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/ MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Cell (0092-8674) 2002 imex curation Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu jyoti Only protein-protein interactions 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 Accepted 2011-MAR-25 by JYOTI Cell (0092-8674) 2002 jyoti Only protein-protein interactions imex curation MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Cell (0092-8674) 2002 imex curation Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu jyoti Only protein-protein interactions 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 Accepted 2011-MAR-25 by JYOTI Cell (0092-8674) 2002 jyoti Only protein-protein interactions imex curation MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Cell (0092-8674) 2002 imex curation Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu jyoti Only protein-protein interactions 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. I tried to link features (forMEP-1 ZnF domains 2+3 to PIE-1 Proline rich region) - but could not - no way to do it in the new editor, and old editor crashed when I tried there. However the Manual says, under:- Some examples where Features should be linked are:"Authors have shown that 2 specific domains interact. (If it is only the fragment used without precision on the real interacting domains, no link is needed). So maybe NO link is even needed to be added. (have added a Comment at interaction level instead.) Early embryo extracts were used. craig.mello@umassmed.edu Accepted 2011-MAR-25 by JYOTI Cell (0092-8674) 2002 jyoti Only protein-protein interactions imex curation MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Cell (0092-8674) 2002 imex curation Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu jyoti Only protein-protein interactions 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 Accepted 2011-MAR-25 by JYOTI Cell (0092-8674) 2002 jyoti Only protein-protein interactions imex curation MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Cell (0092-8674) 2002 imex curation Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu jyoti Only protein-protein interactions 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 Accepted 2011-MAR-25 by JYOTI 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 jyoti Only protein-protein interactions imex curation MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Cell (0092-8674) 2002 imex curation Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu jyoti Only protein-protein interactions 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 Accepted 2011-MAR-25 by JYOTI 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 jyoti Only protein-protein interactions imex curation MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans. Cell (0092-8674) 2002 imex curation Unhavaithaya Y., Shin TH., Miliaras N., Lee J., Oyama T., Mello CC. Early embryo extracts were used. craig.mello@umassmed.edu jyoti Only protein-protein interactions 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. fig 6b/c cannot be added as no species of Histone given nor sequence of peptide. Early embryo extracts were used. craig.mello@umassmed.edu Accepted 2011-MAR-25 by JYOTI Cell (0092-8674) 2002 jyoti Only protein-protein interactions imex curation hda1_caeel Histone deacetylase 1 hda-1 C53A5.3 protein protein caeel Caenorhabditis elegans MNSNGPLMEHGKRRVAYYYDSNIGNYYYGQGHVMKPHRIRMTHHLVLNYGLYRNLEIFRPFPASFEDMTRFHSDEYMTFLKSANPDNLKSFNKQMLKFNVGEDCPLFDGLYEFCQLSSGGSLAAATKLNKQKVDIAINWMGGLHHAKKSEASGFCYTNDIVLGILELLKYHKRVLYVDIDVHHGDGVEEAFYTTDRVMTVSFHKYGDFFPGTGDLKDIGAGKGKLYSVNVPLRDGITDVSYQSIFKPIMTKVMERFDPCAVVLQCGADSLNGDRLGPFNLTLKGHGECARFFRSYNVPLMMVGGGGYTPRNVARCWTYETSIAVDKEVPNELPYNDYFEYFGPNYRLHIESSNAANENSSDMLAKLQTDVIANLEQLTFVPSVQMRPIPEDALSALNDDSLIADQANPDKRLPPQITDGMIQDDGDFYDGEREGDDRRNESDAKRAAQFESEGGEKRQKTE 9A104E88C5A1C07A le418_caeel Protein let-418 let-418 Lethal protein 418 evl-11 F26F12.7 protein protein caeel Caenorhabditis elegans MSTEEDPSLVDAEESMEEGSVTQDATEETEEEEEQEQGDEAGPSERKRSSRKKGGKGGKKGSKKSAAAASKVEIPDPYNSTSEEVCAAIGLTDVEFDYDEEEFQGISNLKTFSSIIKPQILEANPGTNVSKMYPMFQVKYKEYQDHMAAQGKPVQKQARGSKTPAVSTPVIPPRSAPTKTRSARRKRRDSDAPDSDQEFEAFIKQQEQLEDDLVKDKEDARIKRAAEREEKKKGALEAARAAKKAKLEKGEEAENNDYCEECKQDGELLLCDTCPRAYHTVCIDENMEEPPEGDWSCAHCIEHGPEVVKEEPAKQNDEFCKICKETENLLLCDSCVCSFHAYCIDPPLTEVPKEETWSCPRCETVKPEHKIEKILCWRWKEIPYPEPLEAGKEASSDDAMLKPPRKMEPRREREFFVKWKYLSYWQCSWVSEMLLEVHFRMLILLYWRKNDSDAPPEFEESVTSRHHSDNDPYKLRERFYQYGIKPEWMQIHRIINHQSYAKSQQDYLVKWKELSYDQATWERDDSNIANYEEAIIKYWQHRESKLNEDIPKNVQKMIAKHREAKGLPPKEDEKKKKKREKIDIRKKYEVQPDYVTETGGKLHPYQLEGLNWLRHCWSNGTDAILADEMGLGKTVQSLTFLYSLMKEGHCKGPFLIAAPLSTIINWEREAEQWCPDFYVVTYVGLRDARVVLREHEFSFVEGAVRSGPKASKMKTTENMKFHVLLTSYETINMDKTILSSIEWGALVVDEAHRLKNNQSLFFKNLNEYTIHYRVLLTGTPLQNNLEELFHLLNFLSKERFNQLEAFTAEFNEISKEDQIEKLHNLLGPHMLRRLKADVLTGMPSKSELIVRVELSAMQKKWYKNILTRNFDALNVKNGGTQMSLMNVLMELKKCCNHPYLFVKAELEAPKEKNGMYEGTALIKNSGKFVLLQKMLRKLKDGGHRVLIFSQMTRMLDIMEDLCEYEGYRYERIDGSIMGQMRQDAIDRYNAPGAQQFIFLLSTRAGGLGINLATADTVIIYDSDWNPHNDIQAFSRAHRLGQKHKVMIYRFVTKKSVEEKITSVAKKKMLLNHLVVRAGLGGKEGKTMSKTELDDVLRWGTEELFSEDLDAAEGEGSEKKGAAAQEIVWDDAAVDALLDRSNKEETPAGEDGEEKAEWQNEYLSSFKVASYQTKETEGQEEEEEEETEVIKEDEKEPDPDYWEKLLKHHYEQDREIELQKLGKGKRVRKQINYASENMGTDWSKQNQTQDDDDDNESYRGSDNGDGLNSDEDDYDEKKKRRRDEEKMPPLMAKVNGQVEILGFNPRQRKAFYGAVMRWGMPPQDSHQSQWLVRDLRNKSEKVFRAYASLFMRHLCEPGADGHDTFNDGVPREGLNRQHVLGRIGLLSLVRRKVQEFEQYNGQWSMPEIQDEVLAKAANGSAQGSSRSTPKPKEEPKEEPMEKEDATETVNGATSEPATDAESEQNAPVDEPMDTDEAKEPKEEPIETEKPRAARPSFKFNICDGGFTELHSLWANEEKVARNGKEYEIWYRRHDYWLLAGVVVHGYGRFQANFNDIINDPRFSVLNEPFKEVGAEATGSDIKAKFMQRRFKLIEQSLVIEEQLRRAAHANRHLQPDNVGPLAQRFADLENIAESQANIAKESSAGNRNANAVLHKTLVQLDEILSDMKADVSRLPSTFTQLATVTERLNMTERQILSRLTTKDEDAIANRSVLPPPGPFVTPILRQQMDGIQPKFAALYSKFMSENGERMEEDEPVEAEEEEGVKQEPDDETQDSAEAPPVLSAEVNSDDSNDVPSTSAAAAVSSETAADAEPASAEDQAPTDEPEPMET 1A887E990C63B661 mep1_caeel MOG interacting and ectopic P-granules protein 1 M04B2.1 Nuclear zinc finger protein mep-1 protein protein caeel Caenorhabditis elegans MVTADETVLATTTNTTSMSVEPTDPRSAGESSSDSEPDTIEQLKAEQREVMADAANGSEVNGNQENGKEEAASADVEVIEIDDTEESTDPSPDGSDENGDAASTSVPIEEEARKKDEGASEVTVASSEIEQDDDGDVMEITEEPNGKSEDTANGTVTEEVLDEEEPEPSVNGTTEIATEKEPEDSSMPVEQNGKGVKRPVECIELDDDDDDEIQEISTPAPAKKAKIDDVKATSVPEEDNNEQAQKRLLDKLEEYVKEQKDQPSSKSRKVLDTLLGAINAQVQKEPLSVRKLILDKVLVLPNTISFPPSQVCDLLIEHDPEMPLTKVINRMFGEERPKLSDSEKRERAQLKQHNPVPNMTKLLVDIGQDLVQEATYCDIVHAKNLPEVPKNLETYKQVAAQLKPVWETLKRKNEPYKLKMHRCDVCGFQTESKLVMSTHKENLHFTGSKFQCTMCKETDTSEQRMKDHYFETHLVIAKSEEKESKYPCAICEEDFNFKGVREQHYKQCKKDYIRIRNIMMPKQDDHLYINRWLWERPQLDPSILQQQQQAALQQAQQKKQQQLLHQQQAAQAAAAAQLLRKQQLQQQQQQQQARLREQQQAAQFRQVAQLLQQQSAQAQRAQQNQGNVNHNTLIAAMQASLRRGGQQGNSLAVSQLLQKQMAALKSQQGAQQLQAAVNSMRSQNSQKTPTHRSSKLVTTPSHATVGSSSAPTFVCEICDASVQEKEKYLQHLQTTHKQMVGKVLQDMSQGAPLACSRCRDRFWTYEGLERHLVMSHGLVTADLLLKAQKKEDGGRCKTCGKNYAFNMLQHLVADHQVKLCSAEIMYSCDVCAFKCSSYQTLEAHLTSNHPKGDKKTSTPAKKDDCITLDD 3BF8924F86B5A6E3 pie1_caeel Pharynx and intestine in excess protein 1 pie-1 pic-1 Y49E10.14 protein protein caeel Caenorhabditis elegans MAQTKPIAEQMAALNNSDDTSFAADRSNSLLNATCPARIQNSVDQRKINRSFNDSLSSGYSGKWLRPKREALKITPLAQIDEAPATKRHSSAKDKHTEYKTRLCDAFRREGYCPYNDNCTYAHGQDELRVPRRRQEYYSRDPPRERRDSRSRRDDVDTTINRSSSSASKHHDENRRPSNNHGSSNRRQICHNFERGNCRYGPRCRFIHVEQMQHFNANATVYAPPSSDCPPPIAYYHHHPQHQQQFLPFPMPYFLAPPPQAQQGAPFPVQYIPQQHDLMNSQPMYAPMAPTYYYQPINSNGMPMMDVTIDPNATGGAFEVFPDGFFSQPPPTIIS 31513EE4E72B4880 pie_1-mep_1 5 11 unspecified role unspecified role bait bait 10 unspecified role unspecified role prey prey physical association physical association mep_1-q19815 6 9 unspecified role unspecified role prey prey 10 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 physical association physical association 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 1 11 unspecified role unspecified role bait bait 8 unspecified role unspecified role prey prey 9 unspecified role unspecified role prey prey 10 unspecified role unspecified role prey prey association association Fig 4A. pie_1-hda_1-1 2 8 unspecified role unspecified role prey prey 11 unspecified role unspecified role bait bait physical association physical association 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 4 9 unspecified role unspecified role prey prey 10 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 8 unspecified role unspecified role prey prey association association Fig 4B. mep_1-pie_1 3 10 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 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 glutamine_rich_region binding region binding-associated region binding region deletion analysis deletion analysis range range range range ecoli Escherichia coli (strain K12) 11 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 c-terminal proline rich region required to bind necessary binding region required to bind deletion analysis deletion analysis range range range range in vitro In vitro direct interaction direct interaction Fig 4 There is NO mention of an anti-HA antibody in the paper - so participant detection entered as "WB" rather than "anti-tag WB". 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 7 11 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 region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 8 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 Fig 6A