An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing

Cell Research

Volumn 21, Issue 12, 2011, Pages 1691-1700

  Liu, Jun ^a   Bai, Ge ^b,c   Zhang, Cuijun ^a   Chen, Wei ^b   Zhou, Jinxing ^a   Zhang, Suwei ^a   Chen, Qing ^a   Deng, Xin ^b,d   He, Xin Jian ^a   Zhu, Jian Kang ^b  

^a NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^b PURDUE UNIVERSITY   (United States)

^c SHANGHAI JIAO TONG UNIVERSITY   (China)

^d INSTITUTE OF BOTANY   (China)

Author keywords

DNA methylation; DTF1; RdDM; siRNA; transcriptional gene silencing

Indexed keywords

ARABIDOPSIS PROTEIN; RD29A PROTEIN, ARABIDOPSIS; SMALL INTERFERING RNA;

ARABIDOPSIS; ARTICLE; DNA METHYLATION; DRUG ANTAGONISM; GENE LOCUS; GENE SILENCING; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; RNA INTERFERENCE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA METHYLATION; GENE SILENCING; GENETIC LOCI; RNA INTERFERENCE; RNA, SMALL INTERFERING; TRANSCRIPTION, GENETIC;

ARABIDOPSIS;

EID: 82655168764     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2011.173     Document Type: Article

References (54)

1. Xie Z, Johansen L K, Gustafson A M, et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2004;2:E104.
2. Kanno T, Huettel B, Mette MF, et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 2005;37:761-765. (Pubitemid 41754895)
3. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. RNA polymerase IV directs silencing of endogenous DNA. Science 2005;308:118-120. (Pubitemid 40471011)
4. Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Rev Genet 2010;11:204-220.
5. He XJ, Chen T, Zhu JK. Regulation of and function DNA methylation in plants and animals. Cell Res 2011;21:442-465.
6. Matzke MA, Birchler JA. RNAi-mediated pathways in the nucleus. Nat Rev Genet 2005;6:24-35. (Pubitemid 39657895)
7. Mosher RA, Melnyk CW, Kelly KA, et al. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 2009;460:283-286.
8. Hsieh TF, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm. Science 2009;324:1451-1454.
9. Gehring M, Bubb KL, Henikoff S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 2009;324:1447-1451.
10. Ito H, Gaubert H, Bucher E, et al. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 2011;472:115-119.
11. Wierzbicki AT, Haag JR, Pikaard CS. Non-coding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008;135:635-648.
12. Pontier D, Yahubyan G, Vega D, et al. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev 2005;19:2030-2040. (Pubitemid 41247960)
13. Pontes O, Li C F, Nunes PC, et al. The Arabidopsis chromatinmodifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 2006;126:79-92. (Pubitemid 44026550)
14. Li CF, Pontes O, El-Shami M, et al. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 2006;126:93-106.
15. Kanno T, Mette MF, Kreil DP, et al. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 2004;14:801-805. (Pubitemid 38583716)
16. Kanno T, Bucher E, Daxinger L, et al. A structural-maintenance-of chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet 2008;40:670-675. (Pubitemid 351601208)
17. Law JA, Ausin I, Johnson LM, et al. A protein complex required for polymerase V transcripts and RNA-directed DNA methylation in Arabidopsis. Curr Biol 2010;20:951-956.
18. Gao Z, Liu HL, Daxinger L, et al. An RNA polymerase II-and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 2010;465:106-109.
19. He XJ, Hsu YF, Zhu S, et al. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4-and RNA-binding protein. Cell 2009;137:498-508.
20. Bies-Etheve N, Pontier D, Lahmy S, et al. RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep 2009;10:649-654.
21. He XJ, Hsu YF, Zhu S, et al. A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes Dev 2009;23:2717-2722.
22. Kanno T, Bucher E, Daxinger L, et al. RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep 2010;11:65-71.
23. Cao X, Jacobsen SE. Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 2002;12:1138-1144. (Pubitemid 34766938)
24. Naumann U, Daxinger L, Kanno T, et al. Genetic evidence that DNA methyltransferase DRM2 has a direct catalytic role in RNA-directed DNA methylation in Arabidopsis thaliana. Genetics 2011;187:977-979.
25. Greenberg MV, Ausin I, Chan SW, et al. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics 2011;6:344-354.
26. Henderson IR, Deleris A, Wong W, et al. The de novo cytosine methyltransferase DRM2 requires intact UBA domains and a catalytically mutated paralog DRM3 during RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet 2010;6:e1001182.
27. Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature 2009;457:413-420.
28. Motamedi MR, Verdel A, Colmenares SU, et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 2004;119:789-802. (Pubitemid 40017686)
29. Verdel A, Jia S, Gerber S, et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 2004;303:672-676. (Pubitemid 38141633)
30. Debeauchamp JL, Moses A, Noffsinger VJ, et al. Chp1-Tas3 interaction is required to recruit RITS to fission yeast centromeres and for maintenance of centromeric heterochromatin. Mol Cell Biol 2008;28:2154-2166. (Pubitemid 351429963)
31. Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SI. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 2001;292:110-113. (Pubitemid 32289138)
32. Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002;416:556-560. (Pubitemid 34288860)
33. Lindroth AM, Shultis D, Jasencakova Z, et al. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 2004;23:4286-4296. (Pubitemid 39546166)
34. Johnson LM, Bostick M, Zhang X, et al. The SRA methylcytosine-binding domain links DNA and histone methylation. Curr Biol 2007;17:379-384. (Pubitemid 46241885)
35. Yokthongwattana C, Bucher E, Caikovski M, et al. MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. EMBO J 2010;29:340-351.
36. Numa H, Kim JM, Matsui A, et al. Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. EMBO J 2010;29:352-362.
37. Amedeo P, Habu Y, Afsar K, Mittelsten Scheid O, Paszkowski J. Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 2000;405:203-206. (Pubitemid 30313541)
38. Zhou Y, Zhang J, Lin H, Guo G, Guo Y. MORPHEUS' MOL-ECULE1 is required to prevent aberrant RNA transcriptional read-through in Arabidopsis. Plant Physiol 2010;154:1272-1280.
39. Caikovski M, Yokthongwattana C, Habu Y, et al. Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants. PLoS Genet 2008;4:e1000165.
40. Petty TJ, Nishimura T, Emamzadah S, et al. Expression, crystallization and preliminary X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus' molecule 1 protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010;66:916-918.
41. Gong Z, Morales-Ruiz T, Ariza RR, et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 2002;111:803-814. (Pubitemid 36106402)
42. Agius F, Kapoor A, Zhu JK. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 2006;103:11796-11801. (Pubitemid 44182530)
43. Zhu J, Kapoor A, Sridhar VV, et al. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 2007;17:54-59. (Pubitemid 46027567)
44. Penterman J, Zilberman D, Huh JH, et al. DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 2007;104:6752-6757. (Pubitemid 47175573)
45. He XJ, Hsu YF, Pontes O, et al. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev 2009;23:318-330.
46. Kapoor A, Agarwal M, Andreucci A, et al. Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis. Curr Biol 2005;15:1912-1918. (Pubitemid 41566137)
47. Huettel B, Kanno T, Daxinger L, et al. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J 2006;25:2828-2836. (Pubitemid 43980389)
48. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 2007;130:851-862. (Pubitemid 47334929)
49. Penterman J, Uzawa R, Fischer RL. Genetic interactions between DNA demethylation and methylation in Arabidopsis. Plant Physiol 2007;145:1549-1557. (Pubitemid 350276775)
50. Zheng B, Wang Z, Li S, et al. 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.
51. Jacob Y, Feng S, LeBlanc CA, et al. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 2009;16:763-768.
52. Law JA, Vashisht AA, Wohlschlegel JA, Jacobsen SE. 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.
53. Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA 2008;105:3145-3150. (Pubitemid 351723682)
54. Ishitani M, Xiong L, Stevenson B, Zhu JK. Genetic analysis of osmotic and cold stress signal transductionin Arabidopsis: Interactions and convergence of abscisic acid-dependent and abscisic acid-independent pathways. Plant Cell 1997;9:1935-1949. (Pubitemid 28174067)