DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ wang-2018-6 yeast Saccharomyces cerevisiae 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 predetermined predetermined participant predetermined Wang Z., Ma Z., Castillo-González C., Sun D., Li Y., Yu B., Zhao B., Li P., Zhang X. xiuren.zhang@tamu.edu Nature 2018 imex curation Only protein-protein interactions imex curation wang-2018-7 arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Wang Z., Ma Z., Castillo-González C., Sun D., Li Y., Yu B., Zhao B., Li P., Zhang X. xiuren.zhang@tamu.edu Nature 2018 imex curation Only protein-protein interactions imex curation wang-2018-9 arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress anti tag coip anti tag coimmunoprecipitation anti tag coip ms participant Identification by mass spectrometry ms participant Wang Z., Ma Z., Castillo-González C., Sun D., Li Y., Yu B., Zhao B., Li P., Zhang X. xiuren.zhang@tamu.edu Nature 2018 imex curation Only protein-protein interactions imex curation wang-2018-10 arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress confocal microscopy confocal microscopy tag fluorescence tag visualisation by fluorescence tag fluorescence Wang Z., Ma Z., Castillo-González C., Sun D., Li Y., Yu B., Zhao B., Li P., Zhang X. xiuren.zhang@tamu.edu Nature 2018 imex curation Only protein-protein interactions imex curation brm_arath ATP-dependent helicase BRM CHR2 Protein CHROMATIN REMODELING 2 F4I18 T3F17.33 At2g46020 BRM Protein BRAHMA protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MQSGGSGGGPARNPAMGPAGRTASTSSAASPSSSSSSVQQQQQQQQQQQQQQQLASRQQQQQHRNSDTNENMFAYQPGGVQGMMGGGNFASSPGSMQMPQQSRNFFESPQQQQQQQQQGSSTQEGQQNFNPMQQAYIQFAMQAQHQKAQQQARMGMVGSSSVGKDQDARMGMLNMQDLNPSSQPQASSSKPSGDQFARGERQTESSSQQRNETKSHPQQQVGTGQLMPGNMIRPMQAPQAQQLVNNMGNNQLAFAQQWQAMQAWARERNIDLSHPANASQMAHILQARMAAQQKAGEGNVASQSPSIPISSQPASSSVVPGENSPHANSASDISGQSGSAKARHALSTGSFASTSSPRMVNPAMNPFSGQGRENPMYPRHLVQPTNGMPSGNPLQTSANETPVLDQNASTKKSLGPAEHLQMQQPRQLNTPTPNLVAPSDTGPLSNSSLQSGQGTQQAQQRSGFTKQQLHVLKAQILAFRRLKKGEGSLPPELLQAISPPPLELQTQRQISPAIGKVQDRSSDKTGEDQARSLECGKESQAAASSNGPIFSKEEDNVGDTEVALTTGHSQLFQNLGKEATSTDVATKEEQQTDVFPVKSDQGADSSTQKNPRSDSTADKGKAVASDGSQSKVPPQANSPQPPKDTASARKYYGPLFDFPFFTRKLDSYGSATANANNNLTLAYDIKDLICEEGAEFLSKKRTDSLKKINGLLAKNLERKRIRPDLVLRLQIEEKKLRLSDLQSRVREEVDRQQQEIMSMPDRPYRKFVRLCERQRLEMNRQVLANQKAVREKQLKTIFQWRKKLLEAHWAIRDARTARNRGVAKYHEKMLREFSKRKDDGRNKRMEALKNNDVERYREMLLEQQTNMPGDAAERYAVLSSFLTQTEDYLHKLGGKITATKNQQEVEEAANAAAVAARLQGLSEEEVRAAATCAREEVVIRNRFTEMNAPKENSSVNKYYTLAHAVNEVVVRQPSMLQAGTLRDYQLVGLQWMLSLYNNKLNGILADEMGLGKTVQVMALIAYLMEFKGNYGPHLIIVPNAVLVNWKSELHTWLPSVSCIYYVGTKDQRSKLFSQEVCAMKFNVLVTTYEFIMYDRSKLSKVDWKYIIIDEAQRMKDRESVLARDLDRYRCQRRLLLTGTPLQNDLKELWSLLNLLLPDVFDNRKAFHDWFAQPFQKEGPAHNIEDDWLETEKKVIVIHRLHQILEPFMLRRRVEDVEGSLPAKVSVVLRCRMSAIQSAVYDWIKATGTLRVDPDDEKLRAQKNPIYQAKIYRTLNNRCMELRKACNHPLLNYPYFNDFSKDFLVRSCGKLWILDRILIKLQRTGHRVLLFSTMTKLLDILEEYLQWRRLVYRRIDGTTSLEDRESAIVDFNDPDTDCFIFLLSIRAAGRGLNLQTADTVVIYDPDPNPKNEEQAVARAHRIGQTREVKVIYMEAVVEKLSSHQKEDELRSGGSVDLEDDMAGKDRYIGSIEGLIRNNIQQYKIDMADEVINAGRFDQRTTHEERRMTLETLLHDEERYQETVHDVPSLHEVNRMIARSEEEVELFDQMDEEFDWTEEMTNHEQVPKWLRASTREVNATVADLSKKPSKNMLSSSNLIVQPGGPGGERKRGRPKSKKINYKEIEDDIAGYSEESSEERNIDSGNEEEGDIRQFDDDELTGALGDHQTNKGEFDGENPVCGYDYPPGSGSYKKNPPRDDAGSSGSSPESHRSKEMASPVSSQKFGSLSALDTRPGSVSKRLLDDLEEGEIAASGDSHIDLQRSGSWAHDRDEGDEEQVLQPTIKRKRSIRLRPRQTAERVDGSEMPAAQPLQVDRSYRSKLRTVVDSHSSRQDQSDSSSRLRSVPAKKVASTSKLHVSSPKSGRLNATQLTVEDNAEASRETWDGTSPISSSNAGARMSHIIQKRCKIVISKLQRRIDKEGQQIVPMLTNLWKRIQNGYAAGGVNNLLELREIDHRVERLEYAGVMELASDVQLMLRGAMQFYGFSHEVRSEAKKVHNLFFDLLKMSFPDTDFREARNALSFSGSAPTLVSTPTPRGAGISQGKRQKLVNEPETEPSSPQRSQQRENSRIRVQIPQKETKLGGTTSHTDESPILAHPGELVICKKKRKDREKSGPKTRTGGSSSPVSPPPAMIGRGLRSPVSGGVPRETRLAQQQRWPNQPTHPNNSGAAGDSVGWANPVKRLRTDSGKRRPSHL srrt_arath Serrate RNA effector molecule SE T20P8.15 At2g27100 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MADVNLPPSDSVDNRLPEKSTSSSPPPPPPSSSLPQQEQEQDQQQLPLRRERDSRERRDERDIERPPPNRRERDRSPLPPPRRDYKRRPSLSPPPPYRDRRHSPPQRRSPPQKRYRRDDNGYDGRRGSPRGGYGPPDRRFGYDHGGGYDREMGGRPGYGDERPHGRFMGRYQDWEGGRGGYGDASNSGNPQRDGLMSYKQFIQELEDDILPSEAERRYQEYKSEYITTQKRAFFNTHKEEDWLKNKYHPTNLLSVIERRNDLAQKVAKDFLLDLQSGTLDLGPAVTALNKSGRTSEPNSEDEAAGVGKRKRHGMGGAKENELLSAAPKAPSFTSDPKRILTDVEQTQALVRKLDSEKKIEENVLQGSETEKSGREKLHSGSTGPVVIIRGLTSVKGLEGVELLDTLVTYLWRVHGLDYYGKVETNEAKGLRHVRAEGKVSDAKGDENESKFDSHWQERLKGQDPLEVMAAKEKIDAAATEALDPHVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVYKHLKLKHTELVTELTTKVREELYFQNYMNDPNAPGGQPATQQSGPRDRPIRRKPSMENRLRDDRGGRRERDGRANGNDRNDRSEDQQRGDNDGGNPGEVGYDAFGGQGGVHVPPFLSDINPPPMLMPVPGAGPLGPFVPAPPEVAMQMFRDPSGPNPPFEGSGRGGPAPFLLSPAFRQDPRRLRSYQDLDAPEEEVTVIDYRSL dcl1_arath Endoribonuclease Dicer homolog 1 Protein CARPEL FACTORY Protein SHORT INTEGUMENTS 1 Protein SUSPENSOR 1 DCL1 ASU1 SUS1 At1g01040 T25K16.4 CAF SIN1 Dicer-like protein 1 Protein ABNORMAL SUSPENSOR 1 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MVMEDEPREATIKPSYWLDACEDISCDLIDDLVSEFDPSSVAVNESTDENGVINDFFGGIDHILDSIKNGGGLPNNGVSDTNSQINEVTVTPQVIAKETVKENGLQKNGGKRDEFSKEEGDKDRKRARVCSYQSERSNLSGRGHVNNSREGDRFMNRKRTRNWDEAGNNKKKRECNNYRRDGRDREVRGYWERDKVGSNELVYRSGTWEADHERDVKKVSGGNRECDVKAEENKSKPEERKEKVVEEQARRYQLDVLEQAKAKNTIAFLETGAGKTLIAILLIKSVHKDLMSQNRKMLSVFLVPKVPLVYQQAEVIRNQTCFQVGHYCGEMGQDFWDSRRWQREFESKQVLVMTAQILLNILRHSIIRMETIDLLILDECHHAVKKHPYSLVMSEFYHTTPKDKRPAIFGMTASPVNLKGVSSQVDCAIKIRNLETKLDSTVCTIKDRKELEKHVPMPSEIVVEYDKAATMWSLHETIKQMIAAVEEAAQASSRKSKWQFMGARDAGAKDELRQVYGVSERTESDGAANLIHKLRAINYTLAELGQWCAYKVGQSFLSALQSDERVNFQVDVKFQESYLSEVVSLLQCELLEGAAAEKVAAEVGKPENGNAHDEMEEGELPDDPVVSGGEHVDEVIGAAVADGKVTPKVQSLIKLLLKYQHTADFRAIVFVERVVAALVLPKVFAELPSLSFIRCASMIGHNNSQEMKSSQMQDTISKFRDGHVTLLVATSVAEEGLDIRQCNVVMRFDLAKTVLAYIQSRGRARKPGSDYILMVERGNVSHAAFLRNARNSEETLRKEAIERTDLSHLKDTSRLISIDAVPGTVYKVEATGAMVSLNSAVGLVHFYCSQLPGDRYAILRPEFSMEKHEKPGGHTEYSCRLQLPCNAPFEILEGPVCSSMRLAQQAVCLAACKKLHEMGAFTDMLLPDKGSGQDAEKADQDDEGEPVPGTARHREFYPEGVADVLKGEWVSSGKEVCESSKLFHLYMYNVRCVDFGSSKDPFLSEVSEFAILFGNELDAEVLSMSMDLYVARAMITKASLAFKGSLDITENQLSSLKKFHVRLMSIVLDVDVEPSTTPWDPAKAYLFVPVTDNTSMEPIKGINWELVEKITKTTAWDNPLQRARPDVYLGTNERTLGGDRREYGFGKLRHNIVFGQKSHPTYGIRGAVASFDVVRASGLLPVRDAFEKEVEEDLSKGKLMMADGCMVAEDLIGKIVTAAHSGKRFYVDSICYDMSAETSFPRKEGYLGPLEYNTYADYYKQKYGVDLNCKQQPLIKGRGVSYCKNLLSPRFEQSGESETVLDKTYYVFLPPELCVVHPLSGSLIRGAQRLPSIMRRVESMLLAVQLKNLISYPIPTSKILEALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYPQKHEGQLTRMRQQMVSNMVLYQFALVKGLQSYIQADRFAPSRWSAPGVPPVFDEDTKDGGSSFFDEEQKPVSEENSDVFEDGEMEDGELEGDLSSYRVLSSKTLADVVEALIGVYYVEGGKIAANHLMKWIGIHVEDDPDEVDGTLKNVNVPESVLKSIDFVGLERALKYEFKEKGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITRHLFFTYTSLPPGRLTDLRAAAVNNENFARVAVKHKLHLYLRHGSSALEKQIREFVKEVQTESSKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLDSGKDTTAAWKVFQPLLQPMVTPETLPMHPVRELQERCQQQAEGLEYKASRSGNTATVEVFIDGVQVGVAQNPQKKMAQKLAARNALAALKEKEIAESKEKHINNGNAGEDQGENENGNKKNGHQPFTRQTLNDICLRKNWPMPSYRCVKEGGPAHAKRFTFGVRVNTSDRGWTDECIGEPMPSVKKAKDSAAVLLLELLNKTFS drb1_arath Double-stranded RNA-binding protein 1 F21M12.9 At1g09700 DRB1 HYL1 Protein HYPONASTIC LEAVES 1 dsRNA-binding protein 1 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MTSTDVSSGVSNCYVFKSRLQEYAQKYKLPTPVYEIVKEGPSHKSLFQSTVILDGVRYNSLPGFFNRKAAEQSAAEVALRELAKSSELSQCVSQPVHETGLCKNLLQEYAQKMNYAIPLYQCQKVETLGRVTQFTCTVEIGGIKYTGAATRTKKDAEISAGRTALLAIQSDTKNNLANYNTQLTVLPCEKKTIQAAIPLKETVKTLKARKAQFKKKAQKGKRTVAKNPEDIIIPPQPTDHCQNDQSEKIETTPNLEPSSCMNGLKEAAFGSVETEKIETTPNLEPPSCMNGLKEAAFGSVETEKIETTPNLEPPSCMNGLKEAAFGSVETEKIETTPNLEPSSCMNGLKEAAFGSVETEKIETTPNLEPPSCMNGLKEAAFGSVETEKIETTPNLESSSCMSGLKEAAFGSVETEASHA pr40b_arath Pre-mRNA-processing protein 40B MMB12.15 At3g19670 PRP40B MED35_2 MED35B protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MANNHQYPGIQPFQHPNASSIDLPRGFAPPMNFQFLPTIQAPQSEQVARLSSQNFQCVGRGGTVLSIGYPPQSYAPQLLQSMHHSHERPSQLNQVQVQHVPLGPPTLISQPNVSIASGTSLHQPYVQTPDIGMPGFGGPRALFSYPSATSYEGSRVPPQVTGPSIHSQAQQRASIIHTSAESSIMNPTFEQPKAAFLKPLPSQKALTDWVEHTSADGRKYFFNKRTKKSTWEKPVELMTLFERADARTDWKEHSSPDGRKYYYNKITKQSTWTMPEEMKIVREQAEIASVQGPHAEGIIDASEVLTRSDTASTAAPTGLPSQTSTSEGVEKLTLTSDLKQPASVPGSSSPVENVDRVQMSADETSQLCDTSETDGLSVPVTETSAATLVEKDEISVGNSGDSDDMSTKNANQGSGSGPKESQKPMVESEKVESQTEEKQIHQESFSFNNKLEAVDVFKSLLKSAKVGSDWTWEQAMREIINDKRYGALRTLGERKQAFNEFLLQTKRAAEEERLARQKKLYEDFKRMLEECVELTPSTRWSKTVTMFEDDERFKALEREKDRRNIFEDHVSELKEKGRVKALEDRKRNIIEYKRFLESCNFIKPNSQWRKVQDRLEVDERCSRLEKIDQLEIFQEYLRDLEREEEEKKKIQKEELKKVERKHRDEFHGLLDEHIATGELTAKTIWRDYLMKVKDLPVYSAIASNSSGATPKDLFEDAVEDLKKRDHELKSQIKDVLKLRKVNLSAGSTFDEFKVSISEDIGFPLIPDVRLKLVFDDLLERAKEKEEKEARKQTRQTEKLVDMLRSFKDITASSSWEELKHLVEGSEKCSTIGDESFRKRCFEDYVSLLKEQSNRIKQNKKVPEDVREEHDKGRDKYGREKDRVRERDSDDHHKKGAAGKYNHDMNEPHGKERRRSGRDSHNRHRERHTSVKENDTDHFKESHKAGGGHKKSRHQRGWVSEAEVEGKEKRRRKEEAREHTKEEELEDGECGRY brm-se-3 3465539 N/A 3465543 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed N/A 3465544 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed sufficient to bind sufficient to bind sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false sufficient to bind sufficient to bind sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Fig 1a, Extended Data Fig 6b, Extended Data Fig 7b brm-se-2 3465539 N/A 3465543 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed Q6EVK6:p.Glu1747Ala p.Glu1747Ala mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false sufficient to bind sufficient to bind sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false required to bind required to bind required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false N/A 3465544 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed physical association physical association false false false Fig 2a, Extended Data Fig 3a, b brm-se-4 3465539 N/A 3465543 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed N/A 3465544 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed required to bind required to bind required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false sufficient to bind sufficient to bind sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Fig 1a, Extended Data Fig 7b, Extended Data Fig 6b se-dcl1-1 3465539 N/A 3465545 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed N/A 3465544 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed sufficient to bind sufficient to bind sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Extended Data Fig 6b, Extended Data Fig 7a se-dcl1-2 3465539 N/A 3465545 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed sufficient to bind sufficient to bind sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 3465544 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed physical association physical association false false false Extended Data Fig 6b, Extended Data Fig 7a se-drb1-2 3465539 N/A 3465544 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed N/A 3465546 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed physical association physical association false false false Extended Dta Fig 6e se-prp40b-1 3465539 N/A 3465544 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed N/A 3465547 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed physical association physical association false false false Extended Data Fig 6f brm-se-1 3465540 N/A 3465543 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed flag tag flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false Myc tag Myc tag myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 3465544 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed physical association physical association false false false Fig 1b se-brm-3 3465541 N/A 3465543 ms participant Identification by mass spectrometry ms participant unspecified role unspecified role prey prey native native N/A 3465544 predetermined predetermined participant predetermined unspecified role unspecified role bait bait over-expressed over expressed level over-expressed Flag tag Flag tag flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Myc tag Myc tag myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false Extended Data Fig 1b se-brm-4 3465542 N/A 3465543 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed YFP tag YFP tag yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 3465544 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed CFP tag CFP tag cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false colocalization colocalization false false false Extended Data Fig 1c