SHH1, a Homeodomain protein required for DNA Methylation, as well as RDR2, RDM4, and Chromatin remodeling factors, associate with RNA Polymerase IV

PLoS Genetics

Volumn 7, Issue 7, 2011, Pages

  Law, Julie A ^a   Vashisht, Ajay A ^b   Wohlschlegel, James A ^b   Jacobsen, Steven E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE; DOMAINS REARRANGED METHYLTRANSFERASE 2; HOMEODOMAIN PROTEIN; NUCLEAR RNA; NUCLEAR RNA POLYMERASE D1; RNA DIRECTED RNA POLYMERASE; RNA DIRECTED RNA POLYMERASE 2; RNA POLYMERASE; RNA POLYMERASE IV; SAWADEE HOMEODOMAIN HOMOLOG 1 PROTEIN; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN; CLASSY1 PROTEIN, ARABIDOPSIS; DMS4 PROTEIN, ARABIDOPSIS; DNA DIRECTED DNA POLYMERASE BETA; DNA DIRECTED RNA POLYMERASE; NRPD1A PROTEIN, ARABIDOPSIS; RDR2 PROTEIN, ARABIDOPSIS; RNA POLYMERASE IV, ARABIDOPSIS; SHH1 PROTEIN, ARABIDOPSIS; SIGNAL PEPTIDE;

ARABIDOPSIS; ARTICLE; BINDING AFFINITY; BIOGENESIS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA METHYLATION; DNA MODIFICATION; EPIGENETICS; GENE LOCUS; GENE SILENCING; NONHUMAN; RNA PURIFICATION; RNA TRANSLATION; GENE EXPRESSION REGULATION; GENETICS; IMMUNOPRECIPITATION; METABOLISM; MUTATION; PROTEIN BINDING; PROTEIN SUBUNIT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSGENIC PLANT;

ARABIDOPSIS THALIANA;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA METHYLATION; DNA POLYMERASE BETA; DNA-DIRECTED RNA POLYMERASES; GENE EXPRESSION REGULATION, PLANT; HOMEODOMAIN PROTEINS; IMMUNOPRECIPITATION; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MUTATION; PLANTS, GENETICALLY MODIFIED; PROTEIN BINDING; PROTEIN SUBUNITS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA REPLICASE; RNA, SMALL INTERFERING;

EID: 79960960568     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002195     Document Type: Article

References (43)

1. Law JA, Jacobsen SE, (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220.
2. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, et al. (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317: 1760-1764.
3. Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, et al. (2007) The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450: 908-912.
4. Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ, (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21: 367-376.
5. Pikaard CS, Haag JR, Ream T, Wierzbicki AT, (2008) Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 13: 390-397.
6. Li J, Yang Z, Yu B, Liu J, Chen X, (2005) Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 15: 1501-1507.
7. Duran-Figueroa N, Vielle-Calzada JP, ARGONAUTE9-dependent silencing of transposable elements in pericentromeric regions of Arabidopsis. Plant Signal Behav 5: 1476-1479.
8. Olmedo-Monfil V, Duran-Figueroa N, Arteaga-Vazquez M, Demesa-Arevalo E, Autran D, et al. Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature 464: 628-632.
9. Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, et al. The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell 22: 321-334.
10. Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, et al. (2007) An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 19: 1507-1521.
11. Wierzbicki AT, Haag JR, Pikaard CS, (2008) Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135: 635-648.
12. He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, et al. (2009) An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 137: 498-508.
13. Bies-Etheve N, Pontier D, Lahmy S, Picart C, Vega D, et al. (2009) RNA-directed DNA methylation requires an AGO4-interacting member of the SPT5 elongation factor family. EMBO Rep.
14. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS, (2009) RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 41: 630-634.
15. Ausin I, Mockler TC, Chory J, Jacobsen SE, (2009) IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat Struct Mol Biol.
16. Lahmy S, Bies-Etheve N, Lagrange T, (2010) Plant-specific multisubunit RNA polymerase in gene silencing. Epigenetics 5: 4-8.
17. Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, et al. (2010) A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol 20: 951-956.
18. Gao Z, Liu HL, Daxinger L, Pontes O, He X, et al. (2010) An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465: 106-109.
19. Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, et al. (2004) Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14: 801-805.
20. Kanno T, Bucher E, Daxinger L, Huettel B, Bohmdorfer G, et al. (2008) A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet 40: 670-675.
21. He XJ, Hsu YF, Zhu S, Liu HL, Pontes O, et al. (2009) A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes Dev 23: 2717-2722.
22. Kanno T, Bucher E, Daxinger L, Huettel B, Kreil DP, et al. (2009) RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep 11: 65-71.
23. Zheng B, Wang Z, Li S, Yu B, Liu JY, et al. (2009) Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev.
24. Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, 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.
25. Lahmy S, Pontier D, Cavel E, Vega D, El-Shami M, et al. (2009) PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc Natl Acad Sci U S A 106: 941-946.
26. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, et al. (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2: e104 doi:10.1371/journal.pbio.0020104.
27. Mukherjee K, Brocchieri L, Burglin TR, (2009) A comprehensive classification and evolutionary analysis of plant homeobox genes. Mol Biol Evol 26: 2775-2794.
28. Cao X, Jacobsen SE, (2002) Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12: 1138-1144.
29. Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, et al. (2004) RNA silencing genes control de novo DNA methylation. Science 303: 1336.
30. Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, et al. (2011) Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics 6.
31. Chan SW, Henderson IR, Zhang X, Shah G, Chien JS, et al. (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis. PLoS Genet 2: e83 doi:10.1371/journal.pgen.0020083.
32. Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, et al. (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16: 69-79.
33. Herr AJ, Jensen MB, Dalmay T, Baulcombe DC, (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308: 118-120.
34. Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, et al. (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.
35. Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, et al. (2010) An endogenous, systemic RNAi pathway in plants. Embo J 29: 1699-1712.
36. Earley KW, Haag JR, Pontes O, Opper K, Juehne T, et al. (2006) Gateway-compatible vectors for plant functional genomics and proteomics. Plant J 45: 616-629.
37. Pontes O, Li CF, Nunes PC, Haag J, Ream T, et al. (2006) The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126: 79-92.
38. Johnson LM, Law JA, Khattar A, Henderson IR, Jacobsen SE, (2008) SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet 4: e1000280 doi:10.1371/journal.pgen.1000280.
39. Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, et al. (2011) A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes Dev 25: 137-152.
40. Clough SJ, Bent AF, (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743.
41. Deleris A, Greenberg MV, Ausin I, Law RW, Moissiard G, et al. (2010) Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep 11: 950-955.
42. Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, et al. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 38: 721-725.
43. Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, et al. (2006) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40: 303-311.