DDM1_ARATH
ID DDM1_ARATH Reviewed; 764 AA.
AC Q9XFH4; Q5C995; Q5C996;
DT 08-MAR-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=ATP-dependent DNA helicase DDM1;
DE EC=3.6.4.12;
DE AltName: Full=Protein CHROMATIN REMODELING 1 {ECO:0000303|PubMed:16547115};
DE Short=AtCHR1;
DE Short=CHR01;
DE AltName: Full=Protein DECREASED DNA METHYLATION 1;
DE Short=AtDDM1;
DE AltName: Full=Protein SOMNIFEROUS 1;
DE AltName: Full=SWI/SNF2-related matrix-associated actin-dependent regulator of chromatin DDM1;
GN Name=DDM1; Synonyms=CHA1, CHR1 {ECO:0000303|PubMed:16547115}, SOM1, SOM4;
GN OrderedLocusNames=At5g66750; ORFNames=MSN2.14;
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 [GENOMIC DNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=10319870; DOI=10.1038/8803;
RA Jeddeloh J.A., Stokes T.L., Richards E.J.;
RT "Maintenance of genomic methylation requires a SWI2/SNF2-like protein.";
RL Nat. Genet. 22:94-97(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [3]
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 [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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-762, FUNCTION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=cv. C24;
RX PubMed=15516340; DOI=10.1074/jbc.m409053200;
RA Chang S., Pikaard C.S.;
RT "Transcript profiling in Arabidopsis reveals complex responses to global
RT inhibition of DNA methylation and histone deacetylation.";
RL J. Biol. Chem. 280:796-804(2005).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=8316832; DOI=10.1126/science.8316832;
RA Vongs A., Kakutani T., Martienssen R.A., Richards E.J.;
RT "Arabidopsis thaliana DNA methylation mutants.";
RL Science 260:1926-1928(1993).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=7870578; DOI=10.1093/nar/23.1.130;
RA Kakutani T., Jeddeloh J.A., Richards E.J.;
RT "Characterization of an Arabidopsis thaliana DNA hypomethylation mutant.";
RL Nucleic Acids Res. 23:130-137(1995).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=8901594; DOI=10.1073/pnas.93.22.12406;
RA Kakutani T., Jeddeloh J.A., Flowers S.K., Munakata K., Richards E.J.;
RT "Developmental abnormalities and epimutations associated with DNA
RT hypomethylation mutations.";
RL Proc. Natl. Acad. Sci. U.S.A. 93:12406-12411(1996).
RN [9]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=9450349; DOI=10.1046/j.1365-313x.1997.12061447.x;
RA Kakutani T.;
RT "Genetic characterization of late-flowering traits induced by DNA
RT hypomethylation mutation in Arabidopsis thaliana.";
RL Plant J. 12:1447-1451(1997).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=9611181; DOI=10.1093/genetics/149.2.651;
RA Furner I.J., Sheikh M.A., Collett C.E.;
RT "Gene silencing and homology-dependent gene silencing in Arabidopsis:
RT genetic modifiers and DNA methylation.";
RL Genetics 149:651-662(1998).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=9620857; DOI=10.1101/gad.12.11.1714;
RA Jeddeloh J.A., Bender J., Richards E.J.;
RT "The DNA methylation locus DDM1 is required for maintenance of gene
RT silencing in Arabidopsis.";
RL Genes Dev. 12:1714-1725(1998).
RN [12]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=10939915; DOI=10.1073/pnas.95.2.632;
RA Mittelsten Scheid O., Afsar K., Paszkowski J.;
RT "Release of epigenetic gene silencing by trans-acting mutations in
RT Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 95:632-637(1998).
RN [13]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=9927473; DOI=10.1093/genetics/151.2.831;
RA Kakutani T., Munakata K., Richards E.J., Hirochika H.;
RT "Meiotically and mitotically stable inheritance of DNA hypomethylation
RT induced by ddm1 mutation of Arabidopsis thaliana.";
RL Genetics 151:831-838(1999).
RN [14]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=10580004; DOI=10.1101/gad.13.22.2971;
RA Vielle-Calzada J.-P., Thomas J., Spillane C., Coluccio A., Hoeppner M.A.,
RA Grossniklaus U.;
RT "Maintenance of genomic imprinting at the Arabidopsis medea locus requires
RT zygotic DDM1 activity.";
RL Genes Dev. 13:2971-2982(1999).
RN [15]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=10715322; DOI=10.2307/3870941;
RA Hirochika H., Okamoto H., Kakutani T.;
RT "Silencing of retrotransposons in arabidopsis and reactivation by the ddm1
RT mutation.";
RL Plant Cell 12:357-369(2000).
RN [16]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=11148284; DOI=10.2307/3871235;
RA Yadegari R., Kinoshita T., Lotan O., Cohen G., Katz A., Choi Y., Katz A.,
RA Nakashima K., Harada J.J., Goldberg R.B., Fischer R.L., Ohad N.;
RT "Mutations in the FIE and MEA genes that encode interacting polycomb
RT proteins cause parent-of-origin effects on seed development by distinct
RT mechanisms.";
RL Plant Cell 12:2367-2382(2000).
RN [17]
RP REVIEW.
RX PubMed=10999404; DOI=10.1023/a:1006427226972;
RA Finnegan E.J., Kovac K.A.;
RT "Plant DNA methyltransferases.";
RL Plant Mol. Biol. 43:189-201(2000).
RN [18]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=11238379; DOI=10.1101/gad.193701;
RA Singer T., Yordan C., Martienssen R.A.;
RT "Robertson's Mutator transposons in A. thaliana are regulated by the
RT chromatin-remodeling gene Decrease in DNA Methylation (DDM1).";
RL Genes Dev. 15:591-602(2001).
RN [19]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=11346800; DOI=10.1038/35075612;
RA Miura A., Yonebayashi S., Watanabe K., Toyama T., Shimada H., Kakutani T.;
RT "Mobilization of transposons by a mutation abolishing full DNA methylation
RT in Arabidopsis.";
RL Nature 411:212-214(2001).
RN [20]
RP FUNCTION.
RX PubMed=11948614; DOI=10.1002/bies.10078;
RA Bourc'his D., Bestor T.H.;
RT "Helicase homologues maintain cytosine methylation in plants and mammals.";
RL Bioessays 24:297-299(2002).
RN [21]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12194816; DOI=10.1016/s0960-9822(02)00976-4;
RA Johnson L.M., Cao X., Jacobsen S.E.;
RT "Interplay between two epigenetic marks: DNA methylation and histone H3
RT lysine 9 methylation.";
RL Curr. Biol. 12:1360-1367(2002).
RN [22]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12456661; DOI=10.1093/emboj/cdf657;
RA Soppe W.J.J., Jasencakova Z., Houben A., Kakutani T., Meister A.,
RA Huang M.S., Jacobsen S.E., Schubert I., Fransz P.F.;
RT "DNA methylation controls histone H3 lysine 9 methylation and
RT heterochromatin assembly in Arabidopsis.";
RL EMBO J. 21:6549-6559(2002).
RN [23]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=11779837; DOI=10.1101/gr.196001;
RA Wright D.A., Voytas D.F.;
RT "Athila4 of Arabidopsis and Calypso of soybean define a lineage of
RT endogenous plant retroviruses.";
RL Genome Res. 12:122-131(2002).
RN [24]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12472695; DOI=10.1046/j.1365-313x.2002.01466.x;
RA Ohta Y., Noma K., Tsuchimoto S., Ohtsubo E., Ohtsubo H.;
RT "Expression of Arabidopsis LINEs from two promoters.";
RL Plant J. 32:809-818(2002).
RN [25]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12370435; DOI=10.1073/pnas.202380499;
RA Mittelsten Scheid O., Probst A.V., Afsar K., Paszkowski J.;
RT "Two regulatory levels of transcriptional gene silencing in Arabidopsis.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:13659-13662(2002).
RN [26]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12077425; DOI=10.1126/science.1074950;
RA Gendrel A.V., Lippman Z., Yordan C., Colot V., Martienssen R.A.;
RT "Dependence of heterochromatic histone H3 methylation patterns on the
RT Arabidopsis gene DDM1.";
RL Science 297:1871-1873(2002).
RN [27]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12663548; DOI=10.1093/genetics/163.3.1109;
RA Kankel M.W., Ramsey D.E., Stokes T.L., Flowers S.K., Haag J.R.,
RA Jeddeloh J.A., Riddle N.C., Verbsky M.L., Richards E.J.;
RT "Arabidopsis MET1 cytosine methyltransferase mutants.";
RL Genetics 163:1109-1122(2003).
RN [28]
RP FUNCTION AS DNA HELICASE AND ATPASE, DISRUPTION PHENOTYPE, ACTIVITY
RP REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=12403775; DOI=10.1074/jbc.m209260200;
RA Brzeski J., Jerzmanowski A.;
RT "Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-
RT remodeling factors.";
RL J. Biol. Chem. 278:823-828(2003).
RN [29]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=14630972; DOI=10.1105/tpc.017467;
RA Mathieu O., Jasencakova Z., Vaillant I., Gendrel A.-V., Colot V.,
RA Schubert I., Tourmente S.;
RT "Changes in 5S rDNA chromatin organization and transcription during
RT heterochromatin establishment in Arabidopsis.";
RL Plant Cell 15:2929-2939(2003).
RN [30]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=12609046; DOI=10.1046/j.1365-313x.2003.01667.x;
RA Probst A.V., Fransz P.F., Paszkowski J., Mittelsten Scheid O.;
RT "Two means of transcriptional reactivation within heterochromatin.";
RL Plant J. 33:743-749(2003).
RN [31]
RP FUNCTION IN TRANSPOSON SILENCING, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14691539; DOI=10.1371/journal.pbio.0000067;
RA Lippman Z., May B., Yordan C., Singer T., Martienssen R.;
RT "Distinct mechanisms determine transposon inheritance and methylation via
RT small interfering RNA and histone modification.";
RL PLoS Biol. 1:E67-E67(2003).
RN [32]
RP REVIEW.
RX PubMed=12597869; DOI=10.1016/s1360-1385(03)00005-0;
RA Stokes T.;
RT "DNA-RNA-protein gang together in silence.";
RL Trends Plant Sci. 8:53-55(2003).
RN [33]
RP FUNCTION IN TRANSPOSON SILENCING, AND DISRUPTION PHENOTYPE.
RX PubMed=15514067; DOI=10.1534/genetics.104.029637;
RA Kato M., Takashima K., Kakutani T.;
RT "Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana.";
RL Genetics 168:961-969(2004).
RN [34]
RP FUNCTION IN TRANSPOSON SILENCING, AND DISRUPTION PHENOTYPE.
RX PubMed=14608503; DOI=10.1007/s00438-003-0943-y;
RA Miura A., Kato M., Watanabe K., Kawabe A., Kotani H., Kakutani T.;
RT "Genomic localization of endogenous mobile CACTA family transposons in
RT natural variants of Arabidopsis thaliana.";
RL Mol. Genet. Genomics 270:524-532(2004).
RN [35]
RP FUNCTION IN TRANSPOSON SILENCING, AND DISRUPTION PHENOTYPE.
RX PubMed=15269773; DOI=10.1038/nature02651;
RA Lippman Z., Gendrel A.-V., Black M., Vaughn M.W., Dedhia N., McCombie W.R.,
RA Lavine K., Mittal V., May B., Kasschau K.D., Carrington J.C., Doerge R.W.,
RA Colot V., Martienssen R.;
RT "Role of transposable elements in heterochromatin and epigenetic control.";
RL Nature 430:471-476(2004).
RN [36]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=15968513; DOI=10.1007/s00425-005-1524-6;
RA Ruiz-Garcia L., Cervera M.T., Martinez-Zapater J.M.;
RT "DNA methylation increases throughout Arabidopsis development.";
RL Planta 222:301-306(2005).
RN [37]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH MBD2; MBD5 AND MBD6.
RX PubMed=15805479; DOI=10.1105/tpc.105.031567;
RA Zemach A., Li Y., Wayburn B., Ben-Meir H., Kiss V., Avivi Y., Kalchenko V.,
RA Jacobsen S.E., Grafi G.;
RT "DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects
RT their subnuclear localization.";
RL Plant Cell 17:1549-1558(2005).
RN [38]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17082818; DOI=10.1038/sj.embor.7400835;
RA Habu Y., Mathieu O., Tariq M., Probst A.V., Smathajitt C., Zhu T.,
RA Paszkowski J.;
RT "Epigenetic regulation of transcription in intermediate heterochromatin.";
RL EMBO Rep. 7:1279-1284(2006).
RN [39]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16547115; DOI=10.1534/genetics.105.051664;
RA Shaked H., Avivi-Ragolsky N., Levy A.A.;
RT "Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family
RT in DNA damage response and recombination.";
RL Genetics 173:985-994(2006).
RN [40]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17012404; DOI=10.1104/pp.106.088849;
RA Xiao W., Brown R.C., Lemmon B.E., Harada J.J., Goldberg R.B., Fischer R.L.;
RT "Regulation of seed size by hypomethylation of maternal and paternal
RT genomes.";
RL Plant Physiol. 142:1160-1168(2006).
RN [41]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17627280; DOI=10.1038/sj.emboj.7601788;
RA Saze H., Kakutani T.;
RT "Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due
RT to lack of the chromatin-remodeling factor DDM1.";
RL EMBO J. 26:3641-3652(2007).
RN [42]
RP FUNCTION IN TRANSPOSON SILENCING, AND DISRUPTION PHENOTYPE.
RX PubMed=17339215; DOI=10.1534/genetics.107.071092;
RA Rangwala S.H., Richards E.J.;
RT "Differential epigenetic regulation within an Arabidopsis retroposon
RT family.";
RL Genetics 176:151-160(2007).
RN [43]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17144899; DOI=10.1111/j.1365-313x.2006.02936.x;
RA Kinoshita Y., Saze H., Kinoshita T., Miura A., Soppe W.J.J., Koornneef M.,
RA Kakutani T.;
RT "Control of FWA gene silencing in Arabidopsis thaliana by SINE-related
RT direct repeats.";
RL Plant J. 49:38-45(2007).
RN [44]
RP FUNCTION IN TRANSPOSON SILENCING, AND DISRUPTION PHENOTYPE.
RX PubMed=18467467; DOI=10.1104/pp.108.117846;
RA Perez-Hormaeche J., Potet F., Beauclair L., Le Masson I., Courtial B.,
RA Bouche N., Lucas H.;
RT "Invasion of the Arabidopsis genome by the tobacco retrotransposon Tnt1 is
RT controlled by reversible transcriptional gene silencing.";
RL Plant Physiol. 147:1264-1278(2008).
RN [45]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19529764; DOI=10.1371/journal.pone.0005932;
RA Blevins T., Pontes O., Pikaard C.S., Meins F. Jr.;
RT "Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA
RT transcripts in Arabidopsis.";
RL PLoS ONE 4:E5932-E5932(2009).
RN [46]
RP GENE FAMILY.
RX PubMed=24265739; DOI=10.1371/journal.pone.0078982;
RA Xu R., Zhang S., Huang J., Zheng C.;
RT "Genome-wide comparative in silico analysis of the RNA helicase gene family
RT in Zea mays and Glycine max: a comparison with Arabidopsis and Oryza
RT sativa.";
RL PLoS ONE 8:E78982-E78982(2013).
CC -!- FUNCTION: ATP-dependent DNA helicase that plays a role in formation,
CC organization, stability and heritability of heterochromatin and thus
CC regulates several physiological traits. Binds to the nucleosome and
CC promotes chromatin remodeling in an ATP-dependent manner; induces
CC nucleosome repositioning on a short DNA fragment, and, possibly, could
CC be guided to target sites (including silent transposable elements) by
CC small interfering RNAs (siRNAs). Can bind both free and nucleosomal
CC DNA. Required for the heritable maintenance of genome integrity and
CC transcriptional gene silencing (TGS), including homology-dependent gene
CC silencing (HDG silencing), via the maintenance of DNA methylation
CC (mostly on cytosine, in both CpG and CpHpG sites, where H is A, T or C)
CC and of histone methylation (e.g. chromatin methylation). May facilitate
CC localization of MBD proteins at specific nuclear domains. Necessary for
CC the maintenance of the genomic imprint at the MEA locus, especially for
CC the silencing of paternally inherited MEA locus. Plays a major role in
CC the inactivation maintenance of retrotransposons (e.g. Tar17, SINE,
CC LINE, ATLN39, CAC1 (CACTAs), Athila elements, and mutator-like elements
CC MULEs and TIR-MULEs) and the silencing of repeated genes and transgenes
CC (e.g. T-DNA insertions). Required for KYP-dependent histone H3 'Lys-9'
CC (H3K9me) methylation, deacetylation of histone H4 'Lys-16' (H4K16) and
CC MET1-dependent DNA methylation. Involved in the chromatin organization
CC of 5S rRNA genes (localized in the pericentromeric heterochromatin of
CC chromosomes 3, 4, and 5) modifications during heterochromatin
CC establishment. Prevents siRNA accumulation (siRNA are probably involved
CC in epigenetic inheritance and in 5S rRNA genes regulation by
CC silencing). Required during plant organogenesis and development, as
CC well as during seed formation. {ECO:0000269|PubMed:10319870,
CC ECO:0000269|PubMed:10580004, ECO:0000269|PubMed:10715322,
CC ECO:0000269|PubMed:10939915, ECO:0000269|PubMed:11148284,
CC ECO:0000269|PubMed:11238379, ECO:0000269|PubMed:11346800,
CC ECO:0000269|PubMed:11779837, ECO:0000269|PubMed:11948614,
CC ECO:0000269|PubMed:12077425, ECO:0000269|PubMed:12194816,
CC ECO:0000269|PubMed:12370435, ECO:0000269|PubMed:12403775,
CC ECO:0000269|PubMed:12456661, ECO:0000269|PubMed:12472695,
CC ECO:0000269|PubMed:12609046, ECO:0000269|PubMed:12663548,
CC ECO:0000269|PubMed:14608503, ECO:0000269|PubMed:14630972,
CC ECO:0000269|PubMed:14691539, ECO:0000269|PubMed:15269773,
CC ECO:0000269|PubMed:15514067, ECO:0000269|PubMed:15516340,
CC ECO:0000269|PubMed:15805479, ECO:0000269|PubMed:15968513,
CC ECO:0000269|PubMed:17012404, ECO:0000269|PubMed:17082818,
CC ECO:0000269|PubMed:17144899, ECO:0000269|PubMed:17339215,
CC ECO:0000269|PubMed:17627280, ECO:0000269|PubMed:18467467,
CC ECO:0000269|PubMed:19529764, ECO:0000269|PubMed:7870578,
CC ECO:0000269|PubMed:8316832, ECO:0000269|PubMed:8901594,
CC ECO:0000269|PubMed:9450349, ECO:0000269|PubMed:9611181,
CC ECO:0000269|PubMed:9620857, ECO:0000269|PubMed:9927473}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC -!- ACTIVITY REGULATION: ATPase activity is stimulated 3-fold by DNA (both
CC free and nucleosomal) binding. {ECO:0000269|PubMed:12403775}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=55 uM for ATP {ECO:0000269|PubMed:12403775};
CC KM=66 uM for ATP (in the presence of free DNA)
CC {ECO:0000269|PubMed:12403775};
CC KM=66 uM for ATP (in the presence of chromatin)
CC {ECO:0000269|PubMed:12403775};
CC Note=All results where obtained at pH 8.0 and 25 degrees Celsius.;
CC -!- SUBUNIT: Interacts with the MBD domains of MBD2, MBD5 and MBD6.
CC {ECO:0000269|PubMed:15805479}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250, ECO:0000255|PROSITE-
CC ProRule:PRU00768}. Note=Closely associated with pericentric
CC heterochromatin. {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Reactivated transcription of heavily methylated
CC silent loci, via chromatin demethylation. Hypomethylated chromatin;
CC gain of histone H3 'Lys-4' methylation (H3K4me) but depletion of
CC histone H3 'Lys-9' methylation (H3K9me). Altered leaf shape, increased
CC cauline leaf number, and delayed flowering onset (due to FWA
CC derepression). Accumulates developmental abnormalities and
CC transcription derepression by slowly inducing heritable lesions
CC (hopymethylation) at unlinked loci. Derepressed paternally inherited
CC MEA locus in male gametophytes and seeds. Reactivation of several
CC silent retrotransposons. Smaller chromocenters with reduced
CC heterochromatin amount. Causes a striking decondensation of centromeric
CC heterochromatin, a redistribution of the remaining methylation of DNA,
CC and a drastic change in the pattern of histone modification. Abnormal
CC subcellular localization of MBD proteins (e.g. MBD2, MBD5, MBD6 and
CC MBD7). Smaller seeds in male inherited disruption, but larger seeds in
CC female inherited ones. The heritable and cumulative hypermethylation
CC and silencing of BNS, leading to the bonsai phenotype, requires the
CC hypomethylation of the flanking LINE transposon.
CC {ECO:0000269|PubMed:10319870, ECO:0000269|PubMed:10580004,
CC ECO:0000269|PubMed:10715322, ECO:0000269|PubMed:10939915,
CC ECO:0000269|PubMed:11148284, ECO:0000269|PubMed:11238379,
CC ECO:0000269|PubMed:11346800, ECO:0000269|PubMed:11779837,
CC ECO:0000269|PubMed:12077425, ECO:0000269|PubMed:12194816,
CC ECO:0000269|PubMed:12370435, ECO:0000269|PubMed:12403775,
CC ECO:0000269|PubMed:12456661, ECO:0000269|PubMed:12472695,
CC ECO:0000269|PubMed:12609046, ECO:0000269|PubMed:12663548,
CC ECO:0000269|PubMed:14608503, ECO:0000269|PubMed:14630972,
CC ECO:0000269|PubMed:14691539, ECO:0000269|PubMed:15269773,
CC ECO:0000269|PubMed:15514067, ECO:0000269|PubMed:15516340,
CC ECO:0000269|PubMed:15805479, ECO:0000269|PubMed:15968513,
CC ECO:0000269|PubMed:17012404, ECO:0000269|PubMed:17082818,
CC ECO:0000269|PubMed:17144899, ECO:0000269|PubMed:17339215,
CC ECO:0000269|PubMed:17627280, ECO:0000269|PubMed:18467467,
CC ECO:0000269|PubMed:19529764, ECO:0000269|PubMed:7870578,
CC ECO:0000269|PubMed:8316832, ECO:0000269|PubMed:8901594,
CC ECO:0000269|PubMed:9450349, ECO:0000269|PubMed:9611181,
CC ECO:0000269|PubMed:9620857, ECO:0000269|PubMed:9927473}.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAX22754.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAX22755.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF143940; AAD28303.1; -; Genomic_DNA.
DR EMBL; AB018119; BAA97281.1; -; Genomic_DNA.
DR EMBL; CP002688; AED98259.1; -; Genomic_DNA.
DR EMBL; AY099638; AAM20489.1; -; mRNA.
DR EMBL; BT002161; AAN72172.1; -; mRNA.
DR EMBL; AY699010; AAX22754.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AY699011; AAX22755.1; ALT_SEQ; Genomic_DNA.
DR RefSeq; NP_201476.1; NM_126073.3.
DR AlphaFoldDB; Q9XFH4; -.
DR SMR; Q9XFH4; -.
DR BioGRID; 22050; 4.
DR IntAct; Q9XFH4; 1.
DR STRING; 3702.AT5G66750.1; -.
DR iPTMnet; Q9XFH4; -.
DR PaxDb; Q9XFH4; -.
DR PRIDE; Q9XFH4; -.
DR ProteomicsDB; 224563; -.
DR EnsemblPlants; AT5G66750.1; AT5G66750.1; AT5G66750.
DR GeneID; 836808; -.
DR Gramene; AT5G66750.1; AT5G66750.1; AT5G66750.
DR KEGG; ath:AT5G66750; -.
DR Araport; AT5G66750; -.
DR TAIR; locus:2173644; AT5G66750.
DR eggNOG; KOG0385; Eukaryota.
DR HOGENOM; CLU_000315_17_1_1; -.
DR InParanoid; Q9XFH4; -.
DR OMA; ELMLPRK; -.
DR OrthoDB; 61251at2759; -.
DR PhylomeDB; Q9XFH4; -.
DR PRO; PR:Q9XFH4; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9XFH4; baseline and differential.
DR Genevisible; Q9XFH4; AT.
DR GO; GO:0000786; C:nucleosome; IDA:TAIR.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:TAIR.
DR GO; GO:0008094; F:ATP-dependent activity, acting on DNA; IBA:GO_Central.
DR GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0003678; F:DNA helicase activity; IMP:UniProtKB.
DR GO; GO:0006346; P:DNA methylation-dependent heterochromatin assembly; IMP:TAIR.
DR GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR.
DR GO; GO:0090241; P:negative regulation of histone H4 acetylation; IMP:UniProtKB.
DR GO; GO:0051574; P:positive regulation of histone H3-K9 methylation; IMP:UniProtKB.
DR GO; GO:0044030; P:regulation of DNA methylation; IMP:UniProtKB.
DR GO; GO:0006349; P:regulation of gene expression by genomic imprinting; IMP:UniProtKB.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:GO_Central.
DR GO; GO:0032197; P:transposition, RNA-mediated; IMP:TAIR.
DR CDD; cd18009; DEXHc_HELLS_SMARCA6; 1.
DR Gene3D; 3.40.50.10810; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR044753; HELLS_N.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR038718; SNF2-like_sf.
DR InterPro; IPR000330; SNF2_N.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00176; SNF2-rel_dom; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Coiled coil; DNA-binding; Helicase; Hydrolase;
KW Nucleotide-binding; Nucleus; Reference proteome; Repeat; Transcription;
KW Transcription regulation.
FT CHAIN 1..764
FT /note="ATP-dependent DNA helicase DDM1"
FT /id="PRO_0000405276"
FT DOMAIN 214..382
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 528..695
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 129..152
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 62..88
FT /evidence="ECO:0000255"
FT MOTIF 145..152
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 333..336
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOTIF 429..436
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT BINDING 227..234
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 176
FT /note="I -> T (in Ref. 5; AAX22754/AAX22755)"
FT /evidence="ECO:0000305"
FT CONFLICT 187
FT /note="I -> M (in Ref. 5; AAX22754/AAX22755)"
FT /evidence="ECO:0000305"
FT CONFLICT 434
FT /note="C -> F (in Ref. 5; AAX22754/AAX22755)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 764 AA; 86638 MW; F7E3F91DC8E1D9F2 CRC64;
MVSLRSRKVI PASEMVSDGK TEKDASGDSP TSVLNEEENC EEKSVTVVEE EILLAKNGDS
SLISEAMAQE EEQLLKLRED EEKANNAGSA VAPNLNETQF TKLDELLTQT QLYSEFLLEK
MEDITINGIE SESQKAEPEK TGRGRKRKAA SQYNNTKAKR AVAAMISRSK EDGETINSDL
TEEETVIKLQ NELCPLLTGG QLKSYQLKGV KWLISLWQNG LNGILADQMG LGKTIQTIGF
LSHLKGNGLD GPYLVIAPLS TLSNWFNEIA RFTPSINAII YHGDKNQRDE LRRKHMPKTV
GPKFPIVITS YEVAMNDAKR ILRHYPWKYV VIDEGHRLKN HKCKLLRELK HLKMDNKLLL
TGTPLQNNLS ELWSLLNFIL PDIFTSHDEF ESWFDFSEKN KNEATKEEEE KRRAQVVSKL
HGILRPFILR RMKCDVELSL PRKKEIIMYA TMTDHQKKFQ EHLVNNTLEA HLGENAIRGQ
GWKGKLNNLV IQLRKNCNHP DLLQGQIDGS YLYPPVEEIV GQCGKFRLLE RLLVRLFANN
HKVLIFSQWT KLLDIMDYYF SEKGFEVCRI DGSVKLDERR RQIKDFSDEK SSCSIFLLST
RAGGLGINLT AADTCILYDS DWNPQMDLQA MDRCHRIGQT KPVHVYRLST AQSIETRVLK
RAYSKLKLEH VVIGQGQFHQ ERAKSSTPLE EEDILALLKE DETAEDKLIQ TDISDADLDR
LLDRSDLTIT APGETQAAEA FPVKGPGWEV VLPSSGGMLS SLNS
