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/ he-2009-1 An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot He XJ., Hsu YF., Zhu S., Wierzbicki AT., Pontes O., Pikaard CS., Liu HL., Wang CS., Jin H., Zhu JK. Plant extracts taken from Myc-AGO4 transgenic plants. jian-kang.zhu@ucr.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation he-2009-2 An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. in vitro In vitro anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western He XJ., Hsu YF., Zhu S., Wierzbicki AT., Pontes O., Pikaard CS., Liu HL., Wang CS., Jin H., Zhu JK. Plant extracts taken from Myc-AGO4 transgenic plants. jian-kang.zhu@ucr.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation he-2009-5 An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress fluorescence imaging fluorescence microscopy fluorescence imaging immunostaining immunostaining He XJ., Hsu YF., Zhu S., Wierzbicki AT., Pontes O., Pikaard CS., Liu HL., Wang CS., Jin H., Zhu JK. Plant extracts taken from Myc-AGO4 transgenic plants. jian-kang.zhu@ucr.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation he-2009-3 An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. arath-flower Arabidopsis thaliana flower flower Flower anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot He XJ., Hsu YF., Zhu S., Wierzbicki AT., Pontes O., Pikaard CS., Liu HL., Wang CS., Jin H., Zhu JK. Plant extracts taken from Myc-AGO4 transgenic plants. jian-kang.zhu@ucr.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation he-2009-4 An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. arath-flower Arabidopsis thaliana flower flower Flower anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western He XJ., Hsu YF., Zhu S., Wierzbicki AT., Pontes O., Pikaard CS., Liu HL., Wang CS., Jin H., Zhu JK. Plant extracts taken from Myc-AGO4 transgenic plants. jian-kang.zhu@ucr.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation he-2009-6 An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. in vitro In vitro emsa electrophoretic mobility shift assay Gel retardation assay band shift band shift Gel retardation assay emsa predetermined predetermined participant predetermined He XJ., Hsu YF., Zhu S., Wierzbicki AT., Pontes O., Pikaard CS., Liu HL., Wang CS., Jin H., Zhu JK. Plant extracts taken from Myc-AGO4 transgenic plants. jian-kang.zhu@ucr.edu Cell (0092-8674) 2009 Only protein-protein interactions 8 imex curation ago4_arath Protein argonaute 4 At2g27040 AGO4 OCP11 Protein OVEREXPRESSOR OF CATIONIC PEROXIDASE 11 T20P8.9 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDSTNGNGADLESANGANGSGVTEALPPPPPVIPPNVEPVRVKTELAEKKGPVRVPMARKGFGTRGQKIPLLTNHFKVDVANLQGHFFHYSVALFYDDGRPVEQKGVGRKILDKVHQTYHSDLDGKEFAYDGEKTLFTYGALPSNKMDFSVVLEEVSATRANGNGSPNGNESPSDGDRKRLRRPNRSKNFRVEISYAAKIPLQALANAMRGQESENSQEAIRVLDIILRQHAARQGCLLVRQSFFHNDPTNCEPVGGNILGCRGFHSSFRTTQGGMSLNMDVTTTMIIKPGPVVDFLIANQNARDPYSIDWSKAKRTLKNLRVKVSPSGQEFKITGLSDKPCREQTFELKKRNPNENGEFETTEVTVADYFRDTRHIDLQYSADLPCINVGKPKRPTYIPLELCALVPLQRYTKALTTFQRSALVEKSRQKPQERMTVLSKALKVSNYDAEPLLRSCGISISSNFTQVEGRVLPAPKLKMGCGSETFPRNGRWNFNNKEFVEPTKIQRWVVVNFSARCNVRQVVDDLIKIGGSKGIEIASPFQVFEEGNQFRRAPPMIRVENMFKDIQSKLPGVPQFILCVLPDKKNSDLYGPWKKKNLTEFGIVTQCMAPTRQPNDQYLTNLLLKINAKLGGLNSMLSVERTPAFTVISKVPTIILGMDVSHGSPGQSDVPSIAAVVSSREWPLISKYRASVRTQPSKAEMIESLVKKNGTEDDGIIKELLVDFYTSSNKRKPEHIIIFRDGVSESQFNQVLNIELDQIIEACKLLDANWNPKFLLLVAQKNHHTKFFQPTSPENVPPGTIIDNKICHPKNNDFYLCAHAGMIGTTRPTHYHVLYDEIGFSADELQELVHSLSYVYQRSTSAISVVAPICYAHLAAAQLGTFMKFEDQSETSSSHGGITAPGPISVAQLPRLKDNVANSMFFC rdm3_arath Protein RNA-directed DNA methylation 3 KOW domain-containing transcription factor 1 KTF1 Protein SPT5-like RDM3 SPT5L T19N18.20 At5g04290 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MDRKGKGKQVAGSDSYSGGQKRKNSVEFRDEGLRIKKRKNPEVLQFFEESAEVGYYGGSSDEDDDGLGFLNDMEDEPEVEESSKAGKGEKGKSSFVFPKEEDLNEEEFDRIMEERYKPGSGFLRYADDDIKDAIEMDALAPTSKDPPIWKVKCAIGRERRSVFCLMHKFVELRKIGTKLEIISVFSVDHVKGFIFIEADKEHDVLEACKSLVGIYATRMVLLPKAETPNLLTVQKKTKKVSEGTWARVKNGKYKGDLAQIVAVSDTRNKALIKLIPRIDIQALTQKYGGGVTVQKGQTPAPRLISSSELEEFRPLIQVRRDRDTGITFEHLDSLMLKDGYLYKKVSLDSISSWGVIPTKDELLKFTPVDRKETGDVEWISEIYGEERKKKILPTCREGGKGEGSGGGKGEGSGGGKGEGSRGGKGEGSSDFKSESSYELYNLVCFSRKDFGLIVGVDDKGDGYKVLKEGIDGPVVVTVGKKEMQNGPFDSKFTALDLNKKQISVNDVVKISKGPSEGKQGVVRQVYRGIIFLYDESEEENGGYFCCKSQSCEKVKLFTEESNEKTGGFDGTAFEDFVSSPKSPLSPEKEWQPRERYNSSNQGDIGSTYSIGQKLRIRVGPLKGYLCRVIALRYSDVTVKLDSQHKIFTVKSEHLAEVRDRNTVLSTSGDAGTGSFQPFGMLGTESSTGDWAIGAGTSSEGGNWNIGGPSTDSHESLNIERNMVQLCREKNPWGGSKPTSDVSPTVADDNTSAWANAAAENKPASASDQPGGWNPWGKTPASEAGTVSGWGDTSASNVEASSWEKQGASTSNVADLGSWGTHGGSSGGNKQDEDSVWGKLCEASESSQKKEESSWGKKGGSDGESSWGNKDGNSSASKKDGVSWGQQDKGSDESKGGSAWSNQCGDFGSGKKKDGSSGWNKSAEDSNANSKGVPDWGQPNDGSSWGKKGDGAASWGKKDDGGSWGKKDDGNKDDGGSSWGKKDDGQKDDGGSSWEKKFDGGSSWGKKDDGGSSWGKKDDGGSLWGKKDDGGSSWGKEDDGGSLWGKKDDGESSWGKKDDGESSWGKKDDGGSSWGKKDEGGYSEQTFDRGGRGFGGRRGGGRRGGRDQFGRGSSFGNSEDPAPWSKPSGGSSWGKQDGDGGGSSWGKENDAGGGSSWGKQDNGVGSSWGKQNDGSGGGSSWGKQNDAGGGSSWGKQDSGGDGSSWGKQDGGGDSGSAWGKQNNTSGGSSWGKQSDAGGGSSWGKQDGGGGGSSWGKQDGGGGSGSAWGKQNETSNGSSWGKQNDSGGGSSWGKQDGGGGGSSWGKQNDGGGGSSWGKQGDGGSKPWNEHSGGGRGFGERRGGGGFRGGRNQSGRGGRSFDGGRSSSWKTDNQENTWKSDQSGGSDWKKGWGEDSNNSKPSGSSAGGCAGNWPSWDTNSKKETNDKPGDDSKSAWGTSNDQVNTDNNNDSWNKKPNNDVGTSGEADNAWGGKTNAVAPSPSGSAAWGTGDKKTGW nrpe1_arath DNA-directed RNA polymerase V subunit 1 NRPE1 DMS5 At2g40030 DRD3 NRPD1b RMD1 RPE1 DNA-directed RNA polymerase D subunit 1b Protein DEFECTIVE IN MERISTEM SILENCING 5 Protein DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 3 Protein RNA-DIRECTED DNA METHYLATION DEFECTIVE 1 RNA polymerase IV subunit 1 T28M21.19 DNA-directed RNA polymerase E subunit 1 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MEEESTSEILDGEIVGITFALASHHEICIQSISESAINHPSQLTNAFLGLPLEFGKCESCGATEPDKCEGHFGYIQLPVPIYHPAHVNELKQMLSLLCLKCLKIKKAKGTSGGLADRLLGVCCEEASQISIKDRASDGASYLELKLPSRSRLQPGCWNFLERYGYRYGSDYTRPLLAREVKEILRRIPEESRKKLTAKGHIPQEGYILEYLPVPPNCLSVPEASDGFSTMSVDPSRIELKDVLKKVIAIKSSRSGETNFESHKAEASEMFRVVDTYLQVRGTAKAARNIDMRYGVSKISDSSSSKAWTEKMRTLFIRKGSGFSSRSVITGDAYRHVNEVGIPIEIAQRITFEERVSVHNRGYLQKLVDDKLCLSYTQGSTTYSLRDGSKGHTELKPGQVVHRRVMDGDVVFINRPPTTHKHSLQALRVYVHEDNTVKINPLMCSPLSADFDGDCVHLFYPQSLSAKAEVMELFSVEKQLLSSHTGQLILQMGSDSLLSLRVMLERVFLDKATAQQLAMYGSLSLPPPALRKSSKSGPAWTVFQILQLAFPERLSCKGDRFLVDGSDLLKFDFGVDAMGSIINEIVTSIFLEKGPKETLGFFDSLQPLLMESLFAEGFSLSLEDLSMSRADMDVIHNLIIREISPMVSRLRLSYRDELQLENSIHKVKEVAANFMLKSYSIRNLIDIKSNSAITKLVQQTGFLGLQLSDKKKFYTKTLVEDMAIFCKRKYGRISSSGDFGIVKGCFFHGLDPYEEMAHSIAAREVIVRSSRGLAEPGTLFKNLMAVLRDIVITNDGTVRNTCSNSVIQFKYGVDSERGHQGLFEAGEPVGVLAATAMSNPAYKAVLDSSPNSNSSWELMKEVLLCKVNFQNTTNDRRVILYLNECHCGKRFCQENAACTVRNKLNKVSLKDTAVEFLVEYRKQPTISEIFGIDSCLHGHIHLNKTLLQDWNISMQDIHQKCEDVINSLGQKKKKKATDDFKRTSLSVSECCSFRDPCGSKGSDMPCLTFSYNATDPDLERTLDVLCNTVYPVLLEIVIKGDSRICSANIIWNSSDMTTWIRNRHASRRGEWVLDVTVEKSAVKQSGDAWRVVIDSCLSVLHLIDTKRSIPYSVKQVQELLGLSCAFEQAVQRLSASVRMVSKGVLKEHIILLANNMTCSGTMLGFNSGGYKALTRSLNIKAPFTEATLIAPRKCFEKAAEKCHTDSLSTVVGSCSWGKRVDVGTGSQFELLWNQKETGLDDKEETDVYSFLQMVISTTNADAFVSSPGFDVTEEEMAEWAESPERDSALGEPKFEDSADFQNLHDEGKPSGANWEKSSSWDNGCSGGSEWGVSKSTGGEANPESNWEKTTNVEKEDAWSSWNTRKDAQESSKSDSGGAWGIKTKDADADTTPNWETSPAPKDSIVPENNEPTSDVWGHKSVSDKSWDKKNWGTESAPAAWGSTDAAVWGSSDKKNSETESDAAAWGSRDKNNSDVGSGAGVLGPWNKKSSETESNGATWGSSDKTKSGAAAWNSWDKKNIETDSEPAAWGSQGKKNSETESGPAAWGAWDKKKSETEPGPAGWGMGDKKNSETELGPAAMGNWDKKKSDTKSGPAAWGSTDAAAWGSSDKNNSETESDAAAWGSRNKKTSEIESGAGAWGSWGQPSPTAEDKDTNEDDRNPWVSLKETKSREKDDKERSQWGNPAKKFPSSGGWSNGGGADWKGNRNHTPRPPRSEDNLAPMFTATRQRLDSFTSEEQELLSDVEPVMRTLRKIMHPSAYPDGDPISDDDKTFVLEKILNFHPQKETKLGSGVDFITVDKHTIFSDSRCFFVVSTDGAKQDFSYRKSLNNYLMKKYPDRAEEFIDKYFTKPRPSGNRDRNNQDATPPGEEQSQPPNQSIGNGGDDFQTQTQSQSPSQTRAQSPSQAQAQSPSQTQSQSQSQSQSQSQSQSQSQSQSQSQSQSQSQSQSPSQTQTQSPSQTQAQAQSPSSQSPSQTQT rd29a_arath_prom_rna RNA corresponding to the Arabidopsis RD29A promoter region rna ribonucleic acid RNA rna chemical synthesis Chemical synthesis (Chemical synthesis) RNA corresponding to region described in EMBL record AY973635 ago4-ktf1-1 Interaction between Ago4 (At2g27040) and Ktf1 (At5g04290) identified by pulldown 826997 n/a 827003 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 false arath-flower Arabidopsis thaliana flower flower Flower n/a 827004 unspecified role unspecified role bait bait 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 region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) physical association physical association false false false Fig. 4D ago4-nrpe1-1 Interaction between Ago4 (At2g27040) and NRPE1 identified by pulldown 826997 n/a 827005 unspecified role unspecified role bait bait 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 c-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 827003 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 false arath-flower Arabidopsis thaliana flower flower Flower physical association physical association false false false Fig. 4D The TAIR/UniProtKB NRPE1 protein transcript is longer (1976aa) than that described in the text (1874) therefore the c-terminal domain has not been accurately described as a feature. ago4-ktf1-2 Interaction between Ago4 (At2g27040) and Ktf1 (At5g04290) identified by coimmunoprecipitation 826998 n/a 827004 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain 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 ecoli Escherichia coli (strain K12) n/a 827003 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 false arath-flower Arabidopsis thaliana flower flower Flower physical association physical association false false false Fig. 4E ago4-nrpe1-2 Interaction between Ago4 (At2g27040) and NRPE1 identified by pulldown 826998 n/a 827005 unspecified role unspecified role prey prey 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 c-terminal sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 827003 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 false arath-flower Arabidopsis thaliana flower flower Flower physical association physical association false false false Fig. 4E The TAIR/UniProtKB NRPE1 protein transcript is longer (1976aa) than that described in the text (1874) therefore the c-terminal domain has not been accurately described as a feature. ago4-ktf1-5 Colocalisation of Ago4 (At2g27040) and Ktf1 (At5g04290) 826999 n/a 827004 unspecified role unspecified role neutral component neutral component n/a 827003 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false colocalization colocalization false false false Fig. 5B ago4-npre1-1 Colocalisation of Ago4 (At2g27040) and NPRE1 826999 n/a 827005 unspecified role unspecified role neutral component neutral component n/a 827003 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false colocalization colocalization false false false Fig. 5B ago4-ktf1-3 Interaction between Ago4 (At2g27040) and Ktf1 (At5g04290) identified by coimmunoprecipitation 827000 n/a 827003 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 false n/a 827004 unspecified role unspecified role prey prey physical association physical association false false false Fig. 4G ago4-ktf1-4 Interaction between Ago4 (At2g27040) and Ktf1 (At5g04290) identified by coimmunoprecipitation 827001 n/a 827003 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 false n/a 827004 unspecified role unspecified role bait bait physical association physical association false false false Fig. 4F rd25a-ktf1-1 Binding of Ktf1 to the RNA corresponding to the promoter region of RD29A 827002 n/a 827006 unspecified role unspecified role bait bait n/a 827004 unspecified role unspecified role prey prey p3 region required to bind necessary binding region required to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain false direct interaction direct interaction false false false RNA is 32P radio-labelled. The KTF1 P3 region binds to both the forward and reverse strands of the 40 nt RD25A RNA. RNA must be single stranded and KTF1 P3 region does not bind to the corresponding DNA region. Fig. 6