RNA ‐directed DNA methylation requires stepwise binding of silencing factors to long non‐coding RNA
dc.contributor.author | Böhmdorfer, Gudrun | en_US |
dc.contributor.author | Rowley, M. Jordan | en_US |
dc.contributor.author | Kuciński, Jan | en_US |
dc.contributor.author | Zhu, Yongyou | en_US |
dc.contributor.author | Amies, Ivan | en_US |
dc.contributor.author | Wierzbicki, Andrzej T. | en_US |
dc.date.accessioned | 2014-08-06T16:49:43Z | |
dc.date.available | WITHHELD_12_MONTHS | en_US |
dc.date.available | 2014-08-06T16:49:43Z | |
dc.date.issued | 2014-07 | en_US |
dc.identifier.citation | Böhmdorfer, Gudrun ; Rowley, M. Jordan; Kuciński, Jan ; Zhu, Yongyou; Amies, Ivan; Wierzbicki, Andrzej T. (2014). " RNA â directed DNA methylation requires stepwise binding of silencing factors to long nonâ coding RNA ." The Plant Journal 79(2): 181-191. | en_US |
dc.identifier.issn | 0960-7412 | en_US |
dc.identifier.issn | 1365-313X | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/108033 | |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | Non‐Coding RNA | en_US |
dc.subject.other | DNA Methyltransferase | en_US |
dc.subject.other | Argonaute | en_US |
dc.subject.other | INVOLVED IN DE NOVO 2 | en_US |
dc.subject.other | A Rabidopsis Thaliana | en_US |
dc.title | RNA ‐directed DNA methylation requires stepwise binding of silencing factors to long non‐coding RNA | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Natural Resources and Environment | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/108033/1/tpj12563.pdf | |
dc.identifier.doi | 10.1111/tpj.12563 | en_US |
dc.identifier.source | The Plant Journal | en_US |
dc.identifier.citedreference | Rowley, M.J., Böhmdorfer, G. and Wierzbicki, A.T. ( 2013 ) Analysis of long non‐coding RNAs produced by a specialized RNA polymerase in Arabidopsis thaliana. Methods, 63, 160 – 169. | en_US |
dc.identifier.citedreference | Li, C.F., Pontes, O., El‐Shami, M., Henderson, I.R., Bernatavichute, Y.V., Chan, S.W.‐L., Lagrange, T., Pikaard, C.S. and Jacobsen, S.E. ( 2006 ) An ARGONAUTE4‐containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell, 126, 93 – 106. | en_US |
dc.identifier.citedreference | Mohammad, F., Mondal, T., Guseva, N., Pandey, G.K. and Kanduri, C. ( 2010 ) Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development, 137, 2493 – 2499. | en_US |
dc.identifier.citedreference | Mosher, R.A., Schwach, F., Studholme, D. and Baulcombe, D.C. ( 2008 ) PolIVb influences RNA‐directed DNA methylation independently of its role in siRNA biogenesis. Proc. Natl Acad. Sci. USA, 105, 3145 – 3150. | en_US |
dc.identifier.citedreference | Naumann, U., Daxinger, L., Kanno, T., Eun, C., Long, Q., Lorkovic, Z.J., Matzke, M. and Matzke, A.J.M. ( 2011 ) Genetic evidence that DNA methyltransferase DRM2 has a direct catalytic role in RNA‐directed DNA methylation in Arabidopsis thaliana. Genetics, 187, 977 – 979. | en_US |
dc.identifier.citedreference | Onodera, Y., Haag, J.R., Ream, T., Costa Nunes, P., Pontes, O. and Pikaard, C.S. ( 2005 ) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation‐dependent heterochromatin formation. Cell, 120, 613 – 622. | en_US |
dc.identifier.citedreference | Qi, Y., He, X., Wang, X.‐J., Kohany, O., Jurka, J. and Hannon, G.J. ( 2006 ) Distinct catalytic and non‐catalytic roles of ARGONAUTE4 in RNA‐directed DNA methylation. Nature, 443, 1008 – 1012. | en_US |
dc.identifier.citedreference | Rowley, M.J., Avrutsky, M.I., Sifuentes, C.J., Pereira, L. and Wierzbicki, A.T. ( 2011 ) Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet. 7, e1002120. | en_US |
dc.identifier.citedreference | Schmitz, K.‐M., Mayer, C., Postepska, A. and Grummt, I. ( 2010 ) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev. 24, 2264 – 2269. | en_US |
dc.identifier.citedreference | Stroud, H., Greenberg, M.V.C., Feng, S., Bernatavichute, Y.V. and Jacobsen, S.E. ( 2013 ) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell, 152, 352 – 364. | en_US |
dc.identifier.citedreference | Taliaferro, J.M., Aspden, J.L., Bradley, T., Marwha, D., Blanchette, M. and Rio, D.C. ( 2013 ) Two new and distinct roles for Drosophila Argonaute‐2 in the nucleus: alternative pre‐mRNA splicing and transcriptional repression. Genes Dev. 27, 378 – 389. | en_US |
dc.identifier.citedreference | Wierzbicki, A.T. ( 2012 ) The role of long non‐coding RNA in transcriptional gene silencing. Curr. Opin. Plant Biol. 15, 517 – 522. | en_US |
dc.identifier.citedreference | Wierzbicki, A.T., Haag, J.R. and Pikaard, C.S. ( 2008 ) Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell, 135, 635 – 648. | en_US |
dc.identifier.citedreference | Wierzbicki, A.T., Ream, T.S., Haag, J.R. and Pikaard, C.S. ( 2009 ) RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat. Genet. 41, 630 – 634. | en_US |
dc.identifier.citedreference | Wierzbicki, A.T., Cocklin, R., Mayampurath, A., Lister, R., Rowley, M.J., Gregory, B.D., Ecker, J.R., Tang, H. and Pikaard, C.S. ( 2012 ) Spatial and functional relationships among Pol V‐associated loci, Pol IV‐dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 26, 1825 – 1836. | en_US |
dc.identifier.citedreference | Xie, Z., Johansen, L.K., Gustafson, A.M., Kasschau, K.D., Lellis, A.D., Zilberman, D., Jacobsen, S.E. and Carrington, J.C. ( 2004 ) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104. | en_US |
dc.identifier.citedreference | Xie, M., Ren, G., Costa‐Nunes, P., Pontes, O. and Yu, B. ( 2012a ) A subgroup of SGS3‐like proteins act redundantly in RNA‐directed DNA methylation. Nucleic Acids Res. 40, 4422 – 4431. | en_US |
dc.identifier.citedreference | Xie, M., Ren, G., Zhang, C. and Yu, B. ( 2012b ) The DNA‐ and RNA‐binding protein FACTOR of DNA METHYLATION 1 requires XH domain‐mediated complex formation for its function in RNA‐directed DNA methylation. Plant J. 72, 491 – 500. | en_US |
dc.identifier.citedreference | Yoshikawa, M., Peragine, A., Park, M.Y. and Poethig, R.S. ( 2005 ) A pathway for the biogenesis of trans‐acting siRNAs in Arabidopsis. Genes Dev. 19, 2164 – 2175. | en_US |
dc.identifier.citedreference | Zheng, Z., Xing, Y., He, X.‐J., Li, W., Hu, Y., Yadav, S.K., Oh, J. and Zhu, J.‐K. ( 2010 ) An SGS3‐like protein functions in RNA‐directed DNA methylation and transcriptional gene silencing in Arabidopsis. Plant J. 62, 92 – 99. | en_US |
dc.identifier.citedreference | Zheng, Q., Rowley, M.J., Böhmdorfer, G., Sandhu, D., Gregory, B.D. and Wierzbicki, A.T. ( 2013 ) RNA polymerase V targets transcriptional silencing components to promoters of protein‐coding genes. Plant J. 73, 179 – 189. | en_US |
dc.identifier.citedreference | Zhong, X., Hale, C.J., Law, J.A., Johnson, L.M., Feng, S., Tu, A. and Jacobsen, S.E. ( 2012 ) DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat. Struct. Mol. Biol. 19, 870 – 875. | en_US |
dc.identifier.citedreference | Zhu, Y., Rowley, M.J., Böhmdorfer, G. and Wierzbicki, A.T. ( 2013 ) A SWI/SNF chromatin‐remodeling complex acts in noncoding RNA‐mediated transcriptional silencing. Mol. Cell, 49, 298 – 309. | en_US |
dc.identifier.citedreference | Zilberman, D., Cao, X. and Jacobsen, S.E. ( 2003 ) ARGONAUTE4 control of locus‐specific siRNA accumulation and DNA and histone methylation. Science, 299, 716 – 719. | en_US |
dc.identifier.citedreference | Herr, A.J., Jensen, M.B., Dalmay, T. and Baulcombe, D.C. ( 2005 ) RNA polymerase IV directs silencing of endogenous DNA. Science, 308, 118 – 120. | en_US |
dc.identifier.citedreference | Holz‐Schietinger, C. and Reich, N.O. ( 2012 ) RNA modulation of the human DNA methyltransferase 3A. Nucleic Acids Res. 40, 8550 – 8557. | en_US |
dc.identifier.citedreference | Jiang, C. and Pugh, B.F. ( 2009 ) Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10, 161 – 172. | en_US |
dc.identifier.citedreference | Ausin, I., Mockler, T.C., Chory, J. and Jacobsen, S.E. ( 2009 ) IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat. Struct. Mol. Biol. 16, 1325 – 1327. | en_US |
dc.identifier.citedreference | Ausin, I., Greenberg, M.V.C., Simanshu, D.K. et al. ( 2012 ) INVOLVED IN DE NOVO 2‐containing complex involved in RNA‐directed DNA methylation in Arabidopsis. Proc. Natl Acad. Sci. USA, 109, 8374 – 8381. | en_US |
dc.identifier.citedreference | Belancio, V.P., Roy‐Engel, A.M. and Deininger, P.L. ( 2010 ) All y'all need to know ‘bout retroelements in cancer. Semin. Cancer Biol. 20, 200 – 210. | en_US |
dc.identifier.citedreference | Bernstein, E. and Hake, S.B. ( 2006 ) The nucleosome: a little variation goes a long way. Biochem. Cell Biol. 84, 505 – 517. | en_US |
dc.identifier.citedreference | Butt, H., Graner, S. and Luschnig, C. ( 2014 ) Expression analysis of Arabidopsis XH/XS‐domain proteins indicates overlapping and distinct functions for members of this gene family. J. Exp. Bot. 65, 1217 – 1227. Available at: [Accessed April 1, 2014]. | en_US |
dc.identifier.citedreference | Cao, X. and Jacobsen, S.E. ( 2002 ) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr. Biol. 12, 1138 – 1144. | en_US |
dc.identifier.citedreference | Cao, X., Aufsatz, W., Zilberman, D., Mette, M.F., Huang, M.S., Matzke, M. and Jacobsen, S.E. ( 2003 ) Role of the DRM and CMT3 methyltransferases in RNA‐directed DNA methylation. Curr. Biol. 13, 2212 – 2217. | en_US |
dc.identifier.citedreference | Chan, S.W.‐L., Henderson, I.R. and Jacobsen, S.E. ( 2005 ) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6, 351 – 360. | en_US |
dc.identifier.citedreference | Di Ruscio, A., Ebralidze, A.K., Benoukraf, T. et al. ( 2013 ) DNMT1‐interacting RNAs block gene‐specific DNA methylation. Nature, 503, 371 – 376. | en_US |
dc.identifier.citedreference | Fukunaga, R. and Doudna, J.A. ( 2009 ) dsRNA with 5′ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO J. 28, 545 – 555. | en_US |
dc.identifier.citedreference | Gao, Z., Liu, H.‐L., Daxinger, L. et al. ( 2010 ) An RNA polymerase II‐ and AGO4‐associated protein acts in RNA‐directed DNA methylation. Nature, 465, 106 – 109. | en_US |
dc.identifier.citedreference | Grewal, S.I.S. and Elgin, S.C.R. ( 2007 ) Transcription and RNA interference in the formation of heterochromatin. Nature, 447, 399 – 406. | en_US |
dc.identifier.citedreference | Haag, J.R. and Pikaard, C.S. ( 2011 ) Multisubunit RNA polymerases IV and V: purveyors of non‐coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol. 12, 483 – 492. | en_US |
dc.identifier.citedreference | Hancks, D.C. and Kazazian, H.H. Jr ( 2012 ) Active human retrotransposons: variation and disease. Curr. Opin. Genet. Dev. 22, 191 – 203. | en_US |
dc.identifier.citedreference | Hargreaves, D.C. and Crabtree, G.R. ( 2011 ) ATP‐dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 21, 396 – 420. | en_US |
dc.identifier.citedreference | Havecker, E.R., Wallbridge, L.M., Hardcastle, T.J., Bush, M.S., Kelly, K.A., Dunn, R.M., Schwach, F., Doonan, J.H. and Baulcombe, D.C. ( 2010 ) The Arabidopsis RNA‐directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell, 22, 321 – 334. | en_US |
dc.identifier.citedreference | He, X.‐J., Hsu, Y.‐F., Zhu, S. et al. ( 2009 ) An effector of RNA‐directed DNA methylation in Arabidopsis is an ARGONAUTE 4‐ and RNA‐binding protein. Cell, 137, 498 – 508. | en_US |
dc.identifier.citedreference | Kanno, T., Huettel, B., Mette, M.F., Aufsatz, W., Jaligot, E., Daxinger, L., Kreil, D.P., Matzke, M. and Matzke, A.J.M. ( 2005 ) Atypical RNA polymerase subunits required for RNA‐directed DNA methylation. Nat. Genet. 37, 761 – 765. | en_US |
dc.identifier.citedreference | Kasschau, K.D., Fahlgren, N., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A. and Carrington, J.C. ( 2007 ) Genome‐wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 5, e57. | en_US |
dc.identifier.citedreference | Law, J.A., Ausin, I., Johnson, L.M., Vashisht, A.A., Zhu, J.‐K., Wohlschlegel, J.A. and Jacobsen, S.E. ( 2010 ) A protein complex required for polymerase V transcripts and RNA‐ directed DNA methylation in Arabidopsis. Curr. Biol. 20, 951 – 956. | en_US |
dc.identifier.citedreference | Law, J.A., Vashisht, A.A., Wohlschlegel, J.A. and Jacobsen, S.E. ( 2011 ) SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet. 7, e1002195. | en_US |
dc.identifier.citedreference | Le Thomas, A., Rogers, A.K., Webster, A., Marinov, G.K., Liao, S.E., Perkins, E.M., Hur, J.K., Aravin, A.A. and Tóth, K.F. ( 2013 ) Piwi induces piRNA‐guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev. 27, 390 – 399. | en_US |
dc.identifier.citedreference | Lee, T., Gurazada, S.G.R., Zhai, J., Li, S., Simon, S.A., Matzke, M.A., Chen, X. and Meyers, B.C. ( 2012 ) RNA polymerase V‐dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics, 7, 781 – 795. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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