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/ unhavaithaya-2002-1 MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. yeasx Saccharomyces cerevisiae (Baker's yeast) Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid nucleotide sequence nucleotide sequence identification sequence cloning sequence cloning nucleotide sequence Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu C. elegans cDNA libraries used were a gift from R. Barstead (Oklahoma Medical Research Foundation) and Z. Zhou (Baylor College of Medicine). Cell (0092-8674) 2002 Only protein-protein interactions imex curation unhavaithaya-2002-2 MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. caeel Caenorhabditis elegans anti tag coip anti tag coimmunoprecipitation anti tag coip ms participant Identification by mass spectrometry ms participant Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu C. elegans cDNA libraries used were a gift from R. Barstead (Oklahoma Medical Research Foundation) and Z. Zhou (Baylor College of Medicine). Cell (0092-8674) 2002 Only protein-protein interactions imex curation unhavaithaya-2002-3 MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. caeel-embryo Caenorhabditis elegans embryo embryo Embryo Defined as the development stage prior to the initiation of tissue differentiation. anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu Cell (0092-8674) 2002 Only protein-protein interactions imex curation unhavaithaya-2002-4 MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. caeel Caenorhabditis elegans anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu Cell (0092-8674) 2002 Only protein-protein interactions imex curation unhavaithaya-2002-5 MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. caeel Caenorhabditis elegans anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu Cell (0092-8674) 2002 Only protein-protein interactions imex curation unhavaithaya-2002-6 MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu Cell (0092-8674) 2002 Only protein-protein interactions imex curation unhavaithaya-2002-7 MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. chlae-cos_7 Cercopithecus aethiops simian cells transformed with SV40 Grivet cos_7 cercopithecus aethiops, by transformation with SV40 anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu Cell (0092-8674) 2002 Only protein-protein interactions imex curation pie1_caeel Pharynx and intestine in excess protein 1 pie-1 pic-1 Y49E10.14 protein protein caeel Caenorhabditis elegans MAQTKPIAEQMAALNNSDDTSFAADRSNSLLNATCPARIQNSVDQRKINRSFNDSLSSGYSGKWLRPKREALKITPLAQIDEAPATKRHSSAKDKHTEYKTRLCDAFRREGYCPYNDNCTYAHGQDELRVPRRRQEYYSRDPPRERRDSRSRRDDVDTTINRSSSSASKHHDENRRPSNNHGSSNRRQICHNFERGNCRYGPRCRFIHVEQMQHFNANATVYAPPSSDCPPPIAYYHHHPQHQQQFLPFPMPYFLAPPPQAQQGAPFPVQYIPQQHDLMNSQPMYAPMAPTYYYQPINSNGMPMMDVTIDPNATGGAFEVFPDGFFSQPPPTIIS mep1_caeel MOG interacting and ectopic P-granules protein 1 M04B2.1 Nuclear zinc finger protein mep-1 protein protein caeel Caenorhabditis elegans MVTADETVLATTTNTTSMSVEPTDPRSAGESSSDSEPDTIEQLKAEQREVMADAANGSEVNGNQENGKEEAASADVEVIEIDDTEESTDPSPDGSDENGDAASTSVPIEEEARKKDEGASEVTVASSEIEQDDDGDVMEITEEPNGKSEDTANGTVTEEVLDEEEPEPSVNGTTEIATEKEPEDSSMPVEQNGKGVKRPVECIELDDDDDDEIQEISTPAPAKKAKIDDVKATSVPEEDNNEQAQKRLLDKLEEYVKEQKDQPSSKSRKVLDTLLGAINAQVQKEPLSVRKLILDKVLVLPNTISFPPSQVCDLLIEHDPEMPLTKVINRMFGEERPKLSDSEKRERAQLKQHNPVPNMTKLLVDIGQDLVQEATYCDIVHAKNLPEVPKNLETYKQVAAQLKPVWETLKRKNEPYKLKMHRCDVCGFQTESKLVMSTHKENLHFTGSKFQCTMCKETDTSEQRMKDHYFETHLVIAKSEEKESKYPCAICEEDFNFKGVREQHYKQCKKDYIRIRNIMMPKQDDHLYINRWLWERPQLDPSILQQQQQAALQQAQQKKQQQLLHQQQAAQAAAAAQLLRKQQLQQQQQQQQARLREQQQAAQFRQVAQLLQQQSAQAQRAQQNQGNVNHNTLIAAMQASLRRGGQQGNSLAVSQLLQKQMAALKSQQGAQQLQAAVNSMRSQNSQKTPTHRSSKLVTTPSHATVGSSSAPTFVCEICDASVQEKEKYLQHLQTTHKQMVGKVLQDMSQGAPLACSRCRDRFWTYEGLERHLVMSHGLVTADLLLKAQKKEDGGRCKTCGKNYAFNMLQHLVADHQVKLCSAEIMYSCDVCAFKCSSYQTLEAHLTSNHPKGDKKTSTPAKKDDCITLDD le418_caeel Protein let-418 let-418 Lethal protein 418 evl-11 F26F12.7 protein protein caeel Caenorhabditis elegans MSTEEDPSLVDAEESMEEGSVTQDATEETEEEEEQEQGDEAGPSERKRSSRKKGGKGGKKGSKKSAAAASKVEIPDPYNSTSEEVCAAIGLTDVEFDYDEEEFQGISNLKTFSSIIKPQILEANPGTNVSKMYPMFQVKYKEYQDHMAAQGKPVQKQARGSKTPAVSTPVIPPRSAPTKTRSARRKRRDSDAPDSDQEFEAFIKQQEQLEDDLVKDKEDARIKRAAEREEKKKGALEAARAAKKAKLEKGEEAENNDYCEECKQDGELLLCDTCPRAYHTVCIDENMEEPPEGDWSCAHCIEHGPEVVKEEPAKQNDEFCKICKETENLLLCDSCVCSFHAYCIDPPLTEVPKEETWSCPRCETVKPEHKIEKILCWRWKEIPYPEPLEAGKEASSDDAMLKPPRKMEPRREREFFVKWKYLSYWQCSWVSEMLLEVHFRMLILLYWRKNDSDAPPEFEESVTSRHHSDNDPYKLRERFYQYGIKPEWMQIHRIINHQSYAKSQQDYLVKWKELSYDQATWERDDSNIANYEEAIIKYWQHRESKLNEDIPKNVQKMIAKHREAKGLPPKEDEKKKKKREKIDIRKKYEVQPDYVTETGGKLHPYQLEGLNWLRHCWSNGTDAILADEMGLGKTVQSLTFLYSLMKEGHCKGPFLIAAPLSTIINWEREAEQWCPDFYVVTYVGLRDARVVLREHEFSFVEGAVRSGPKASKMKTTENMKFHVLLTSYETINMDKTILSSIEWGALVVDEAHRLKNNQSLFFKNLNEYTIHYRVLLTGTPLQNNLEELFHLLNFLSKERFNQLEAFTAEFNEISKEDQIEKLHNLLGPHMLRRLKADVLTGMPSKSELIVRVELSAMQKKWYKNILTRNFDALNVKNGGTQMSLMNVLMELKKCCNHPYLFVKAELEAPKEKNGMYEGTALIKNSGKFVLLQKMLRKLKDGGHRVLIFSQMTRMLDIMEDLCEYEGYRYERIDGSIMGQMRQDAIDRYNAPGAQQFIFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRLGQKHKVMIYRFVTKKSVEEKITSVAKKKMLLNHLVVRAGLGGKEGKTMSKTELDDVLRWGTEELFSEDLDAAEGEGSEKKGAAAQEIVWDDAAVDALLDRSNKEETPAGEDGEEKAEWQNEYLSSFKVASYQTKETEGQEEEEEEETEVIKEDEKEPDPDYWEKLLKHHYEQDREIELQKLGKGKRVRKQINYASENMGTDWSKQNQTQDDDDDNESYRGSDNGDGLNSDEDDYDEKKKRRRDEEKMPPLMAKVNGQVEILGFNPRQRKAFYGAVMRWGMPPQDSHQSQWLVRDLRNKSEKVFRAYASLFMRHLCEPGADGHDTFNDGVPREGLNRQHVLGRIGLLSLVRRKVQEFEQYNGQWSMPEIQDEVLAKAANGSAQGSSRSTPKPKEEPKEEPMEKEDATETVNGATSEPATDAESEQNAPVDEPMDTDEAKEPKEEPIETEKPRAARPSFKFNICDGGFTELHSLWANEEKVARNGKEYEIWYRRHDYWLLAGVVVHGYGRFQANFNDIINDPRFSVLNEPFKEVGAEATGSDIKAKFMQRRFKLIEQSLVIEEQLRRAAHANRHLQPDNVGPLAQRFADLENIAESQANIAKESSAGNRNANAVLHKTLVQLDEILSDMKADVSRLPSTFTQLATVTERLNMTERQILSRLTTKDEDAIANRSVLPPPGPFVTPILRQQMDGIQPKFAALYSKFMSENGERMEEDEPVEAEEEEGVKQEPDDETQDSAEAPPVLSAEVNSDDSNDVPSTSAAAAVSSETAADAEPASAEDQAPTDEPEPMET hda1_caeel Histone deacetylase 1 hda-1 C53A5.3 protein protein caeel Caenorhabditis elegans MNSNGPLMEHGKRRVAYYYDSNIGNYYYGQGHVMKPHRIRMTHHLVLNYGLYRNLEIFRPFPASFEDMTRFHSDEYMTFLKSANPDNLKSFNKQMLKFNVGEDCPLFDGLYEFCQLSSGGSLAAATKLNKQKVDIAINWMGGLHHAKKSEASGFCYTNDIVLGILELLKYHKRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKYGDFFPGTGDLKDIGAGKGKLYSVNVPLRDGITDVSYQSIFKPIMTKVMERFDPCAVVLQCGADSLNGDRLGPFNLTLKGHGECARFFRSYNVPLMMVGGGGYTPRNVARCWTYETSIAVDKEVPNELPYNDYFEYFGPNYRLHIESSNAANENSSDMLAKLQTDVIANLEQLTFVPSVQMRPIPEDALSALNDDSLIADQANPDKRLPPQITDGMIQDDGDFYDGEREGDDRRNESDAKRAAQFESEGGEKRQKTE pie_1-mep_1 1129576 n/a 1129583 unspecified role unspecified role bait bait n/a 1129584 unspecified role unspecified role prey prey physical association physical association false false false mep_1-q19815 1129577 n/a 1129585 unspecified role unspecified role prey prey n/a 1129584 unspecified role unspecified role bait bait region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig 3A Figure 3A identifies a 280 kDa protein as a product of the gene let-418. However the only let-418 protein in UniProt and WormBase has a molecular weight of ~209 kDa. pie_1-hda_1 1129578 n/a 1129583 unspecified role unspecified role bait bait n/a 1129586 unspecified role unspecified role prey prey n/a 1129585 unspecified role unspecified role prey prey n/a 1129584 unspecified role unspecified role prey prey association association false false false Fig 4A. pie_1-hda_1-1 1129579 n/a 1129586 unspecified role unspecified role prey prey n/a 1129583 unspecified role unspecified role bait bait physical association physical association false false false Fig 4A Identical immunoprecipitation assays on extracts prepared from mixed-stage animals where PIE-1 protein itself is undetectable (Figure 4A, lane 1) failed to recover detectable quantities of MEP-1 and LET-418 (Figure 4A, lane 3). mep_1-hda_1 1129580 n/a 1129585 unspecified role unspecified role prey prey n/a 1129584 unspecified role unspecified role bait bait region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1129586 unspecified role unspecified role prey prey association association false false false Fig 4B. mep_1-pie_1 1129581 n/a 1129584 unspecified role unspecified role bait bait zn_fingers_2+3 binding region binding-associated region binding region deletion analysis deletion analysis range range range range false region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false glutamine_rich_region binding region binding-associated region binding region deletion analysis deletion analysis range range range range false ecoli Escherichia coli (strain K12) n/a 1129583 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false c-terminal proline rich region required to bind necessary binding region required to bind deletion analysis deletion analysis range range range range false in vitro In vitro direct interaction direct interaction false false false Fig 4 The proline-rich domain of PIE-1 interacts primarily with the second and third Zn-fingers of MEP-1 (Figure 4E). hda_1-pie_1 1129582 n/a 1129583 unspecified role unspecified role prey prey c_terminal_proline_rich_region required to bind necessary binding region required to bind c-term range C-terminal range c-term range c-term range C-terminal range c-term range false region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1129586 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 false physical association physical association false false false Fig 6A