RNA-directed DNA methylation

References

• Wassenegger M, Heimes S, Riedel L, Sanger HL. RNA-directed de novo methylation of genomic sequences in plants. Cell 1994; 76:567 - 576
   PubMed Web of Science ®Google Scholar
• Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992; 69:915 - 926
   PubMed Web of Science ®Google Scholar
• Finnegan EJ, Peacock WJ, Dennis ES. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci USA 1996; 93:8449 - 8454
   PubMed Web of Science ®Google Scholar
• Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, et al. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 2003; 163:1109 - 1122
   PubMed Web of Science ®Google Scholar
• Bender J. DNA methylation and epigenetics. Annu Rev Plant Biol 2004; 55:41 - 68
   PubMed Web of Science ®Google Scholar
• Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16:6 - 21
   PubMed Web of Science ®Google Scholar
• El-Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev 2007; 21:2539 - 2544
   PubMed Web of Science ®Google Scholar
• Chinnusamy V, Zhu JK. RNA-directed DNA methylation and demethylation in plants. Sci China C Life Sci 2009; 52:331 - 343
   PubMedGoogle Scholar
• Pikaard CS, Haag JR, Ream T, Wierzbicki AT. Roles of RNA polymerase IV in gene silencing. Trends Plant Sci 2008; 13:390 - 397
   PubMed Web of Science ®Google Scholar
• Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, Zhu JK, et al. 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
   PubMed Web of Science ®Google Scholar
• Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. RNA polymerase IV directs silencing of endogenous DNA. Science 2005; 308:118 - 120
   PubMed Web of Science ®Google Scholar
• Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet 2005; 37:761 - 765
   PubMed Web of Science ®Google Scholar
• Onodera Y, Haag JR, Ream T, Nunes PC, Pontes O, Pikaard CS. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 2005; 120:613 - 622
   PubMed Web of Science ®Google Scholar
• Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, 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
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Pontes O, Li CF, Nunes PC, Haag J, Ream T, Vitins A, et al. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell 2006; 126:79 - 92
   PubMed Web of Science ®Google Scholar
• Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, Chan SW, et al. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell 2006; 126:93 - 106
   PubMed Web of Science ®Google Scholar
• Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2005; 123:1279 - 1291
   PubMed Web of Science ®Google Scholar
• He XJ, Hsu YF, Pontes O, Zhu J, Lu J, Bressan RA, 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
   PubMed Web of Science ®Google Scholar
• Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, Feuerbach F, et al. Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 2002; 14:629 - 639
   PubMed Web of Science ®Google Scholar
• Nonomura K, Morohoshi A, Nakano M, Eiguchi M, Miyao A, Hirochika H, et al. A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. Plant Cell 2007; 19:2583 - 2594
   PubMed Web of Science ®Google Scholar
• Tolia NH, Joshua-Tor L. Slicer and the argonautes. Nat Chem Biol 2007; 3:36 - 43
   PubMed Web of Science ®Google Scholar
• Hutvagner G, Simard MJ. Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 2008; 9:22 - 32
   PubMed Web of Science ®Google Scholar
• Vaucheret H. Plant ARGONAUTES. Trends Plant Sci 2008; 13:350 - 358
   PubMed Web of Science ®Google Scholar
• Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Benning C. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J 1998; 17:170 - 180
   PubMed Web of Science ®Google Scholar
• Fagard M, Boutet S, Morel JB, Bellini C, Vaucheret H. AGO1, QDE-2 and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc Natl Acad Sci USA 2000; 97:11650 - 11654
   PubMed Web of Science ®Google Scholar
• Zilberman D, Cao X, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 2003; 299:716 - 719
   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 - 1220
   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 - 1012
   PubMed Web of Science ®Google Scholar
• Zheng X, Zhu J, Kapoor A, Zhu JK. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J 2007; 26:1691 - 1701
   PubMed Web of Science ®Google Scholar
• Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004; 430:471 - 476
   PubMed Web of Science ®Google Scholar
• Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 2007; 39:61 - 69
   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 - 1201
   PubMed Web of Science ®Google Scholar
• Vaughn MW, Tanurdzic M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, et al. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 2007; 5:174
   PubMed Web of Science ®Google Scholar
• Sieburth LE, Meyerowitz EM. Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell 1997; 9:355 - 365
   PubMed Web of Science ®Google Scholar
• Ito T, Sakai H, Meyerowitz EM. Whorl-specific expression of the SUPERMAN gene of Arabidopsis is mediated by cis elements in the transcribed region. Curr Biol 2003; 13:1524 - 1530
   PubMed Web of Science ®Google Scholar
• Kakutani T, Munakata K, Richards EJ, Hirochika H. Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 1999; 151:831 - 838
   PubMed Web of Science ®Google Scholar
• Papa CM, Springer NM, Muszynski MG, Meeley R, Kaeppler SM. Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 2001; 13:1919 - 1928
   PubMed Web of Science ®Google Scholar
• Bestor TH. The DNA methyltransferases of mammals. Hum Mol Genet 2000; 9:2395 - 2402
   PubMed Web of Science ®Google Scholar
• Cheng X. Structure and function of DNA methyltransferases. Annu Rev Biophys Biomol Struct 1995; 24:293 - 318
   PubMedGoogle Scholar
• Finnegan EJ, Kovac KA. Plant DNA methyltransferases. Plant Mol Biol 2000; 43:189 - 201
   PubMed Web of Science ®Google Scholar
• Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL. Demethylation-induced developmental pleiotropy in Arabidopsis. Science 1996; 273:654 - 657
   PubMed Web of Science ®Google Scholar
• Saze H, Mittelsten Scheid O, Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 2003; 34:65 - 69
   PubMed Web of Science ®Google Scholar
• Henikoff S, Comai L. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics 1998; 149:307 - 318
   PubMed Web of Science ®Google Scholar
• Bartee L, Malagnac F, Bender J. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev 2001; 15:1753 - 1758
   PubMed Web of Science ®Google Scholar
• Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 2001; 292:2077 - 2080
   PubMed Web of Science ®Google Scholar
• Cao X, Springer NM, Muszynski MG, Phillips RL, Kaeppler S, Jacobsen SE. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc Natl Acad Sci USA 2000; 97:4979 - 4984
   PubMed Web of Science ®Google Scholar
• Cao X, Jacobsen SE. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 2002; 12:1138 - 1144
   PubMed Web of Science ®Google Scholar
• Cao X, Jacobsen SE. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 2002; 99:16491 - 16498
   PubMed Web of Science ®Google 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 - 757
   PubMed Web of Science ®Google Scholar
• Zaratiegui M, Irvine DV, Martienssen RA. Noncoding RNAs and gene silencing. Cell 2007; 128:763 - 766
   PubMed Web of Science ®Google Scholar
• Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 2003; 13:2212 - 2217
   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 2004; 303:1336
   PubMed Web of Science ®Google Scholar
• Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 2007; 17:54 - 59
   PubMed Web of Science ®Google Scholar
• Zhu JK. Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 2009;
   PubMed Web of Science ®Google Scholar
• Burn JE, Bagnall DJ, Metzger JD, Dennis ES, Peacock WJ. DNA methylation, vernalization, and the initiation of flowering. Proc Natl Acad Sci USA 1993; 90:287 - 291
   PubMed Web of Science ®Google Scholar
• Jenuwein T, Allis CD. Translating the histone code. Science 2001; 293:1074 - 1080
   PubMed Web of Science ®Google Scholar
• Richards EJ, Elgin SC. Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects. Cell 2002; 108:489 - 500
   PubMed Web of Science ®Google Scholar
• Kouzarides T. Chromatin modifications and their function. Cell 2007; 128:693 - 705
   PubMed Web of Science ®Google Scholar
• Dobosy JR, Selker EU. Emerging connections between DNA methylation and histone acetylation. Cell Mol Life Sci 2001; 58:721 - 727
   PubMed Web of Science ®Google Scholar
• Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJ. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 2002; 21:6832 - 6841
   PubMed Web of Science ®Google Scholar
• Matzke MA, Birchler JA. RNAi-mediated pathways in the nucleus. Nat Rev Genet 2005; 6:24 - 35
   PubMed Web of Science ®Google Scholar
• Jackson JP, Lindroth AM, Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002; 416:556 - 560
   PubMed Web of Science ®Google Scholar
• Malagnac F, Bartee L, Bender J. An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 2002; 21:6842 - 6852
   PubMed Web of Science ®Google Scholar
• Ebbs ML, Bartee L, Bender J. H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol 2005; 25:10507 - 10515
   PubMed Web of Science ®Google Scholar
• Huettel B, Kanno T, Daxinger L, Bucher E, van der Winden J, Matzke AJ, Matzke M. RNA-directed DNA methylation mediated by DRD1 and Pol IVb: a versatile pathway for transcriptional gene silencing in plants. Biochim Biophys Acta 2007; 1769:358 - 374
   PubMed Web of Science ®Google Scholar
• Vongs A, Kakutani T, Martienssen RA, Richards EJ. Arabidopsis thaliana DNA methylation mutants. Science 1993; 260:1926 - 1928
   PubMed Web of Science ®Google Scholar
• Jacobsen SE, Sakai H, Finnegan EJ, Cao X, Meyerowitz EM. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr Biol 2000; 10:179 - 186
   PubMed Web of Science ®Google Scholar
• Bartee L, Bender J. Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family. Nucl Acids Res 2001; 29:2127 - 2134
   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; 99:16499 - 16506
   PubMed Web of Science ®Google Scholar
• Schoft VK, Chumak N, Mosiolek M, Slusarz L, Komnenovic V, Brownfield L, et al. Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep 2009; 10:1015 - 1021
   PubMed Web of Science ®Google Scholar
• Rangwala SH, Richards EJ. Differential epigenetic regulation within an Arabidopsis retroposon family. Genetics 2007; 176:151 - 160
   PubMed Web of Science ®Google Scholar
• Habu Y, Mathieu O, Tariq M, Probst AV, Smathajitt C, Zhu T, Paszkowski J. Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep 2006; 7:1279 - 1284
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 2002; 111:803 - 814
   PubMed Web of Science ®Google Scholar
• Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marin MI, Martinez-Macias MI, Ariza RR, Roldan-Arjona T. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci USA 2006; 103:6853 - 6858
   PubMed Web of Science ®Google Scholar
• Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell 2002; 110:33 - 42
   PubMed Web of Science ®Google Scholar
• Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. Demethylation of the zygotic paternal genome. Nature 2000; 403:501 - 502
   PubMed Web of Science ®Google Scholar
• Miller CA, Sweatt JD. Covalent modification of DNA regulates memory formation. Neuron 2007; 53:857 - 869
   PubMed Web of Science ®Google Scholar
• Reiner SL. Epigenetic control in the immune response. Hum Mol Genet 2005; 14:41 - 46
   PubMed Web of Science ®Google Scholar
• Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, et al. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 2006; 124:495 - 506
   PubMed Web of Science ®Google Scholar
• Arnaud P, Feil R. MEDEA takes control of its own imprinting. Cell 2006; 124:468 - 470
   PubMed Web of Science ®Google Scholar
• Penterman J, Uzawa R, Fischer RL. Genetic interactions between DNA demethylation and methylation in Arabidopsis. Plant Physiol 2007; 145:1549 - 1557
   PubMed Web of Science ®Google Scholar
• Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, et al. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 2004; 303:521 - 523
   PubMed Web of Science ®Google Scholar
• Jullien PE, Kinoshita T, Ohad N, Berger F. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 2006; 18:1360 - 1372
   PubMed Web of Science ®Google Scholar
• Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008; 133:523 - 536
   PubMed Web of Science ®Google Scholar
• Bennetzen JL, Ma J, Devos KM. Mechanisms of recent genome size variation in flowering plants. Ann Bot 2005; 95:127 - 132
   PubMed Web of Science ®Google Scholar
• Feschotte C, Jiang N, Wessler SR. Plant transposable elements: where genetics meets genomics. Nat Rev Genet 2002; 3:329 - 341
   PubMed Web of Science ®Google Scholar
• Choi CS, Sano H. Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics 2007; 277:589 - 600
   PubMed Web of Science ®Google Scholar
• Douet J, Blanchard B, Cuvillier C, Tourmente S. Interplay of RNA Pol IV and ROS1 during post-embryonic 5S rDNA chromatin remodeling. Plant Cell Physiol 2008; 49:1783 - 1791
   PubMed Web of Science ®Google Scholar
• Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJ, Matzke M. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J 2006; 25:2828 - 2836
   Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Zemach A, Grafi G. Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation. Trends Plant Sci 2007; 12:80 - 85
   Google Scholar
• Zheng X, Pontes O, Zhu J, Miki D, Zhang F, Li WX, et al. ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 2008; 455:1259 - 1262
   PubMed Web of Science ®Google Scholar
• Zhu JK. Epigenome sequencing comes of age. Cell 2008; 133:395 - 397
   PubMed Web of Science ®Google Scholar
• Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 2004; 427:164 - 167
   PubMed Web of Science ®Google Scholar
• Sung S, Amasino RM. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 2004; 427:159 - 164
   PubMed Web of Science ®Google Scholar
• Swiezewski S, Crevillen P, Liu F, Ecker JR, Jerzmanowski A, Dean C. Small RNA-mediated chromatin silencing directed to the 3′ region of the Arabidopsis gene encoding the developmental regulator, FLC. Proc Natl Acad Sci USA 2007; 104:3633 - 3638
   PubMed Web of Science ®Google Scholar
• Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006; 442:295 - 298
   PubMed Web of Science ®Google Scholar
• Hale CJ, Stonaker JL, Gross SM, Hollick JB. A novel Snf2 protein maintains trans-generational regulatory states established by paramutation in maize. PLoS Biol 2007; 5:275
   PubMed Web of Science ®Google Scholar
• Dorweiler JE, Carey CC, Kubo KM, Hollick JB, Kermicle JL, Chandler VL. mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. Plant Cell 2000; 12:2101 - 2118
   PubMed Web of Science ®Google Scholar
• Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, et al. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell 2003; 5:891 - 901
   PubMed Web of Science ®Google Scholar
• Jeddeloh JA, Bender J, Richards EJ. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev 1998; 12:1714 - 1725
   PubMed Web of Science ®Google Scholar
• Saze H, Sasaki T, Kakutani T. Negative regulation of DNA methylation in plants. Epigenetics 2008; 3:122 - 124
   PubMed Web of Science ®Google Scholar
• Miura A, Nakamura M, Inagaki S, Kobayashi A, Saze H, Kakutani T. An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J 2009; 28:1078 - 1086
   Google Scholar
• Saze H, Shiraishi A, Miura A, Kakutani T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science 2008; 319:462 - 465
   PubMed Web of Science ®Google Scholar
• Chinnusamy V, Zhu JK. Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 2009; 12:133 - 139
   PubMed Web of Science ®Google Scholar
• Mahfouz MM, Kim S, Delauney AJ, Verma DP. Arabidopsis TARGET OF RAPAMYCIN interacts with RAPTOR, which regulates the activity of S6 kinase in response to osmotic stress signals. Plant Cell 2006; 18:477 - 490
   PubMed Web of Science ®Google Scholar
• Woo HR, Richards EJ. Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana. BMC Plant Biol 2008; 8:92
   PubMed Web of Science ®Google Scholar
• Sharma R, Mohan Singh RK, Malik G, Deveshwar P, Tyagi AK, Kapoor S, Kapoor M. Rice cytosine DNA methyltransferases—gene expression profiling during reproductive development and abiotic stress. FEBS J 2009; 276:6301 - 6311
   PubMed Web of Science ®Google Scholar
• Labra M, Ghiani A, Citterio S, Sgorbati S, Sala F, Vannini C, et al. Analysis of cytosine methylation pattern in response to water deficit in pea root tips. Plant Biol 2002; 4:694 - 699
   Web of Science ®Google Scholar
• Kovarik A, Matyasek R, Leitch A, Gazdova B, Fulnecek J, Bezdek M. Variability in CpNpG methylation in higher plant genomes. Gene 1997; 204:25 - 33
   PubMed Web of Science ®Google Scholar
• Kashkush K, Khasdan V. Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 2007; 177:1975 - 1985
   PubMed Web of Science ®Google Scholar
• Duan K, Ding X, Zhang Q, Zhu H, Pan A, Huang J. AtCopeg1, the unique gene originated from AtCopia95 retrotransposon family, is sensitive to external hormones and abiotic stresses. Plant Cell Rep 2008; 27:1065 - 1073
   PubMed Web of Science ®Google Scholar
• Kinoshita Y, Saze H, Kinoshita T, Miura A, Soppe WJ, Koornneef M, Kakutani T. Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J 2007; 49:38 - 45
   PubMed Web of Science ®Google Scholar
• Kato M, Takashima K, Kakutani T. Epigenetic control of CACTA transposon mobility in Arabidopsis thaliana. Genetics 2004; 168:961 - 969
   PubMed Web of Science ®Google Scholar
• Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 2003; 13:421 - 426
   PubMedGoogle Scholar
• Jacobsen SE, Meyerowitz EM. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 1997; 277:1100 - 1103
   PubMed Web of Science ®Google Scholar
• Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 2002; 21:6549 - 6559
   PubMed Web of Science ®Google Scholar
• Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 2003; 100:8823 - 8827
   PubMed Web of Science ®Google Scholar
• Mathieu O, Probst AV, Paszkowski J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 2005; 24:2783 - 2791
   PubMed Web of Science ®Google Scholar
• Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 1996; 93:12406 - 12411
   Google Scholar
• Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, et al. A role for RNAi in the selective correction of DNA methylation defects. Science 2009; 323:1600 - 1604
   PubMed Web of Science ®Google Scholar
• Cullis CA. Mechanisms and control of rapid genomic changes in flax. Ann Bot 2005; 95:201 - 206
   PubMed Web of Science ®Google Scholar
• Richards EJ. DNA methylation and plant development. Trends Genet 1997; 13:319 - 323
   PubMed Web of Science ®Google Scholar