RDM4_ARATH
ID RDM4_ARATH Reviewed; 346 AA.
AC Q8GYP3; O22924;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=RNA-directed DNA methylation 4;
DE AltName: Full=Protein DEFECTIVE IN MERISTEM SILENCING 4;
GN Name=RDM4; Synonyms=DMS4; OrderedLocusNames=At2g30280; ORFNames=T9D9.9;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH POL II AND POL V
RP COMPLEXES.
RX PubMed=19903758; DOI=10.1101/gad.1851809;
RA He X.J., Hsu Y.F., Zhu S., Liu H.L., Pontes O., Zhu J., Cui X., Wang C.S.,
RA Zhu J.K.;
RT "A conserved transcriptional regulator is required for RNA-directed DNA
RT methylation and plant development.";
RL Genes Dev. 23:2717-2722(2009).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=20010803; DOI=10.1038/embor.2009.246;
RA Kanno T., Bucher E., Daxinger L., Huettel B., Kreil D.P., Breinig F.,
RA Lind M., Schmitt M.J., Simon S.A., Gurazada S.G., Meyers B.C.,
RA Lorkovic Z.J., Matzke A.J., Matzke M.;
RT "RNA-directed DNA methylation and plant development require an IWR1-type
RT transcription factor.";
RL EMBO Rep. 11:65-71(2010).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH NRPD1.
RX PubMed=21811420; DOI=10.1371/journal.pgen.1002195;
RA Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E.;
RT "SHH1, a homeodomain protein required for DNA methylation, as well as RDR2,
RT RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.";
RL PLoS Genet. 7:E1002195-E1002195(2011).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Probable regulatory factor for several RNA polymerases.
CC Effector involved in facilitation of Pol V transcription as RNA
CC scaffold and recruitment of silencing complex to target genomic sites.
CC {ECO:0000269|PubMed:19903758, ECO:0000269|PubMed:20010803}.
CC -!- SUBUNIT: Interacts with NRPD1. Associates with Pol II and Pol V
CC complexes. {ECO:0000269|PubMed:19903758, ECO:0000269|PubMed:21811420}.
CC -!- DISRUPTION PHENOTYPE: Reduced DNA methylation at RdDM target loci and
CC pleiotropic developmental phenotype. {ECO:0000269|PubMed:19903758,
CC ECO:0000269|PubMed:20010803}.
CC -!- SIMILARITY: Belongs to the IWR1/SLC7A6OS family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC16933.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC002338; AAC16933.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC08365.1; -; Genomic_DNA.
DR EMBL; AK117472; BAC42136.1; -; mRNA.
DR EMBL; BT005437; AAO63857.1; -; mRNA.
DR PIR; E84706; E84706.
DR RefSeq; NP_180587.2; NM_128581.4.
DR AlphaFoldDB; Q8GYP3; -.
DR BioGRID; 2927; 1.
DR STRING; 3702.AT2G30280.1; -.
DR iPTMnet; Q8GYP3; -.
DR PaxDb; Q8GYP3; -.
DR PRIDE; Q8GYP3; -.
DR ProteomicsDB; 235076; -.
DR EnsemblPlants; AT2G30280.1; AT2G30280.1; AT2G30280.
DR GeneID; 817578; -.
DR Gramene; AT2G30280.1; AT2G30280.1; AT2G30280.
DR KEGG; ath:AT2G30280; -.
DR Araport; AT2G30280; -.
DR TAIR; locus:2065764; AT2G30280.
DR eggNOG; ENOG502QS78; Eukaryota.
DR HOGENOM; CLU_067940_0_0_1; -.
DR InParanoid; Q8GYP3; -.
DR OMA; NPFPLVQ; -.
DR OrthoDB; 1173564at2759; -.
DR PhylomeDB; Q8GYP3; -.
DR PRO; PR:Q8GYP3; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q8GYP3; baseline and differential.
DR Genevisible; Q8GYP3; AT.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IMP:TAIR.
DR GO; GO:0006306; P:DNA methylation; IMP:TAIR.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:0009791; P:post-embryonic development; IMP:TAIR.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IGI:TAIR.
DR InterPro; IPR013883; TF_Iwr1_dom.
DR Pfam; PF08574; Iwr1; 1.
PE 1: Evidence at protein level;
KW Acetylation; Reference proteome; RNA-mediated gene silencing.
FT CHAIN 1..346
FT /note="RNA-directed DNA methylation 4"
FT /id="PRO_0000423312"
FT REGION 253..346
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 276..307
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 308..325
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 326..346
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 346 AA; 40079 MW; 1178E4F6937BCAAD CRC64;
MDGVGESSTQ NEVEEKPVIV RVKRKVGQSL LDAFWLEINE RPLKRPTLDF SKLSISDSGE
RGPSVAEDVK PKKVLVRHLE TVTDSETTAD IIHSFFESDH NEKSCSKGKF EERKIAFKKD
NRKEQRLTKS VQKQQIASEN ARFEQIWRSR KGNKEGIHEK CHFFDVIRVD TEERRDNAQE
FTSLEDQKML ASFLPLLREC IPTAAEEIEA DIQSSHTEEY VYDYYAVNEE MDISEDSSKN
QFPLVIVEDE EEFCDGSDES DYDSEDSNAE DHPKTDYPEE EEEEEEEDDD DDDDDESEEE
KSEASDESDD EETSKRHVRS VLGDDEFDDY AEDVYGYSES DEEFES
