A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing

Molecular Cell

Volumn 49, Issue 2, 2013, Pages 298-309

  Zhu, Yongyou ^a   Rowley, M Jordan ^a   Böhmdorfer, Gudrun ^a   Wierzbicki, Andrzej T ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; RNA BINDING PROTEIN; RNA BINDING PROTEIN IDN2; RNA POLYMERASE; RNA POLYMERASE V; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR SNF; TRANSCRIPTION FACTOR SWI3B; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA METHYLATION; GENE EXPRESSION REGULATION; GENE LOCUS; GENE SILENCING; NUCLEOSOME; PROTEIN PROTEIN INTERACTION; RNA TRANSCRIPTION;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; DNA-DIRECTED RNA POLYMERASES; GENE EXPRESSION REGULATION, PLANT; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN SUBUNITS; RNA INTERFERENCE; RNA, LONG UNTRANSLATED; RNA, PLANT; RNA-BINDING PROTEINS; TWO-HYBRID SYSTEM TECHNIQUES;

ARABIDOPSIS THALIANA;

EID: 84872787042     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2012.11.011     Document Type: Article

References (56)

1. Ausin I., Mockler T.C., Chory J., Jacobsen S.E. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat. Struct. Mol. Biol. 2009, 16:1325-1327.
2. Ausin I., Greenberg M.V.C., Simanshu D.K., Hale C.J., Vashisht A.A., Simon S.A., Lee T.-F., Feng S., Española S.D., Meyers B.C., et al. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc. Natl. Acad. Sci. USA 2012, 109:8374-8381.
3. Bezhani S., Winter C., Hershman S., Wagner J.D., Kennedy J.F., Kwon C.S., Pfluger J., Su Y., Wagner D. Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED. Plant Cell 2007, 19:403-416.
4. Bies-Etheve N., Pontier D., Lahmy S., Picart C., Vega D., Cooke R., Lagrange T. RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep. 2009, 10:649-654.
5. Brzeski J., Jerzmanowski A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 2003, 278:823-828.
6. Cam H.P., Chen E.S., Grewal S.I.S. Transcriptional scaffolds for heterochromatin assembly. Cell 2009, 136:610-614.
7. Chodavarapu R.K., Feng S., Bernatavichute Y.V., Chen P.-Y., Stroud H., Yu Y., Hetzel J.A., Kuo F., Kim J., Cokus S.J., et al. Relationship between nucleosome positioning and DNA methylation. Nature 2010, 466:388-392.
8. Farrona S., Hurtado L., Bowman J.L., Reyes J.C. The Arabidopsis thaliana SNF2 homolog AtBRM controls shoot development and flowering. Development 2004, 131:4965-4975.
9. Farrona S., Hurtado L., March-Díaz R., Schmitz R.J., Florencio F.J., Turck F., Amasino R.M., Reyes J.C. Brahma is required for proper expression of the floral repressor FLC in Arabidopsis. PLoS ONE 2011, 6:e17997.
10. Faulkner G.J., Kimura Y., Daub C.O., Wani S., Plessy C., Irvine K.M., Schroder K., Cloonan N., Steptoe A.L., Lassmann T., et al. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 2009, 41:563-571.
11. Girard A., Hannon G.J. Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol. 2008, 18:136-148.
12. Haag J.R., Pikaard C.S. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol. 2011, 12:483-492.
13. Haag J.R., Ream T.S., Marasco M., Nicora C.D., Norbeck A.D., Pasa-Tolic L., Pikaard C.S. In vitro transcription activities of Pol IV, Pol V, and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing. Mol. Cell. 2012, Published online November 8, 2012. 10.1016/j.molcel.2012.09.027.
14. Hargreaves D.C., Crabtree G.R. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 2011, 21:396-420.
15. He X.-J., Hsu Y.-F., Zhu S., Wierzbicki A.T., Pontes O., Pikaard C.S., Liu H.-L., Wang C.-S., Jin H., Zhu J.-K. An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 2009, 137:498-508.
16. Huang L., Jones A.M.E., Searle I., Patel K., Vogler H., Hubner N.C., Baulcombe D.C. An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat. Struct. Mol. Biol. 2009, 16:91-93.
17. Huettel B., Kanno T., Daxinger L., Aufsatz W., Matzke A.J.M., Matzke M. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J. 2006, 25:2828-2836.
18. Jeddeloh J.A., Stokes T.L., Richards E.J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 1999, 22:94-97.
19. Jiang C., Pugh B.F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 2009, 10:161-172.
20. Kanno T., Mette M.F., Kreil D.P., Aufsatz W., Matzke M., Matzke A.J.M. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 2004, 14:801-805.
21. Knizewski L., Ginalski K., Jerzmanowski A. Snf2 proteins in plants: gene silencing and beyond. Trends Plant Sci. 2008, 13:557-565.
22. Kumar S.V., Wigge P.A. H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis. Cell 2010, 140:136-147.
23. Kwon C.S., Hibara K., Pfluger J., Bezhani S., Metha H., Aida M., Tasaka M., Wagner D. A role for chromatin remodeling in regulation of CUC gene expression in the Arabidopsis cotyledon boundary. Development 2006, 133:3223-3230.
24. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
25. Law J.A., Jacobsen S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 2010, 11:204-220.
26. Law J.A., Ausin I., Johnson L.M., Vashisht A.A., Zhu J.-K., Wohlschlegel J.A., Jacobsen S.E. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr. Biol. 2010, 20:951-956.
27. Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet. 2011, 7:e1002195.
28. McDonnell A.V., Jiang T., Keating A.E., Berger B. Paircoil2: improved prediction of coiled coils from sequence. Bioinformatics 2006, 22:356-358.
29. Pontes O., Li C.F., Costa Nunes P., Haag J., Ream T., Vitins A., Jacobsen S.E., Pikaard C.S. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 2006, 126:79-92.
30. Ream T.S., Haag J.R., Wierzbicki A.T., Nicora C.D., Norbeck A.D., Zhu J.-K., Hagen G., Guilfoyle T.J., Pasa-Tolić L., Pikaard C.S. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell 2009, 33:192-203.
31. Reeves R., Jones A. Genomic transcriptional activity and the structure of chromatin. Nature 1976, 260:495-500.
32. Rowley M.J., Avrutsky M.I., Sifuentes C.J., Pereira L., Wierzbicki A.T. Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet. 2011, 7:e1002120.
33. Sadeh R., Allis C.D. Genome-wide "re" -modeling of nucleosome positions. Cell 2011, 147:263-266.
34. Saez A., Rodrigues A., Santiago J., Rubio S., Rodriguez P.L. HAB1-SWI3B interaction reveals a link between abscisic acid signaling and putative SWI/SNF chromatin-remodeling complexes in Arabidopsis. Plant Cell 2008, 20:2972-2988.
35. Sarnowski T.J., Swiezewski S., Pawlikowska K., Kaczanowski S., Jerzmanowski A. AtSWI3B, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time. Nucleic Acids Res. 2002, 30:3412-3421.
36. Sarnowski T.J., Ríos G., Jásik J., Swiezewski S., Kaczanowski S., Li Y., Kwiatkowska A., Pawlikowska K., Koźbiał M., Koźbiał P., et al. SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play distinct roles during Arabidopsis development. Plant Cell 2005, 17:2454-2472.
37. Shin H., Liu T., Manrai A.K., Liu X.S. CEAS: cis-regulatory element annotation system. Bioinformatics 2009, 25:2605-2606.
38. Smith L.M., Pontes O., Searle I., Yelina N., Yousafzai F.K., Herr A.J., Pikaard C.S., Baulcombe D.C. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 2007, 19:1507-1521.
39. Su W., Liu Y., Xia Y., Hong Z., Li J. Conserved endoplasmic reticulum-associated degradation system to eliminate mutated receptor-like kinases in Arabidopsis. Proc. Natl. Acad. Sci. USA 2011, 108:870-875.
40. Tang X., Hou A., Babu M., Nguyen V., Hurtado L., Lu Q., Reyes J.C., Wang A., Keller W.A., Harada J.J., et al. The Arabidopsis BRAHMA chromatin-remodeling ATPase is involved in repression of seed maturation genes in leaves. Plant Physiol. 2008, 147:1143-1157.
41. Tripet B., Wagschal K., Lavigne P., Mant C.T., Hodges R.S. Effects of side-chain characteristics on stability and oligomerization state of a de novo-designed model coiled-coil: 20 amino acid substitutions in position "d" J. Mol. Biol. 2000, 300:377-402.
42. Wagner D., Meyerowitz E.M. SPLAYED, a novel SWI/SNF ATPase homolog, controls reproductive development in Arabidopsis. Curr. Biol. 2002, 12:85-94.
43. Walley J.W., Rowe H.C., Xiao Y., Chehab E.W., Kliebenstein D.J., Wagner D., Dehesh K. The chromatin remodeler SPLAYED regulates specific stress signaling pathways. PLoS Pathog. 2008, 4:e1000237.
44. Wang K.C., Chang H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 2011, 43:904-914.
45. Weiner A., Hughes A., Yassour M., Rando O.J., Friedman N. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 2010, 20:90-100.
46. Wierzbicki A.T. The role of long non-coding RNA in transcriptional gene silencing. Curr. Opin. Plant Biol. 2012, 15:517-522.
47. Wierzbicki A.T., Haag J.R., Pikaard C.S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008, 135:635-648.
48. Wierzbicki A.T., Ream T.S., Haag J.R., Pikaard C.S. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat. Genet. 2009, 41:630-634.
49. Wierzbicki A.T., Cocklin R., Mayampurath A., Lister R., Rowley M.J., Gregory B.D., Ecker J.R., Tang H., Pikaard C.S. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 2012, 26:1825-1836.
50. Wu M.-F., Sang Y., Bezhani S., Yamaguchi N., Han S.-K., Li Z., Su Y., Slewinski T.L., Wagner D. SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proc. Natl. Acad. Sci. USA 2012, 109:3576-3581.
51. Xie M., Ren G., Costa-Nunes P., Pontes O., Yu B. A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation. Nucleic Acids Res. 2012, 40:4422-4431.
52. Zhang C.-J., Ning Y.-Q., Zhang S.-W., Chen Q., Shao C.-R., Guo Y.-W., Zhou J.-X., Li L., Chen S., He X.-J. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. PLoS Genet. 2012, 8:e1002693.
53. Zheng B., Wang Z., Li S., Yu B., Liu J.-Y., Chen X. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 2009, 23:2850-2860.
54. Zheng Z., Xing Y., He X.-J., Li W., Hu Y., Yadav S.K., Oh J., Zhu J.-K. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. Plant J. 2010, 62:92-99.
55. Zheng Q., Rowley M.J., Böhmdorfer G., Sandhu D., Gregory B.D., Wierzbicki A.T. RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes. Plant J. 2012, Published online September 27, 2012. 10.1111/tpj.12034.
56. Zhong X., Hale C.J., Law J.A., Johnson L.M., Feng S., Tu A., Jacobsen S.E. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat. Struct. Mol. Biol. 2012, 19:870-875.