Revisiting RNA-directed DNA methylation

References

• Matzke M, Mette MF, Jakowitsch J, Kanno T, Moscone EA, van der Winden J, et al. A test for transvection in plants: DNA pairing may lead to trans-activation or silencing of complex heteroalleles in tobacco. Genetics 2001; 158:451 - 61; PMID: 11333252
   PubMed Web of Science ®Google Scholar
• 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/10.1016/0092-8674(94)90119-8; PMID: 8313476
   PubMed Web of Science ®Google Scholar
• Pélissier T, Thalmeir S, Kempe D, Sänger HL, Wassenegger M. Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucleic Acids Res 1999; 27:1625 - 34; http://dx.doi.org/10.1093/nar/27.7.1625; PMID: 10075993
   PubMed Web of Science ®Google Scholar
• Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, et al. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 2004; 1677:129-41;; 10.1016/j.bbaexp.2003.10.015.PMID: 15020054
   PubMedGoogle Scholar
• Jones L, Ratcliff F, Baulcombe DC. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol 2001; 11:747 - 57; http://dx.doi.org/10.1016/S0960-9822(01)00226-3; PMID: 11378384
   PubMed Web of Science ®Google Scholar
• Wang MB, Wesley SV, Finnegan EJ, Smith NA, Waterhouse PM. Replicating satellite RNA induces sequence-specific DNA methylation and truncated transcripts in plants. RNA 2001; 7:16 - 28; http://dx.doi.org/10.1017/S1355838201001224; PMID: 11214177
   PubMed Web of Science ®Google Scholar
• Aufsatz W, Mette MF, van der Winden J, Matzke AJ, Matzke M. RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci USA 2002; 99:Suppl 4 16499 - 506; http://dx.doi.org/10.1073/pnas.162371499; PMID: 12169664
   PubMed Web of Science ®Google Scholar
• Mette MF, van der Winden J, Matzke MA, Matzke AJ. Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J 1999; 18:241 - 8; http://dx.doi.org/10.1093/emboj/18.1.241; PMID: 9878066
   PubMed Web of Science ®Google Scholar
• Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science (New York, NY 2004; 303:1336.
   Google Scholar
• Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2004; 2:E104; http://dx.doi.org/10.1371/journal.pbio.0020104; PMID: 15024409
   PubMed Web of Science ®Google Scholar
• Bender J. RNA-directed DNA methylation: getting a grip on mechanism. Curr Biol 2012; 22:R400 - 1; http://dx.doi.org/10.1016/j.cub.2012.04.010; PMID: 22625855
   PubMedGoogle Scholar
• Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010; 11:204 - 20; http://dx.doi.org/10.1038/nrg2719; PMID: 20142834
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Wierzbicki AT, Ream TS, Haag JR, Pikaard CS. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 2009; 41:630 - 4; http://dx.doi.org/10.1038/ng.365; PMID: 19377477
   PubMed Web of Science ®Google Scholar
• Mlotshwa S, Pruss GJ, Gao Z, Mgutshini NL, Li J, Chen X, et al. Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing. Plant J 2010; 64:699 - 704; http://dx.doi.org/10.1111/j.1365-313X.2010.04358.x; PMID: 21070421
   PubMed Web of Science ®Google Scholar
• Melnyk CW, Molnar A, Bassett A, Baulcombe DC. Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana. Curr Biol 2011; 21:1678 - 83; http://dx.doi.org/10.1016/j.cub.2011.08.065; PMID: 21962713
   PubMed Web of Science ®Google Scholar
• Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 2010; 328:872 - 5; http://dx.doi.org/10.1126/science.1187959; PMID: 20413459
   PubMed Web of Science ®Google Scholar
• Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 2006; 126:1189 - 201; http://dx.doi.org/10.1016/j.cell.2006.08.003; PMID: 16949657
   PubMed Web of Science ®Google Scholar
• Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, et al. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 2006; 38:721 - 5; http://dx.doi.org/10.1038/ng1804; PMID: 16699516
   PubMed Web of Science ®Google Scholar
• Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 2011; 12:483 - 92; http://dx.doi.org/10.1038/nrm3152; PMID: 21779025
   PubMed Web of Science ®Google Scholar
• Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008; 133:523 - 36; http://dx.doi.org/10.1016/j.cell.2008.03.029; PMID: 18423832
   PubMed Web of Science ®Google Scholar
• Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, et al. 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
   PubMed Web of Science ®Google Scholar
• Pontier D, Picart C, Roudier F, Garcia D, Lahmy S, Azevedo J, et al. NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol Cell 2012; 48:121 - 32; http://dx.doi.org/10.1016/j.molcel.2012.07.027; PMID: 22940247
   PubMed Web of Science ®Google Scholar
• Vaistij FE, Jones L. Compromised virus-induced gene silencing in RDR6-deficient plants. Plant Physiol 2009; 149:1399 - 407; http://dx.doi.org/10.1104/pp.108.132688; PMID: 19129420
   PubMed Web of Science ®Google Scholar
• Ausin I, Mockler TC, Chory J, Jacobsen SE. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat Struct Mol Biol 2009; 16:1325 - 7; http://dx.doi.org/10.1038/nsmb.1690; PMID: 19915591
   PubMed Web of Science ®Google Scholar
• Otagaki S, Kawai M, Masuta C, Kanazawa A. Size and positional effects of promoter RNA segments on virus-induced RNA-directed DNA methylation and transcriptional gene silencing. Epigenetics 2011; 6:681 - 91; http://dx.doi.org/10.4161/epi.6.6.16214; PMID: 21610318
   PubMed Web of Science ®Google Scholar
• Dalakouras A, Moser M, Zwiebel M, Krczal G, Hell R, Wassenegger M. A hairpin RNA construct residing in an intron efficiently triggered RNA-directed DNA methylation in tobacco. Plant J 2009; 60:840 - 51; http://dx.doi.org/10.1111/j.1365-313X.2009.04003.x; PMID: 19702668
   PubMed Web of Science ®Google Scholar
• Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, et al. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol 2003; 132:1382 - 90; http://dx.doi.org/10.1104/pp.103.021980; PMID: 12857820
   PubMed Web of Science ®Google Scholar
• Wassenegger M. RNA-directed DNA methylation. Plant Mol Biol 2000; 43:203 - 20; http://dx.doi.org/10.1023/A:1006479327881; PMID: 10999405
   PubMed Web of Science ®Google Scholar
• Ye R, Wang W, Iki T, Liu C, Wu Y, Ishikawa M, et al. Cytoplasmic assembly and selective nuclear import of Arabidopsis Argonaute4/siRNA complexes. Mol Cell 2012; 46:859 - 70; http://dx.doi.org/10.1016/j.molcel.2012.04.013; PMID: 22608924
   PubMed Web of Science ®Google Scholar
• Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 2004; 14:1214 - 20; http://dx.doi.org/10.1016/j.cub.2004.06.055; PMID: 15242620
   PubMed Web of Science ®Google Scholar
• Pikaard CS, Haag JR, Ream T, Wierzbicki AT. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 2008; 13:390 - 7; http://dx.doi.org/10.1016/j.tplants.2008.04.008; PMID: 18514566
   PubMed Web of Science ®Google Scholar
• Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, 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
   PubMed Web of Science ®Google Scholar
• Qi Y, He X, Wang XJ, Kohany O, Jurka J, Hannon GJ. Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 2006; 443:1008 - 12; http://dx.doi.org/10.1038/nature05198; PMID: 16998468
   PubMed Web of Science ®Google Scholar
• Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJ, et al. A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J 2009; 28:48 - 57; http://dx.doi.org/10.1038/emboj.2008.260; PMID: 19078964
   PubMed Web of Science ®Google Scholar