RNA polymerase V targets transcriptional silencing components to promoters of protein‐coding genes
dc.contributor.author | Zheng, Qi | en_US |
dc.contributor.author | Rowley, M. Jordan | en_US |
dc.contributor.author | Böhmdorfer, Gudrun | en_US |
dc.contributor.author | Sandhu, Davinder | en_US |
dc.contributor.author | Gregory, Brian D. | en_US |
dc.contributor.author | Wierzbicki, Andrzej T. | en_US |
dc.date.accessioned | 2013-02-12T19:00:55Z | |
dc.date.available | 2014-03-03T15:09:24Z | en_US |
dc.date.issued | 2013-01 | en_US |
dc.identifier.citation | Zheng, Qi; Rowley, M. Jordan; Böhmdorfer, Gudrun ; Sandhu, Davinder; Gregory, Brian D.; Wierzbicki, Andrzej T. (2013). " RNA polymerase V targets transcriptional silencing components to promoters of proteinâ coding genes." The Plant Journal 73(2): 179-189. <http://hdl.handle.net/2027.42/96338> | en_US |
dc.identifier.issn | 0960-7412 | en_US |
dc.identifier.issn | 1365-313X | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/96338 | |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | Stress | en_US |
dc.subject.other | Gene Silencing | en_US |
dc.subject.other | Nc RNA | en_US |
dc.subject.other | A Rgonaute | en_US |
dc.subject.other | Pol V | en_US |
dc.subject.other | A Rabidopsis Thaliana | en_US |
dc.title | RNA polymerase V targets transcriptional silencing components to promoters of protein‐coding genes | 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/2027.42/96338/1/tpj12034-sup-0010-TableS1.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/2/tpj12034-sup-0006-FigureS4.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/3/tpj12034-sup-0007-FigureS5.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/4/tpj12034-sup-0003-FigureS1.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/5/tpj12034-sup-0008-FigureS6.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/6/tpj12034-sup-0005-FigureS3.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/7/tpj12034-sup-0004-FigureS2.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/8/tpj12034-sup-0009-FigureS7.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/9/tpj12034.pdf | |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/96338/10/tpj12034-sup-0002-MethodsS1.pdf | |
dc.identifier.doi | 10.1111/tpj.12034 | en_US |
dc.identifier.source | The Plant Journal | en_US |
dc.identifier.citedreference | Tittel‐Elmer, M., Bucher, E., Broger, L., Mathieu, O., Paszkowski, J. and Vaillant, I. ( 2010 ) Stress‐induced activation of heterochromatic transcription. PLoS Genet. 6, e1001175. | 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 | Moshkovich, N., Nisha, P., Boyle, P.J., Thompson, B.A., Dale, R.K. and Lei, E.P. ( 2011 ) RNAi‐independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev. 25, 1686 – 1701. | en_US |
dc.identifier.citedreference | Muino, J.M., Kaufmann, K., Ham, R.C., van Angenent, G.C. and Krajewski, P. ( 2011 ) ChIP‐seq analysis in R (CSAR): an R package for the statistical detection of protein‐bound genomic regions. Plant Methods, 7, 11. | 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 | Pecinka, A., Dinh, H.Q., Baubec, T., Rosa, M., Lettner, N. and Mittelsten Scheid, O. ( 2010 ) Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell, 22, 3118 – 3129. | en_US |
dc.identifier.citedreference | Pontes, O., Li, C.F., Costa Nunes, P., Haag, J., Ream, T., Vitins, A., Jacobsen, S.E. and Pikaard, C.S. ( 2006 ) The Arabidopsis chromatin‐modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell, 126, 79 – 92. | en_US |
dc.identifier.citedreference | Pontier, D., Yahubyan, G., Vega, D., Bulski, A., Saez‐Vasquez, J., Hakimi, M.‐A., Lerbs‐Mache, S., Colot, V. and Lagrange, T. ( 2005 ) Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 19, 2030 – 2040. | 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 | Ream, T.S., Haag, J.R., Wierzbicki, A.T. et al. ( 2009 ) Subunit compositions of the RNA‐silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell, 33, 192 – 203. | 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 | Shin, H., Liu, T., Manrai, A.K. and Liu, X.S. ( 2009 ) CEAS: cis ‐regulatory element annotation system. Bioinformatics, 25, 2605 – 2606. | en_US |
dc.identifier.citedreference | Tomato Genome Consortium ( 2012 ) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635 – 641. | en_US |
dc.identifier.citedreference | Wang, H., Zhang, Xiuren, Liu, J. et al. ( 2011 ) Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J. 67, 292 – 304. | en_US |
dc.identifier.citedreference | Wierzbicki, A.T. ( 2012 ) The role of long non‐coding RNA in transcriptional gene silencing. Curr. Opin. Plant Biol. doi: 10.1016/j.pbi.2012.08.008. | 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 | Zhang, X., Yazaki, J., Sundaresan, A. et al. ( 2006 ) Genome‐wide high‐resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell, 126, 1189 – 1201. | en_US |
dc.identifier.citedreference | Zheng, Q. and Wang, X.‐J. ( 2008 ) GOEAST: a web‐based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 36, W358 – W363. | en_US |
dc.identifier.citedreference | Zheng, B., Wang, Z., Li, S., Yu, B., Liu, J.‐Y. and Chen, X. ( 2009 ) Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA‐directed transcriptional gene silencing in Arabidopsis. Genes Dev. 23, 2850 – 2860. | en_US |
dc.identifier.citedreference | Zheng, Q., Ryvkin, P., Li, F., Dragomir, I., Valladares, O., Yang, J., Cao, K., Wang, L.‐S. and Gregory, B.D. ( 2010 ) Genome‐wide double‐stranded RNA sequencing reveals the functional significance of base‐paired RNAs in Arabidopsis. PLoS Genet. 6, e1001141. | 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 | 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 | Agorio, A. and Vera, P. ( 2007 ) ARGONAUTE4 is required for resistance to Pseudomonas syringae in Arabidopsis. Plant Cell, 19, 3778 – 3790. | en_US |
dc.identifier.citedreference | Alleman, M., Sidorenko, L., McGinnis, K., Seshadri, V., Dorweiler, J.E., White, J., Sikkink, K. and Chandler, V.L. ( 2006 ) An RNA‐dependent RNA polymerase is required for paramutation in maize. Nature, 442, 295 – 298. | en_US |
dc.identifier.citedreference | Arabidopsis Genome Initiative ( 2000 ) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796 – 815. | en_US |
dc.identifier.citedreference | Autran, D., Baroux, C., Raissig, M.T. et al. ( 2011 ) Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell, 145, 707 – 719. | en_US |
dc.identifier.citedreference | Cernilogar, F.M., Onorati, M.C., Kothe, G.O. et al. ( 2011 ) Chromatin‐associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature, 480, 391 – 395. | en_US |
dc.identifier.citedreference | Chodavarapu, R.K., Feng, S., Bernatavichute, Y.V. et al. ( 2010 ) Relationship between nucleosome positioning and DNA methylation. Nature, 466, 388 – 392. | en_US |
dc.identifier.citedreference | Dowen, R.H., Pelizzola, M., Schmitz, R.J., Lister, R., Dowen, J.M., Nery, J.R., Dixon, J.E. and Ecker, J.R. ( 2012 ) Widespread dynamic DNA methylation in response to biotic stress. Proc. Natl Acad. Sci. USA, 109, E2183 – E2191. | en_US |
dc.identifier.citedreference | Erhard, K.F. Jr, Stonaker, J.L., Parkinson, S.E., Lim, J.P., Hale, C.J. and Hollick, J.B. ( 2009 ) RNA polymerase IV functions in paramutation in Zea mays. Science, 323, 1201 – 1205. | en_US |
dc.identifier.citedreference | Henderson, I.R. and Jacobsen, S.E. ( 2008 ) Tandem repeats upstream of the Arabidopsis endogene SDC recruit non‐CG DNA methylation and initiate siRNA spreading. Genes Dev. 22, 1597 – 1606. | en_US |
dc.identifier.citedreference | Huettel, B., Kanno, T., Daxinger, L., Aufsatz, W., Matzke, A.J.M. and Matzke, M. ( 2006 ) Endogenous targets of RNA‐directed DNA methylation and Pol IV in Arabidopsis. EMBO J. 25, 2828 – 2836. | en_US |
dc.identifier.citedreference | Hutvagner, G. and Simard, M.J. ( 2008 ) Argonaute proteins: key players in RNA silencing. Nat. Rev. Mol. Cell Biol. 9, 22 – 32. | 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 | Kaplan, N., Moore, I.K., Fondufe‐Mittendorf, Y. et al. ( 2009 ) The DNA‐encoded nucleosome organization of a eukaryotic genome. Nature, 458, 362 – 366. | en_US |
dc.identifier.citedreference | Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. ( 2009 ) Ultrafast and memory‐efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. | en_US |
dc.identifier.citedreference | Law, J.A. and Jacobsen, S.E. ( 2010 ) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204 – 220. | 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 | Lister, R., O'Malley, R.C., Tonti‐Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H. and Ecker, J.R. ( 2008 ) Highly integrated single‐base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523 – 536. | en_US |
dc.identifier.citedreference | Lockton, S. and Gaut, B.S. ( 2009 ) The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J. Mol. Evol. 68, 80 – 89. | en_US |
dc.identifier.citedreference | López, A., Ramírez, V., García‐Andrade, J., Flors, V. and Vera, P. ( 2011 ) The RNA silencing enzyme RNA polymerase V is required for plant immunity. PLoS Genet. 7, e1002434. | en_US |
dc.identifier.citedreference | Mathieu, O., Reinders, J., Caikovski, M., Smathajitt, C. and Paszkowski, J. ( 2007 ) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell, 130, 851 – 862. | en_US |
dc.identifier.citedreference | McClintock, B. ( 1956 ) Controlling elements and the gene. Cold Spring Harbor Symp. Quant. Biol. 21, 197 – 216. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
Files in this item
Remediation of Harmful Language
The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.
Accessibility
If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.