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/ http://www.ebi.ac.uk/ kim-2009a-1 Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast ch-ip chromatin immunoprecipitation assay ch-ip primer specific pcr primer specific pcr Kim T., Buratowski S. Chromatin - Epigenetic interactions resulting in chromatin modulation steveb@hms.harvard.edu Cell (0092-8674) 2009 Only protein-protein interactions 4 imex curation kim-2009a-2 Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Kim T., Buratowski S. Chromatin - Epigenetic interactions resulting in chromatin modulation steveb@hms.harvard.edu Cell (0092-8674) 2009 Only protein-protein interactions 4 imex curation kim-2009a-3 Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Kim T., Buratowski S. Chromatin - Epigenetic interactions resulting in chromatin modulation steveb@hms.harvard.edu Cell (0092-8674) 2009 Only protein-protein interactions 4 imex curation kim-2009a-4 Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. in vitro In vitro pull down pull down anti tag western anti tag western blot anti tag western Kim T., Buratowski S. Chromatin - Epigenetic interactions resulting in chromatin modulation steveb@hms.harvard.edu Cell (0092-8674) 2009 Only protein-protein interactions 4 imex curation h3_yeast Histone H3 SIN2 YNL031C N2749 HHT1 YBR010W YBR0201 HHT2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS A6115FEB480AC67A adh1_yeast_gene Yeast ADH1 gene gene gene yeast Saccharomyces cerevisiae Baker's yeast h4_yeast Histone H4 N2752 YBR0122 YBR009C YNL030W HHF1 HHF2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG 69B7D1F89E62DE41 pyk1_yeast_gene Yeast Pyk1 gene gene gene yeast Saccharomyces cerevisiae Baker's yeast pma1_yeast_gene Yeast PMA1 gene gene gene yeast Saccharomyces cerevisiae Baker's yeast yef3_yeast_gene YEF3 gene gene gene yeast Saccharomyces cerevisiae Baker's yeast hos2_yeast Probable histone deacetylase HOS2 G1330 YGL194C HOS2 protein protein yeast Saccharomyces cerevisiae Baker's yeast MSGTFSYDVKTKENEPLFEFNSAYSPRVSYHFNSKVSHYHYGVKHPMKPFRLMLTDHLVSSYGLHKIMDLYETRSATRDELLQFHSEDYVNFLSKVSPENANKLPRGTLENFNIGDDCPIFQNLYDYTTLYTGASLDATRKLINNQSDIAINWSGGLHHAKKNSPSGFCYVNDIVLSILNLLRYHPRILYIDIDLHHGDGVQEAFYTTDRVFTLSFHKYNGEFFPGTGDLTEIGCDKGKHFALNVPLEDGIDDDSYINLFKSIVDPLIMTFKPTLIVQQCGADSLGHDRLGCFNLNIKAHGECVKFVKSFGLPMLVVGGGGYTPRNVSRLWTYETGILNDVLLPEDIPEDIPFRDSFGPDYSLYPMLDDLYENKNSKKLLEDIRIRCLENIRYLQGAPSVRMDAECIPTQDISALTEEEDKIIQEMNEETEADSSNRLEEMEKENSGLIAFS set3_yeast SET domain-containing protein 3 SET3 YKR029C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSVPNSKEQSLLDDASTLLLFSKGKKRAEEASKIGSKTDTIEHDESHEREKKGAIEMAAAALATASTVSLPLKKATEQSAAEAATSTAAKEETENQPQKQPQWPVPDSYIVDPDAGIITCICDLNDDDGFTIQCDHCNRWQHAICYGIKDIGMAPDDYLCNSCDPREVDINLARKIQQERINVKTVEPSSSNNSASNKNNGRDRASSTTISDVGDSFSTDQDNTNHRDKRRKRNPSNNSIDSKNESASVNSSDGLTSMPKKKEHFLSAKDAYGAIYLPLKDNVFKSDLIEPFLNKHMDDNWVIQYPHKTFKSVSIEVKPYADIAYSRTYPGFTKLGVYLKKDCIKGDFIQEILGELDFYKNYLTDPRNHYRIWGTAKRRVIFHSHWPIYIDARLSGNSTRYLRRSCQPNVELVTIKLQDTDNRNDKSSGRKSSRIKFVLRALRDISEDEELYIKWQWDSKHPILKLIKGMTIDSLDDLERYGLINSVETILSNGECGCGNNSKDCYLLKVKRYAQSLYKSVKSRGKMNNRYKLNEILNQYNCKKRREPPILHRLEEKAQNTIERAPILLNNFYRQKFLNRNNGPKIPQKNTIDSTNNPDDIAKPFKFALFAQHSSNISVPKKNETSEKPLIITKSTDYDESHITNIEELPIPVLLPINKTSRQTANDVEESQSKNEHKLSRTPSLSNFNKELSKEAQHSQAKTKEIMTEASVNSRRESTPESIMHLSDFSSSQLHSKKKLSFADYRKKLLK 934621768C36230B h3-adh1-1 Binding of H3 to the Adh1 gene 822345 n/a 822349 unspecified role unspecified role bait bait n/a 822350 unspecified role unspecified role prey prey association association false false false Fig.1C, 3B Identified H3 proteins acetylated to histones 10 and 15 h4-adh1-1 Binding of H4 to the Adh1 gene 822345 n/a 822350 unspecified role unspecified role prey prey n/a 822351 unspecified role unspecified role bait bait association association false false false Fig.1C, 3B Identified tetra-acetylated H4 proteins h3-pyk1-1 Binding of H3 to the Pyk1 gene 822345 n/a 822352 unspecified role unspecified role prey prey n/a 822349 unspecified role unspecified role bait bait association association false false false Fig.1C, 3B Identified H3 proteins acetylated to histones 10 and 15 h4-pyk1-1 Binding of H4 to the Pyk1 gene 822345 n/a 822352 unspecified role unspecified role prey prey n/a 822351 unspecified role unspecified role bait bait association association false false false Fig.1C, 3B Identified tetra-acetylated H4 proteins h3-pma1-1 Binding of H3 to the Pma1 gene 822345 n/a 822349 unspecified role unspecified role bait bait n/a 822353 unspecified role unspecified role prey prey association association false false false Fig.1B, 3B Identified H3 proteins acetylated to histones 10 and 15 h4-pma1-1 Binding of H4 to the Pma1 gene 822345 n/a 822353 unspecified role unspecified role prey prey n/a 822351 unspecified role unspecified role bait bait association association false false false Fig.1B, 3B Identified tetra-acetylated H4 proteins h3-yef3-1 Binding of H3 to the Yef3 gene 822345 n/a 822354 unspecified role unspecified role prey prey n/a 822349 unspecified role unspecified role bait bait association association false false false Figs.1A, 2A, 3A, 3C Identified H3 proteins acetylated to histones 10 and 15 h4-yef3-1 Binding of H4 to the Yef3 gene 822345 n/a 822354 unspecified role unspecified role prey prey n/a 822351 unspecified role unspecified role bait bait association association false false false Figs.1A, 2A, 3A, 3C Identified tetra-acetylated H4 proteins hos2-yef3-1 Binding of Hos2 to the Yef3 gene 822345 n/a 822354 unspecified role unspecified role prey prey n/a 822355 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 false association association false false false Fig. 4C, 4D, 4E set3-h3-1 Binding of Set3 to H3 identified by coimmunopreciptiation 822346 n/a 822349 unspecified role unspecified role prey prey n/a 822356 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 false physical association physical association false false false Interaction required the presence of Set1 Fig. 4A hos2-h3-1 Binding of Hos2 to H3 identified by coimmunopreciptiation 822346 n/a 822355 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 false n/a 822349 unspecified role unspecified role prey prey physical association physical association false false false Interaction required the presence of Set1 Fig. 4A h4-set3-1 Interaction between H4 and Set3 identified by coimmunoprecipitation 822347 n/a 822351 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 false n/a 822356 unspecified role unspecified role prey prey P36124:p.Trp140Ala mutation decreasing mutation decreasing interaction hotspot hotspot mutation decreasing certain certain sequence position certain certain certain sequence position certain false region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 4B hos2-h3-2 Binding of Hos2 to H3 identified by pulldown 822348 n/a 822349 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false lys-5 (required) 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 false in vitro In vitro n/a 822355 unspecified role unspecified role prey prey 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 false yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast physical association physical association false false false Interaction required the presence of Set3 Fig. 5C, 5D