DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu 03-Feb-2009: Contacted by JYOTI. jyoti Only protein-protein interactions in vitro In vitro pull down pull down weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu Accepted 2008-DEC-19 by JYOTI. 03-Feb-2009: Contacted by JYOTI. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 jyoti IMEx The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu 03-Feb-2009: Contacted by JYOTI. jyoti Only protein-protein interactions human-hela Homo sapiens epitheloid cervix carcinoma cells Human hela Human epitheloid cervix carcinoma HeLa cells derivation: cervix; epithelial; adenocarcinoma ATCC no:CCL-2 anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu Accepted 2008-DEC-19 by JYOTI. 03-Feb-2009: Contacted by JYOTI. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 jyoti IMEx The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu 03-Feb-2009: Contacted by JYOTI. jyoti Only protein-protein interactions nicbe Nicotiana benthamiana anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu Accepted 2008-DEC-19 by JYOTI. 03-Feb-2009: Contacted by JYOTI. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 jyoti IMEx The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 imex curation Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu 03-Feb-2009: Contacted by JYOTI. 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 predetermined predetermined participant predetermined Yu B., Bi L., Zheng B., Ji L., Chevalier D., Agarwal M., Ramachandran V., Li W., Lagrange T., Walker JC., Chen X. xuemei.chen@ucr.edu Accepted 2008-DEC-19 by JYOTI. 03-Mar-2009: Contacted by JYOTI. Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2008 jyoti IMEx snip1_human Smad nuclear-interacting protein 1 SNIP1 FHA domain-containing protein SNIP1 protein protein human Homo sapiens Human MKAVKSERERGSRRRHRDGDVVLPAGVVVKQERLSPEVAPPAHRRPDHSGGSPSPPTSEPARSGHRGNRARGVSRSPPKKKNKASGRRSKSPRSKRNRSPHHSTVKVKQEREDHPRRGREDRQHREPSEQEHRRARNSDRDRHRGHSHQRRTSNERPGSGQGQGRDRDTQNLQAQEEEREFYNARRREHRQRNDVGGGGSESQELVPRPGGNNKEKEVPAKEKPSFELSGALLEDTNTFRGVVIKYSEPPEARIPKKRWRLYPFKNDEVLPVMYIHRQSAYLLGRHRRIADIPIDHPSCSKQHAVFQYRLVEYTRADGTVGRRVKPYIIDLGSGNGTFLNNKRIEPQRYYELKEKDVLKFGFSSREYVLLHESSDTSEIDRKDDEDEEEEEEVSDS B183F83EC3184676 ddl_arath FHA domain-containing protein DDL DDL Protein DAWDLE At3g20550 K10D20.9 protein protein arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress MAPSSRSPSPRTKRLRRARGEKEIGRSREREDDGREREKRNSRERDRDIGRDRDRERKGEGERDREVGDKRRRSGREDTEKRRRTRTDDERYSRGRHERSTSPSDRSHRSSRRSPERAIASRHDEGSNARGGSEEPNVEEDSVARMRAVEEALAAKKKEEPSFELSGKLAEETNRYRGITLLFNEPPEARKPSERWRLYVFKDGEPLNEPLCLHRQSCYLFGRERRIADIPTDHPSCSKQHAVIQYREMEKEKPDGMMGKQVKPYIMDLGSTNKTYINESPIEPQRYYELFEKDTIKFGNSSREYVLLHENSAE 42F3A7C9DFF14B68 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 EAA944F0C0C81D4C mir162b-arath-rna pri-miR162b rna ribonucleic acid RNA rna arath Arabidopsis thaliana (Mouse-ear cress) Mouse-ear cress ATTCTCTCTTTCTCTCTCTCTCTCTCTCTCATCCCGGCCCAGTTATGTGGTCGGAGAGAATGATGAAGG D15D40BCFBDD532F rnc_human Ribonuclease 3 Ribonuclease III DROSHA p241 RNASEN RN3 RNASE3L Protein Drosha protein protein human Homo sapiens Human MMQGNTCHRMSFHPGRGCPRGRGGHGARPSAPSFRPQNLRLLHPQQPPVQYQYEPPSAPSTTFSNSPAPNFLPPRPDFVPFPPPMPPSAQGPLPPCPIRPPFPNHQMRHPFPVPPCFPPMPPPMPCPNNPPVPGAPPGQGTFPFMMPPPSMPHPPPPPVMPQQVNYQYPPGYSHHNFPPPSFNSFQNNPSSFLPSANNSSSPHFRHLPPYPLPKAPSERRSPERLKHYDDHRHRDHSHGRGERHRSLDRRERGRSPDRRRQDSRYRSDYDRGRTPSRHRSYERSRERERERHRHRDNRRSPSLERSYKKEYKRSGRSYGLSVVPEPAGCTPELPGEIIKNTDSWAPPLEIVNHRSPSREKKRARWEEEKDRWSDNQSSGKDKNYTSIKEKEPEETMPDKNEEEEEELLKPVWIRCTHSENYYSSDPMDQVGDSTVVGTSRLRDLYDKFEEELGSRQEKAKAARPPWEPPKTKLDEDLESSSESECESDEDSTCSSSSDSEVFDVIAEIKRKKAHPDRLHDELWYNDPGQMNDGPLCKCSAKARRTGIRHSIYPGEEAIKPCRPMTNNAGRLFHYRITVSPPTNFLTDRPTVIEYDDHEYIFEGFSMFAHAPLTNIPLCKVIRFNIDYTIHFIEEMMPENFCVKGLELFSLFLFRDILELYDWNLKGPLFEDSPPCCPRFHFMPRFVRFLPDGGKEVLSMHQILLYLLRCSKALVPEEEIANMLQWEELEWQKYAEECKGMIVTNPGTKPSSVRIDQLDREQFNPDVITFPIIVHFGIRPAQLSYAGDPQYQKLWKSYVKLRHLLANSPKVKQTDKQKLAQREEALQKIRQKNTMRREVTVELSSQGFWKTGIRSDVCQHAMMLPVLTHHIRYHQCLMHLDKLIGYTFQDRCLLQLAMTHPSHHLNFGMNPDHARNSLSNCGIRQPKYGDRKVHHMHMRKKGINTLINIMSRLGQDDPTPSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRHAMANCFEALIGAVYLEGSLEEAKQLFGRLLFNDPDLREVWLNYPLHPLQLQEPNTDRQLIETSPVLQKLTEFEEAIGVIFTHVRLLARAFTLRTVGFNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDWNDPKSQLQQCCLTLRTEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYNFPQMAHQKRFIERKYRQELKEMRWEREHQEREPDETEDIKK DIP protein Q9NRR4 original sequence version: 112 DIP protein Q9NRR4 original sequence version: 70 DIP protein Q9NRR4 original sequence version: 110 DIP protein Q9NRR4 original sequence version: 102 DIP protein Q9NRR4 original sequence version: 121 DIP protein Q9NRR4 original sequence version: 109 ED6FDEA09F3B8092 ddl-dcl1-2 4 7 unspecified role unspecified role bait bait n-terminal required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain 6 unspecified role unspecified role prey prey physical association physical association Figure 5A DDL was found to interact with an N-terminal portion (amino acids 1-833), but not a C-terminal portion (amino acids 814-1909), of DCL1 in the yeast two-hybrid assay ddl-dcl1-1 3 7 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 6 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 physical association physical association Figure 5B As shown in Fig. 5B, an anti-HA antibody detected the enrichment of HA-DDL in the DCL1-YFP immunoprecipitate relative to the control immunoprecipitate, suggesting the association between DDL and DCL1. The authors cautioned "it should be noted that only a small portion of the inputHA-DDL was associated with DCL1-YFP in this assay. In fact, HA-DDL was not detected in the DCL1-YFP immunoprecipitate when the levels of DCL1-YFP were low (i.e., in the absence of p19). These observations suggested that only a portion of DCL1 molecules could interact with DDL or that DDL interacted transiently with DCL1". ddl-rna 1 8 unspecified role unspecified role prey prey 6 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 physical association physical association Figure 7A Figure 7B Labeled pri-miR162b was added to the beads containing GST-DDL or GST. After washes and elution, the RNA was resolved on a polyacrylamide gel. Pri-miR162b was retained by GST-DDL but not GST alone snip1-drosha-1 2 9 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 5 unspecified role unspecified role bait bait region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Figure 6D After immunoprecipitation of HA-SNIP1with an anti-HAantibody, we were able to detect the presence of Drosha-Flag in the SNIP1 immunoprecipitate, but not in the control immunoprecipitate, with an anti-Flag antibody