8674) 2007 imex curation Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org 01-April-2008: Contacted by JYOTI. davet Only protein-protein interactions 4 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org Accepted 2008-FEB-9 by DAVET. 01-April-2008: Contacted by JYOTI. Cell (0092-8674) 2007 davet Only protein-protein interactions 4 imex curation Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Cell (0092-8674) 2007 imex curation Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org 01-April-2008: Contacted by JYOTI. davet Only protein-protein interactions 4 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa full dna sequence full identification by DNA sequencing full dna sequence Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org Accepted 2008-FEB-9 by DAVET. 01-April-2008: Contacted by JYOTI. Cell (0092-8674) 2007 davet Only protein-protein interactions 4 imex curation Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Histone Crosstalk between H2B Monoubiquitination and H3 Methylation Mediated by COMPASS. Cell (0092-8674) 2007 imex curation Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org 01-April-2008: Contacted by JYOTI. davet Only protein-protein interactions 4 yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast tap tandem affinity purification TAP TAP tap mudpit multidimensional protein identification technology mudpit Lee JS., Shukla A., Schneider J., Swanson SK., Washburn MP., Florens L., Bhaumik SR., Shilatifard A. Chromatin - Epigenetic interactions resulting in chromatin modulation Superose 6 HR column ash@stowers-institute.org Accepted 2008-FEB-9 by DAVET. 01-April-2008: Contacted by JYOTI. Cell (0092-8674) 2007 davet Only protein-protein interactions 4 imex curation sdc1_yeast COMPASS component SDC1 SDC1 SAF19 CPS25 YDR469W Complex proteins associated with SET1 protein SDC1 Set1C component SDC1 Suppressor of CDC25 protein 1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNESENSPQHNEVTVPMVEDTSSNADIPMEQIQREDNKNYDKHDNECFDMNGNHNNNSDNLQFDSVPSSATKDLKNIKSVTNQNVKIEESSSTNSVIEESSEPKISKLENVNLAATVGGSQTRKYLNTNVTPHLLAGMRLIAVQQPEDPLRVLGEYLIEQSNILKSGEKESNASK B40247D641124306 B40247D641124306 adh1_yeast_gene Yeast ADH1 gene gene gene yeast Saccharomyces cerevisiae Baker's yeast dot1_yeast Histone-lysine N-methyltransferase, H3 lysine-79 specific DOT1 PCH1 YDR440W D9461.26 KMT4 Histone H3-K79 methyltransferase Disrupter of telomere silencing protein 1 Lysine N-methyltransferase 4 protein protein yeast Saccharomyces cerevisiae Baker's yeast MGGQESISNNNSDSFIMSSPNLDSQESSISPIDEKKGTDMQTKSLSSYSKGTLLSKQVQNLLEEANKYDPIYGSSLPRGFLRDRNTKGKDNGLVPLVEKVIPPIHKKTNNRNTRKKSSTTTKKDVKKPKAAKVKGKNGRTNHKHTPISKQEIDTAREKKPLKKGRANKKNDRDSPSSTFVDWNGPCLRLQYPLFDIEYLRSHEIYSGTPIQSISLRTNSPQPTSLTSDNDTSSVTTAKLQSILFSNYMEEYKVDFKRSTAIYNPMSEIGKLIEYSCLVFLPSPYAEQLKETILPDLNASFDNSDTKGFVNAINLYNKMIREIPRQRIIDHLETIDKIPRSFIHDFLHIVYTRSIHPQANKLKHYKAFSNYVYGELLPNFLSDVYQQCQLKKGDTFMDLGSGVGNCVVQAALECGCALSFGCEIMDDASDLTILQYEELKKRCKLYGMRLNNVEFSLKKSFVDNNRVAELIPQCDVILVNNFLFDEDLNKKVEKILQTAKVGCKIISLKSLRSLTYQINFYNVENIFNRLKVQRYDLKEDSVSWTHSGGEYYISTVMEDVDESLFSPAARGRRNRGTPVKYTR 05CAA6A8F8CBAB9A swd3_yeast COMPASS component SWD3 CPS30 YBR175W YBR1237 SWD3 SAF35 Complex proteins associated with SET1 protein SWD3 Set1C component SWD3 protein protein yeast Saccharomyces cerevisiae Baker's yeast MFQFVTPVGTQNGLKATCAKISPDGQFLAITQGLNILIYDINRRTVSQTLVTSHARPFSELCWSPDGQCIATASDDFSVEIIHLSYGLLHTFIGHTAPVISLTFNRKGNLLFTSSMDESIKIWDTLNGSLMKTISAHSEAVVSVDVPMNDSSILSSGSYDGLIRIFDAETGHCLKTLTYDKDWKRENGVVPISQVKFSENARYLLVKSLDGVVKIWDCIGGCVVRTFQVQPLEKGVLHHSCGMDFLNPEDGSTPLVISGYENGDIYCWNSDTKSLLQLLDGSLYHHSSPVMSIHCFGNIMCSLALNGDCCLWRWV E8E88C483D1CD776 E8E88C483D1CD776 swd1_yeast COMPASS component SWD1 CPS50 YAR003W FUN16 SWD1 SAF49 Complex proteins associated with SET1 protein SWD1 Set1C component SWD1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MNILLQDPFAVLKEHPEKLTHTIENPLRTECLQFSPCGDYLALGCANGALVIYDMDTFRPICVPGNMLGAHVRPITSIAWSPDGRLLLTSSRDWSIKLWDLSKPSKPLKEIRFDSPIWGCQWLDAKRRLCVATIFEESDAYVIDFSNDPVASLLSKSDEKQLSSTPDHGYVLVCTVHTKHPNIIIVGTSKGWLDFYKFHSLYQTECIHSLKITSSNIKHLIVSQNGERLAINCSDRTIRQYEISIDDENSAVELTLEHKYQDVINKLQWNCILFSNNTAEYLVASTHGSSAHELYIWETTSGTLVRVLEGAEEELIDINWDFYSMSIVSNGFESGNVYVWSVVIPPKWSALAPDFEEVEENVDYLEKEDEFDEVDEAEQQQGLEQEEEIAIDLRTREQYDVRGNNLLVERFTIPTDYTRIIKMQSS 90C389612AB66231 90C389612AB66231 h3_yeast Histone H3 SIN2 YNL031C N2749 HHT1 YBR010W YBR0201 HHT2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS A6115FEB480AC67A A6115FEB480AC67A bre2_yeast COMPASS component BRE2 Complex proteins associated with SET1 protein BRE2 Set1C component BRE2 Brefeldin-A sensitivity protein 2 CPS60 YLR015W BRE2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MKLGIIPYQEGTDIVYKNALQGQQEGKRPNLPQMEATHQIKSSVQGTSYEFVRTEDIPLNRRHFVYRPCSANPFFTILGYGCTEYPFDHSGMSVMDRSEGLSISRDGNDLVSVPDQYGWRTARSDVCIKEGMTYWEVEVIRGGNKKFADGVNNKENADDSVDEVQSGIYEKMHKQVNDTPHLRFGVCRREASLEAPVGFDVYGYGIRDISLESIHEGKLNCVLENGSPLKEGDKIGFLLSLPSIHTQIKQAKEFTKRRIFALNSHMDTMNEPWREDAENGPSRKKLKQETTNKEFQRALLEDIEYNDVVRDQIAIRYKNQLFFEATDYVKTTKPEYYSSDKRERQDYYQLEDSYLAIFQNGKYLGKAFENLKPLLPPFSELQYNEKFYLGYWQHGEARDESNDKNTTSAKKKKQQQKKKKGLILRNKYVNNNKLGYYPTISCFNGGTARIISEEDKLEYLDQIRSAYCVDGNSKVNTLDTLYKEQIAEDIVWDIIDELEQIALQQ D5B33221E9F10379 D5B33221E9F10379 pho84_yeast_gene Inorganic phosphate transporter PHO84 gene gene yeast Saccharomyces cerevisiae Baker's yeast swd2_yeast COMPASS component SWD2 CPS35 YKL018W SWD2 SAF37 Complex proteins associated with SET1 protein SWD2 Set1C component SWD2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MTTVSINKPNLLKFKHVKSFQPQEKDCGPVTSLNFDDNGQFLLTSSSNDTMQLYSATNCKFLDTIASKKYGCHSAIFTHAQNECIYSSTMKNFDIKYLNLETNQYLRYFSGHGALVNDLKMNPVNDTFLSSSYDESVRLWDLKISKPQVIIPSLVPNCIAYDPSGLVFALGNPENFEIGLYNLKKIQEGPFLIIKINDATFSQWNKLEFSNNGKYLLVGSSIGKHLIFDAFTGQQLFELIGTRAFPMREFLDSGSACFTPDGEFVLGTDYDGRIAIWNHSDSISNKVLRPQGFIPCVSHETCPRSIAFNPKYSMFVTADETVDFYVYDE 5453C193A5C0AEEC 5453C193A5C0AEEC shg1_yeast COMPASS component SHG1 CPS15 YBR258C YBR1726 SHG1 Complex proteins associated with SET1 protein SHG1 Set1C component SHG1 protein protein yeast Saccharomyces cerevisiae Baker's yeast MAYNQEDSKRLSDKYKKEGHFDKLKREILSNPWNNTEENSESFEQALRKRVASTVKEMVNEDEELIFKNRGLTSALIESQLVKDNYLKLGSKMEGDNGDGEKKFDLDVYVRSKLQDPKLLEMIKGQLQETLNSYEEEANGST 12E73F0C3DD225D7 spp1_yeast COMPASS component SPP1 SPP1 SAF41 Complex proteins associated with SET1 protein SPP1 Set1C component SPP1 Suppressor of PRP protein 1 CPS40 YPL138C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSLPQWCPPHSTLKRNPTTGEDVYCICKRPDYGELMVGCDGCDDWFHFTCLHIPEQFKDLVFSFYCPYCQAGITGKNKDAIINGEGSLPKTLWKRKCRISDCYKPCLQDSKYCSEEHGREFVNDIWSRLKTDEDRAVVKKMVEQTGHIDKFKKFGQLDFIDNNIVVKTDDEKEIFDQIVVRDMTLKTLEDDLQEVQEISLPLFKKKLELLEVYLGWLDNVYTEMRKLDDDAASHVECGKEDSKGTKRKKKKNSSRSRARKNICGYCSTYERIPCSVEEFVRDFGSNEEATKIHEVCTKWKCNRHLDWVSTNQEQYLQQIDSLESMQERLQHLIQARKKQLNIQYYEEILRRGL F4B8DFE0CB358CA4 F4B8DFE0CB358CA4 set1_yeast Histone-lysine N-methyltransferase, H3 lysine-4 specific SET1 YTX1 KMT2 COMPASS component SET1 SET domain-containing protein 1 Lysine N-methyltransferase 2 YHR119W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSNYYRRAHASSGSYRQPQEQPQYSRSGHYQYSNGHSHQQYSSQYNQRRRYNHNDGTRRRYNDDRPHSSNNASTRQYYATNNSQSGPYVNKKSDISSRRGMSQSRYSNSNVHNTLASSSGSLPTESALLLQQRPPSVLRYNTDNLKSKFHYFDPIKGEFFNKDKMLSWKATDKEFSETGYYVVKELQDGQFKFKIKHRHPEIKASDPRNENGIMTSGKVATHRKCRNSLILLPRISYDRYSLGPPPSCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKHSILNNIISKFVEINVKKLQKLQENLKKAKEKEAENEKAKELQGKDITLPKEPKVDTLSHSSGSEKRIPYDLLGVVNNRPVLHVSKIFVAKHRFCVEDFKYKLRGYRCAKFIDHPTGIYIIFNDIAHAQTCSNAESGNLTIMSRSRRIPILIKFHLILPRFQNRTRFNKSSSSSNSTNVPIKYESKEEFIEATAKQILKDLEKTLHVDIKKRLIGPTVFDALDHANFPELLAKRELKEKEKRQQIASKIAEDELKRKEEAKRDFDLFGLYGGYAKSNKRNLKRHNSLALDHTSLKRKKLSNGIKPMAHLLNEETDSKETTPLNDEGITRVSKEHDEEDENMTSSSSEEEEEEAPDKKFKSESEPTTPESDHLHGIKPLVPDQNGSSDVLDASSMYKPTATEIPEPVYPPEEYDLKYSQTLSSMDLQNAIKDEEDMLILKQLLSTYTPTVTPETSAALEYKIWQSRRKVLEEEKASDWQIELNGTLFDSELQPGSSFKAEGFRKIADKLKINYLPHRRRVHQPLNTVNIHNERNEYTPELCQREESSNKEPSDSVPQEVSSSRDNRASNRRFQQDIEAQKAAIGTESELLSLNQLNKRKKPVMFARSAIHNWGLYALDSIAAKEMIIEYVGERIRQPVAEMREKRYLKNGIGSSYLFRVDENTVIDATKKGGIARFINHCCDPNCTAKIIKVGGRRRIVIYALRDIAASEELTYDYKFEREKDDEERLPCLCGAPNCKGFLN B7FA5D60F71063FD B7FA5D60F71063FD gal1_yeast_gene Yeast Gal1 gene gene gene yeast Saccharomyces cerevisiae Baker's yeast set1-bre2-9 1 11 unspecified role unspecified role neutral component neutral component 16 unspecified role unspecified role neutral component neutral component physical association physical association As shown in Figure 2I and 2J, both Set1 and Cps60 coelute on analytical size exclusion column at about the same fractions near the 670 kDa molecular weight marker (Figure 2I and 2J, fractions 23-27) Fig. 2I and 2J A point lys124arg mutation in Histone 2B prevents this interaction from occuring set1-swd2-1 1 16 unspecified role unspecified role neutral component neutral component 13 unspecified role unspecified role neutral component neutral component physical association physical association Both Set1 and Cps35 from WT strains coelute from size exclusion at about the same fractions near the 670 kDa molecular weight marker (Figure 3) Fig. 3 A point lys124arg mutation in Histone 2B prevents this interaction from occuring compass_yeast-1 4 13 unspecified role unspecified role prey prey 15 unspecified role unspecified role prey prey 11 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 5 unspecified role unspecified role prey prey 8 unspecified role unspecified role prey prey 16 unspecified role unspecified role prey prey 14 unspecified role unspecified role prey prey 9 unspecified role unspecified role prey prey association association Loss of H2B monoubiquitination (lys124arg mutation) in the cell results in the loss of the association of Swd2 and Shg1 within the complex Fig. 4 swd2-gal1-1 3 17 unspecified role unspecified role prey prey 13 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Both Cps35p and Cps60p are recruited to the coding sequence of the active GAL1 gene The presence of Cps35 at GAL1 is reduced by 90% in the strains lacking rad6 or bearing the Histone H2B K124R single point mutation Fig. 5 and 6E bre2-gal1-2 3 11 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 17 unspecified role unspecified role prey prey physical association physical association Both Cps35p and Cps60p are recruited to the coding sequence of the active GAL1 gene Fig. 5 swd2-adh1-1 3 6 unspecified role unspecified role prey prey 13 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association we performed similar ChIP studies on two constitutively active genes, ADH1 and PHO84 (Figure 5D and 5E) The presence of Cps35 at ADH1 is reduced by 90% in the strains lacking rad6 or bearing the Histone H2B K124R single point mutation Fig. 5D swd2-pho84-1 3 12 unspecified role unspecified role prey prey 13 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association we performed similar ChIP studies on two constitutively active genes, ADH1 and PHO84 (Figure 5D and 5E) The presence of Cps35 at pho84 is reduced by 90% in the strains lacking rad6 or bearing the Histone H2B K124R single point mutation Fig. 5E swd2-dot1-1 2 7 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 13 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 physical association physical association Cps35's interaction with Dot1 was determined in strains bearing FLAG::Cps35 tag and Dot1::9Myc tag. Fig. 6A h3-gal1-1 3 10 unspecified role unspecified role bait bait lys-5 n6me2lys N6,N6-dimethyl-L-lysine (2S)-2-amino-6-(dimethylamino)hexanoic acid MOD_RES N6,N6-dimethyllysine N(zeta)-dimethyllysine N6,N6-dimethyl-L-lysine N6,N6-dimethylated L-lysine epsilon-dimethyllysine lysine derivative Lys(y) Dimethyl N6Me2Lys di-Methylation dimethylk certain certain sequence position certain certain certain sequence position certain 17 unspecified role unspecified role prey prey physical association physical association Histone H3K4-dimethylation at the GAL1 coding sequence is lost in deltaset1. This interaction cannot be detected using anti-H3-dimethyl K5 Abs in the absence of Set1 Fig. 5 and 6D