RNA-directed DNA methylation in plants: Where to start?

RNA Biology

Volumn 10, Issue 10, 2013, Pages 1593-1596

  Zhang, Heng ^a   He, Xinjian ^b   Zhu, Jian Kang ^a,c  

^a Chinese Academy of Sciences   (China)

^b NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^c PURDUE UNIVERSITY   (United States)

Author keywords

DNA methylation; Histone modifcation; LncRNA; RdDM; SiRNA

Indexed keywords

ARGONAUTE PROTEIN; DDR PROTEIN; DNA TRANSCRIPTION FACTOR 1; DOUBLE STRANDED RNA; HISTONE 3 LYSINE 9; HISTONE H3; HOMEODOMAIN PROTEIN; KOW DOMAIN CONTAINING TRANSCRIPTION FACTOR 1; LONG UNTRANSLATED RNA; MULTIPROTEIN COMPLEX; PIWI INTERACTING RNA; PRIMER RNA; RNA BINDING PROTEIN; RNA POLYMERASE; RNA POLYMERASE II; RNA POLYMERASE IV; RNA POLYMERASE V; SAWADEE HOMEODOMAIN HOMOLOG 1; SINGLE STRANDED RNA; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN; DNA DIRECTED RNA POLYMERASE; PLANT RNA; RNA POLYMERASE IV, ARABIDOPSIS; RNA POLYMERASE V, ARABIDOPSIS;

AFFINITY PURIFICATION; ARABIDOPSIS THALIANA; BASE PAIRING; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA BINDING; DNA METHYLATION; DNA SEQUENCE; DNA TEMPLATE; GENE MUTATION; GENE SILENCING; GENOME; HETEROCHROMATIN; HISTONE MODIFICATION; NUCLEIC ACID STRUCTURE; PHYLOGENY; PLANT; PURIFICATION; REVIEW; RNA DIRECTED DNA METHYLATION; SEQUENCE HOMOLOGY; TANDEM MASS SPECTROMETRY; TRANSCRIPTIONAL GENE SILENCING; TRANSPOSON; ARABIDOPSIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA METHYLATION; DNA-DIRECTED RNA POLYMERASES; GENE EXPRESSION REGULATION, PLANT; RNA, PLANT; RNA, SMALL INTERFERING;

EID: 84885975303     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.26312     Document Type: Review

References (30)

1. Castel SE, Martienssen RA. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 2013;14:100-12 http://dx.doi.org/10.1038/nrg 3355; PMID:23329111
2. Grewal SI, Elgin SC. Transcription and RNA interference in the formation of heterochromatin. Nature 2007;447:399-406 http://dx.doi.org/10.1038/ nature05914; PMID:17522672 (Pubitemid 46816745)
3. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. Landscape of transcription in human cells. Nature 2012;489:101-8 http://dx.doi.org/10.1038/nature1 1233; PMID:22955620
4. Wassenegger M, Heimes S, Riedel L, Sänger HL. RNA-directed de novo methylation of genomic sequences in plants. Cell 1994;76:567-76 http://dx.doi.org/1 0.1 016/0 092-8674 (94) 90119-8; PMID: 8313476 (Pubitemid 24064176)
5. Vaucheret H. Plant ARGONAUTES. Trends Plant Sci 2008;13:350-8 http://dx.doi.org/10.1016/j. tplants.2008.04.007; PMID: 18508405
6. Haag JR, Ream TS, Marasco M, Nicora CD, Norbeck AD, Pasa-Tolic L, Pikaard CS. 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;48:811-8 http://dx.doi.org/10.1016/j.molcel.2012.09.027; PMID:23142082
7. Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 2007;19:1507-21 http://dx.doi.org/10.1105/tpc.107.051540; PMID: 17526749 (Pubitemid 47025373)
8. Wierzbicki AT, Haag JR, Pikaard CS. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008;135:635-48 http://dx.doi.org/10.1016/j.cell.2008.09. 035; PMID: 19013275
9. Zheng B, Wang Z, Li S, Yu B, Liu JY, 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;23:2850-60 http://dx.doi.org/10. 1101/gad.1868009; PMID:19948763
10. Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol 2012;19:870-5 http://dx.doi.org/10.1038/nsmb.2354; PMID:22864289
11. Pikaard CS, Haag JR, Pontes OM, Blevins T, Cocklin R. A Transcription Fork Model for Pol IV and Pol V-dependent RNA-Directed DNA Methylation. Cold Spring Harb Symp Quant Biol 2013.
12. Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, et al. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 2010;465:106-9 http://dx.doi.org/10.1038/ nature09025; PMID:20410883
13. He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK. An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell 2009;137:498-508 http://dx.doi.org/10.1016/j.cell.2009.04.028; PMID:19410546
14. Rowley MJ, Avrutsky MI, Sifuentes CJ, Pereira L, Wierzbicki AT. Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet 2011;7:e1002120 http://dx.doi.org/10. 1371/journal. pgen. 1002120; PMID:21738482
15. Zhang CJ, Ning YQ, Zhang SW, Chen Q, Shao CR, Guo YW, Zhou JX, Li L, Chen S, He XJ. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. PLoS Genet 2012;8:e1002693 http://dx.doi.org/10.1371/journal. pgen. 1002693; PMID:22570638
16. Zhu Y, Rowley MJ, Böhmdorfer G, Wierzbicki A T A. A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell 2013;49:298-309 http://dx.doi.org/10.1016/j.molcel.2012.11. 011; PMID:23246435
17. Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, Zhu JK, Hagen G, Guilfoyle TJ, Pasa-Tolic L, Pikaard CS. 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 http://dx.doi.org/10.1016/j. molcel.2008.12.015; PMID:19110459
18. Tucker SL, Reece J, Ream TS, Pikaard CS. Evolutionary history of plant multisubunit RNA polymerases IV and V: subunit origins via genomewide and segmental gene duplications, retrotransposition, and lineage-specifc subfunctionalization. Cold Spring Harb Symp Quant Biol 2010;75:285-97 http://dx.doi.org/10.1101/sqb.2010.75.037; PMID:21447813
19. Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev 2012;26:1825-36 http://dx.doi.org/10.1101/gad. 197772.112; PMID:22855789
20. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009;458:223-7 http://dx.doi.org/10.1038/nature07672; PMID:19182780
21. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 2010;8:e1000384 http://dx.doi.org/10.1371/journal. pbio.1000384; PMID:20485488
22. 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 http://dx.doi.org/10.1371/journal.pgen. 1002195; PMID:21811420
23. Liu J, Bai G, Zhang C, Chen W, Zhou J, Zhang S, Chen Q, Deng X, He XJ, Zhu JK. An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specifc transcriptional gene silencing. Cell Res 2011;21:1691-700 http://dx.doi.org/10. 1038/cr.2011.173; PMID:22064704
24. Mukherjee K, Brocchieri L, Bürglin TR. A comprehensive classifcation and evolutionary analysis of plant homeobox genes. Mol Biol Evol 2009;26:2775-94 http://dx.doi.org/10.1093/molbev/msp201; PMID:19734295
25. Billeter M. Homeodomain-type DNA recognition. Prog Biophys Mol Biol 1996;66:211-25 http://dx.doi.org/10.1016/S0079-6107 (97) 00006-0; PMID:9284 451 (Pubitemid 27323427)
26. Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, et al. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol I V. Proc Natl Acad Sci U S A 2013;110:8290-5 http://dx.doi.org/10.1073/pnas.1300585110; PMID:23637343
27. Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM, Strahl BD, Patel DJ, Jacobsen SE. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 2013;498:385-9 http://dx.doi.org/10.1038/nature12178; PMID:23636332
28. Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 2009;4:363-71 http://dx.doi.org/10. 1038/nprot.2009.2; PMID:19247286
29. Nielsen PR, Nietlispach D, Buscaino A, Warner RJ, Akhtar A, Murzin AG, Murzina NV, Laue ED. Structure of the chromo barrel domain from the MOF acetyltransferase. J Biol Chem 2005;280:32326-31 http://dx.doi.org/10.1074/jbc. M501347200; PMID:15964847 (Pubitemid 41361842)
30. Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A 2012;109:E2183-91 http://dx.doi.org/10.1073/pnas. 1209329109; PMID:22733782