DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 20, 2013, Pages 8290-8295

  Zhang, Heng ^a   Ma, Ze Yang ^b   Zeng, Liang ^a   Tanaka, Kaori ^c   Zhang, Cui Jun ^b   Ma, Jun ^b   Bai, Ge ^b   Wang, Pengcheng ^d   Zhang, Su Wei ^b   Liu, Zhang Wei ^b   Cai, Tao ^b   Tang, Kai ^d   Liu, Renyi ^e   Shi, Xiaobing ^c   He, Xin Jian ^b   Zhu, Jian Kang ^a,d  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^d PURDUE UNIVERSITY   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Gene silencing; Histone modifications; Small RNA; Transposon

Indexed keywords

DNA BINDING PROTEIN; DTF1 PROTEIN; HISTONE H3; RNA DIRECTED DNA POLYMERASE; RNA POLYMERASE IV; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DEMETHYLATION; DNA METHYLATION; FEEDBACK SYSTEM; IN VITRO STUDY; NEGATIVE FEEDBACK; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY; TRANSPOSON;

GENE SILENCING; HISTONE MODIFICATIONS; SMALL RNA; TRANSPOSON;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CLONING, MOLECULAR; DNA METHYLATION; DNA POLYMERASE BETA; DNA-BINDING PROTEINS; GENE SILENCING; HISTONES; HOMEODOMAIN PROTEINS; MUTATION; RNA, PLANT; RNA, SMALL INTERFERING; RNA-DIRECTED DNA POLYMERASE; TRANSCRIPTION, GENETIC; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 84877866795     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1300585110     Document Type: Article

References (37)

1. He X-J, Chen T, Zhu J-K (2011) Regulation and function of DNA methylation in plants and animals. Cell Res 21(3):442-465.
2. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11(3):204-220.
3. Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJM (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21(3):367-376.
4. Zhang H, Zhu J-K (2011) RNA-directed DNA methylation. Curr Opin Plant Biol 14(2): 142-147.
5. Haag JR, Pikaard CS (2011) Multisubunit RNA polymerases IV and V: Purveyors of noncoding RNA for plant gene silencing. Nat Rev Mol Cell Biol 12(8):483-492.
6. 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(4):635-648.
7. Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends Genet 20(6):244-251. (Pubitemid 38625682)
8. Du J, et al. (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151(1):167-180.
9. Johnson LM, et al. (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17(4):379-384. (Pubitemid 46241885)
10. Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJM (2002) HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 21(24):6832-6841. (Pubitemid 36014555)
11. Searle IR, Pontes O, Melnyk CW, Smith LM, Baulcombe DC (2010) JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev 24(10):986-991.
12. Deleris A, et al. (2010) Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep 11(12):950-955.
13. Sridhar VV, et al. (2007) Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature 447(7145):735-738. (Pubitemid 46889731)
14. Liu J, et al. (2011) An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and-independent roles in locus-specific transcriptional gene silencing. Cell Res 21(12):1691-1700.
15. Law JA, Vashisht AA, Wohlschlegel JA, Jacobsen SE (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(7):e1002195.
16. Wierzbicki AT, et al. (2012) Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev 26(16):1825-1836.
17. Zhong X, et al. (2012) DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol 19(9):870-875.
18. Ausin I, et al. (2012) INVOLVED IN DE NOVO 2-containing complex involved in RNAdirected DNA methylation in Arabidopsis. Proc Nat Acad Sci USA 109(22):8374-8381.
19. Zhu J-K (2009) Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 43:143-166.
20. He X-J, et al. (2009) A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes Dev 23(23):2717-2722.
21. Kanno T, et al. (2010) RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep 11(1):65-71.
22. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS (2009) RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 41(5):630-634.
23. Pontes O, et al. (2006) The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 126(1):79-92. (Pubitemid 44026550)
24. Mukherjee K, Brocchieri L, Bürglin TR (2009) A comprehensive classification and evolutionary analysis of plant homeobox genes. Mol Biol Evol 26(12):2775-2794.
25. Wolberger C (1996) Homeodomain interactions. Curr Opin Struct Biol 6(1):62-68. (Pubitemid 26073945)
26. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: A case study using the Phyre server. Nat Protoc 4(3):363-371.
27. Nielsen PR, et al. (2005) Structure of the chromo barrel domain from the MOF acetyltransferase. J Biol Chem 280(37):32326-32331. (Pubitemid 41361842)
28. Schalch T, et al. (2009) High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin. Mol Cell 34(1):36-46.
29. Yap KL, et al. (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38(5):662-674.
30. Rajakumara E, et al. (2011) PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell 43(2):275-284.
31. Numa H, et al. (2010) Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. EMBO J 29(2):352-362.
32. Li X, et al. (2012) Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis. Proc Natl Acad Sci USA 109(28): 11425-11430.
33. Tucker SL, Reece J, Ream TS, Pikaard CS (2010) Evolutionary history of plant multisubunit RNA polymerases IV and V: Subunit origins via genome-wide and segmental gene duplications, retrotransposition, and lineage-specific subfunctionalization. Cold Spring Harb Symp Quant Biol 75:285-297.
34. Lister R, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523-536.
35. Qian W, et al. (2012) A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336(6087):1445-1448.
36. He X-J, et al. (2009) 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 23(3):318-330.
37. Zhang C-J, et al. (2012) IDN2 and its paralogs form a complex required for RNAdirected DNA methylation. PLoS Genet 8(5):e1002693.