Abstract
DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it may be one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Aleksandrushkina NI, Kudryashova IB, Kirnos MD, Vanyushin BF (1990) Synthesis of “heavy” miniplasmid-like mitochondrial DNA and its adenine methylation in coleoptile and initial leaf of wheat seedlings: influence of phytohormones. Biochemistry (Mosc) 55:2038–2045
Ammermann D, Steinbruck G, Baur R, Wohlert H (1981) Methylated bases in the DNA of the ciliate Stylonychia mytilus. Eur J Cell Biol 24:154–156
Arber W (1974) DNA modification and restriction. Prog Nucleic Acid Res Mol Biol 14:1–37
Arnaud P, Goubely C, Pelissier T, Deragon JM (2000) SINE retroposons can be used in vivo as nucleation centers for de novo methylation. Mol Cell Biol 20:3434–3441
Ashapkin VV, Antoniv TT, Vanyushin BF (1993) Multiple nuclear protein binding to 135 bp subrepeat element of wheat ribosomal intergenic spacer. Biochem Mol Biol Int 30:755–761
Ashapkin VV, Kutueva LI, Vanyushin BF (2002) The gene for domains rearranged methyltransferase (DRM2) in Arabidopsis thaliana plants is methylated at both cytosine and adenine residues. FEBS Lett 532:367–372
Ashikawa I (2001) Surveying CpG methylation at 5′-CCGG in the genomes of rice cultivars. Plant Mol Biol 45:31–39
Aufsatz W, Mette MF, van der Winden J, Matzke AJM, Matzke M (2002a) RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci USA 99Suppl 4:16499–16506
Aufsatz W, Mette MF, van der Winden J, Matzke M, Matzke AJ (2002b) HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA. EMBO J 21:6832–6841
Babinger P, Kobl I, Mages W, Schmitt R (2001) A link between DNA methylation and epigenetic silencing in transgenic Volvox carteri. Nucleic Acids Res 29:1261–1271
Bae SH, Cheong HK, Cheong C, Kang S, Hwang DS, Choi BS (2003) Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition. J Biol Chem 278:45987–45993
Bakeeva LE, Kirnos MD, Aleksandrushkina NI, Kazimirchyuk SB, Shorning BYu, Zamyatnina VA, Yaguzhinsky LS, Vanyushin BF (1999) Subcellular reorganization of mitochondria producing heavy DNA in aging wheat coleoptiles. FEBS Lett 457:122–125
Ballestar E, Wolffe AP (2001) Methyl-CpG-binding proteins targeting specific gene repression. Eur J Biochem 268:1–6
Barras F, Marinus MG (1989) The great GATC: DNA methylation in E. coli. Trends Genet 5:139–145
Bartee L, Bender J (2001) Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family. Nucleic Acids Res 29:2127–2134
Bartee L, Malagnac F, Bender J (2001) Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Genes Dev 15:1753–1758
Bashkite EA, Kirnos MD, Kiryanov GI, Aleksandrushkina NI, Vanyushin BF (1980) Replication and methylation of DNA in the tobacco suspension culture cells and auxin influence. Biochemistry (Mosc) 45:1448–1456
Baurens FC, Nicolleau J, Legavre T, Verdeil JL, Monteuuis O (2004) Genomic DNA methylation of juvenile and mature Acacia mangium micropropagated in vitro with reference to leaf morphology as a phase change marker. Tree Physiol 24:401–407
Bender J (2001) A vicious cycle: RNA silencing and DNA methylation in plants. Cell 106:129–132
Berg A, Meza TJ, Mahic M, Thorstensen T, Kristiansen K, Aalen RB (2003) Tenmembers of the Arabidopsis gene family encoding methyl-CpG-binding domain proteins are transcriptionally active and at least one, AtMBDH, is crucial for normal development. Nucleic Acids Res 31:5291–5304
Bernacchia G, Primo A, Giorgetti L, Pitto L, Cella R (1998) Carrot DNA-methyltransferase is encoded by two classes of genes with differing patterns of expression. Plant J 13:317–329
Bestor TH (1992) Activation of mammalian DNA methyltransferase by cleavage of a Zn binding regulatory domain. EMBO J 11:2611–2617
Bestor TH (1998) Methylation meets acetylation. Nature 393:311–312
Bezdek M, Koukalova B, Kuhrova V, Vyskot B (1992) Differential sensitivity of CG and CCG DNA sequences to ethionine-induced hypomethylation of the Nicotiana tabacum genome. FEBS Lett 300:268–270
Bianchi MW, Viotti A (1988) DNA methylation and tissue specific transcription of storage protein genes of maize. Plant Mol Biol 11:203–214
Bird A (1992) The essentials of DNA methylation. Cell 70:5–8
Bird A, Wolffe AP (1999) Methylation-induced repression—belts, braces, and chromatin. Cell 99:451–454
Bourc’his D, Bestor TH (2002) Helicase homologues maintain cytosine methylation in plants and mammals. Bioessays 24:297–299
Brodzik R, Hennig J (1998) Adenine methylation of GATC sequences regulates activity of tobacco PR-1 and PR-2 promoters in electroporated protoplasts. Plant Physiol Biochem 36:401–406
Bromberg S, Pratt K, Hattman S (1982) Sequence specificity of the DNA adenine methylase in the protozoan Tetrahymena thermophila. J Bacteriol 150:993–996
Brutnell TP, Dellaporta SL (1994) Somatic inactivation and reactivation of Ac associated with changes in cytosine methylation and transposase expression. Genetics 138:213–225
Bujnicki JM (1999–2000) Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation. In Silico Biol 1:175–182
Bujnicki JM, Radlinska M (1999) Is theHemKfamilyofputative S-adenosylmethionine-dependent methyltransferases a “missing” ζ subfamily of adenine methyltransferases? A hypothesis. IUBMB Life 48:247–249
Burn JE, Smyth DR, Peacock WJ, Dennis ES (1993) Genes conferring late flowering in Arabidopsis thaliana. Genetica 90:147–155
Buryanov YI, Ilyin AV, Skryabin GK (1970) On detection of 6-methylaminopurine in DNA of fungus Mucor hiemalis. Dokl Akad Nauk SSSR 195:728–730
Buryanov YI, Eroshina NV, Vagabova LM, Iliin AV (1972) On the detection of 6-methylaminopurine in DNA of higher plant pollen. Dokl Akad Nauk SSSR 206:992–994
Bushell C, Spielman M, Scott RJ (2003) The basis of natural and artificial postzygotic hybridization barriers in Arabidopsis species. Plant Cell 15:1430–1442
Buzek J, Ebert I, Ruffini-Castiglione M, Siroky J, Vyskot B, Greilhuber J (1998) Structure and DNA methylation pattern of partially heterochromatinised endosperm nuclei in Gagea lutea (Liliaceae). Planta 204:506–514
Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci USA 99Suppl 4:16491–16498
Cao X, Springer NM, Muszynskil MG, Phillips RL, Kaeppler S, Jacobsen SE (2000) Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc Natl Acad Sci USA 97:4979–4984
Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13:2212–2217
Castilho A, Neves N, Rufini-Castiglione M, Viegas W, Heslop-Harrison JS (1999) 5-Methylcytosine distribution and genome organization in triticale before and after treatment with 5-azacytidine. J Cell Sci 112:4397–4404
Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE (2004) RNA silencing genes control de novo DNA methylation. Science 303:1336
Charles MP, Ravanat JL, Adamski D, D’Orazi G, Cadet J, Favier A, Berger F, Wion D (2004) N(6)-Methyldeoxyadenosine, a nucleoside commonly found in prokaryotes, induces C2C12 myogenic differentiation. Biochem Biophys Res Commun 314:476–482
Chaudhury AM, Koltunow A, Payne T, Luo M, Tucker MR, Dennis ES, Peacock WJ (2001) Control of early seed development. Annu Rev Cell Dev Biol 17:677–699
Chen Z, Pikaard CS (1997) Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev 11:2124–2136
Chopra S, Cocciolone SM, Bushman S, Sangar V, McMullen MD, Peterson T (2003) The maize unstable factor for orange1 is a dominant epigenetic modifier of a tissue specifically silent allele of pericarp color1. Genetics 163:1135–1146
Chvojka L, Sulimova GE, Bulgakov R, Bashkite EA, Vanyushin BF (1978) Changes in the 5-methylcytosine content in plant DNA associated with flowering gradient. Biochemistry (Mosc) 43:996–1000
Clark SJ, Harrison J, Frommer M (1995) CpNpG methylation in mammalian cells. Nat Genet 10:20–27
Colot V, Rossignol JL (1999) Eukaryotic DNA methylation as an evolutionary device. Bioessays 21:402–411
Cui H, Fedoroff NV (2002) Inducible DNA demethylation mediated by the maize suppressor-mutator transposon-encoded TnpA protein. Plant Cell 14:2883–2899
Cummings DJ, Tait A, Godard JM (1974) Methylated bases in DNA from Paramecium aurelia. Biochim Biophys Acta 374:1–11
DeLabre ML, Nett JH, Trumpower BL (1999) The cleaved presequence is not required for import of subunit 6 of the cytochrome bc1 complex into yeast mitochondria or assembly into the complex. FEBS Lett 449:201–205
Demidkina NP, Kiryanov GI, Vanyushin BF (1979) Methylation of newly-synthesized DNA in the mouse fibroblast cell culture. Biochemistry (Mosc) 44:1416–1425
Dennis ES, Bilodeau P, Burn J, Finnegan EJ, Genger R, Helliwell C, Kang BJ, Sheldon CC, Peacock WJ (1998) Methylation controls the low temperature induction of flowering in Arabidopsis. Symp Soc Exp Biol 51:97–103
Deplus R, Brenner C, Burgers WA, Putmans P, Kouzarides T, de Launoit Y, Fuks F (2002) Dnmt3L is a transcriptional repressor that recruits histone deacetylase. Nucleic Acids Res 30:3831–3838
Dunn DB, Smith JD (1955) Occurrence of a new base in the deoxyribonucleic acid of a strain of Bacterium coli. Nature 175:336–337
Ehrlich KC (1993) Characterization of DBPm, a plant protein that binds to DNA containing 5-methylcytosine. Biochim Biophys Acta 1172:108–116
Ehrlich KC, Cary JW, Ehrlich M (1992) A broad bean cDNA clone encoding a DN-Abinding protein resembling mammalian CREB in its sequence specificity and DNA methylation sensitivity. Gene 117:169–178
Fantappie MR, Gimba ER, Rumjanek FD (2001) Lack of DNA methylation in Schistosoma mansoni. Exp Parasitol 98:162–166
Fedoreyeva LI, Vanyushin BF (2002) N6-adenine DNA-methyltransferase in wheat seedlings. FEBS Lett 514:305–308
Fedoroff NV (1995) DNA methylation and activity of the maize Spm transposable element. Curr Top Microbiol Immunol 197:143–164
Finnegan EJ, Dennis ES (1993) Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana. Nucleic Acids Res 21:2383–2388
Finnegan EJ, Kovac KA (2000) Plant DNA methyltransferases. Plant Mol Biol 43:189–210
Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci USA 93:8449–8454
Finnegan EJ, Genger RK, Kovac K, Peacock WJ, Dennis ES (1998a) DNA methylation and the promotion of flowering by vernalization. Proc Natl Acad Sci USA 95:5824–5829
Finnegan EJ, Genger RK, Peacock WJ, Dennis ES (1998b) DNA methylation in plants. Annu Rev Plant Physiol Plant Mol Biol 49:223–247
Finnegan EJ, Peacock WJ, Dennis ES (2000) DNA methylation, a key regulator of plant development and other processes. Curr Opin Genet Dev 10:217–223
Finnegan EJ, Sheldon CC, Jardinaud F, Peacock WJ, Dennis ES (2004) A cluster of Arabidopsis genes with a coordinate response to an environmental stimulus. Curr Biol 14:911–916
Fisscher U, Weisbeek P, Smeekens S (1996) Atobacco nuclear protein that preferentially binds to unmethylated CpG-rich DNA. Eur J Biochem 235:585–592
Fojtova M, Kovarik A, Votruba I, Holy A (1998) Evaluation of the impact of Sadenosylhomocysteine metabolic pools on cytosine methylation of the tobacco genome. Eur J Biochem 252:347–352
Fojtova M, Kovarik A, Matyasek R (2001) Cytosine methylation of plastid genome in higher plants. Fact or artefact? Plant Sci 160:585–593
Fraga MF, Rodriguez R, Canal MJ (2002) Genomic DNA methylation-demethylation during aging and reinvigoration of Pinus radiata. Tree Physiol 22:813–816
Fransz P, De Jong JH, Lysak M, Castiglione MR, Schubert I (2002) Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc Natl Acad Sci USA 99:14584–14589
Frediani M, Giraldi E, Castiglione MR (1996) Distribution of 5-methylcytosine-rich regions in the metaphase chromosomes of Vicia faba. Chromosome Res 4:141–146
Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S (2004) Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein. Nucleic Acids Res 32:82–92
Fukuda T, Sakai M, Takano H, Ono K, Takio S (2004) Hypermethylation of retrotransposons in the liverwort Marchantia paleacea var. diptera. Plant Cell Rep 22:594–598
Fulnecek J, Matyasek R, Kovarik A, Bezdek M (1998) Mapping of 5-methylcytosine residues in Nicotiana tabacum 5S rRNA genes by genomic sequencing. Mol Gen Genet 259:133–141
Fulnecek J, Matyasek R, Kovarik A (2002) Distribution of 5-methylcytosine residues in 5S rRNA genes in Arabidopsis thaliana and Secale cereale. Mol Genet Genomics 268:510–517
Galweiler L, Conlan RS, Mader P, Palme K, Moore I (2000) Technical advance: the DNA-binding activity of gal4 is inhibited by methylation of the gal4 binding site in plant chromatin. Plant J 23:143–157
Gendrel A-V, Lippman Z, Yordan C, Colot V, Martienssen RA (2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM 1. Science 297:1871–1873
Genger RK, Kovac KA, Dennis ES, Peacock WJ, Finnegan EJ (1999) Multiple DNA methyltransferase genes in Arabidopsis thaliana. Plant Mol Biol 41:269–278
Gorovsky MA, Hattman S, Pleger GL (1973) [N6]methyladenine in the nuclear DNA of eucaryote, Tetrahymena pyriformis. J Cell Biol 56:697–701
Goubely C, Arnaud P, Tatout C, Heslop-Harrison JS, Deragon JM(1999) S1 SINE retroposons are methylated at symmetrical and non-symmetrical positions in Brassica napus: identification of a preferred target site for asymmetrical methylation. Plant Mol Biol 39:243–255
Gowher H, Leismann O, Jeltsch A (2000) DNA of Drosophila melanogaster contains 5-methylcytosine. EMBO J 19:6918–6923
Graham MW, Larkin PJ (1995) Adenine methylation at dam sites increases transient gene expression in plant cells. Transgenic Res 4:324–331
Gruenbaum Y, Naveh-Many T, Cedar H (1981) Sequence specificity of methylation in higher plant DNA. Nature 292:860–862
Guo HS, Lopez-Moya JJ, Garcia JA (1999) Mitotic stability of infection-induced resistance to plum pox potyvirus associated with transgene silencing and DNA methylation. Mol Plant Microbe Interact 12:103–111
Guseinov VA, Vanyushin BF (1975) Content and localization of 5-methylcytosine in DNA of healthy and wilt-infected cotton plants. Biochim Biophys Acta 395:229–238
Guseinov VA, Kiryanov GI, Vanyushin BF (1975) Intragenome distribution of 5-methylcytosine in DNA of healthy and wilt-infected cotton plants (Gossypium hirsutum L.). Mol Biol Rep 2:59–63
Gutierrez JC, Callejas S, Borniquel S, Martin-Gonzalez A (2000) DNA methylation in ciliates: implications in differentiation processes. Int Microbiol 3:139–146
Harrison GS, Findly RC, Karrer KM (1986) Site-specific methylation of adenine in the nuclear genome of a eukaryote, Tetrahymena thermophila. Mol Cell Biol 6:2364–2370
Hashida SN, Kitamura K, Mikami T, Kishima Y (2003) Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus. Plant Physiol 132:1207–1216
Hattman S, Kenny C, Berger L, Pratt K (1978) Comparative study of DNA methylation in three unicellular eucaryotes. J Bacteriol 135:1156–1157
Hendrich B, Bird A (2000) Mammalian methyltransferases and methyl-CpG-binding domains: proteins involved in DNA methylation. Curr Top Microbiol Immunol 249:55–74
Henikoff S, Comai L (1998) A DNA methyltransferase homologous with a chromodomain exists inmultiple polymorphic forms inArabidopsis. Genetics 149:307–318
Hirochika H, Okamoto H, Kakutani T (2000) Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12:357–369
Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226–232
Inamdar NM, Ehrlich KC, Ehrlich M (1991) CpG methylation inhibits binding of several sequence-specific DNA-binding proteins from pea, wheat, soybean and cauliflower. Plant Mol Biol 17:111–123
Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556–560
Jacobsen SE, Meyerowitz EM (1997) Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277:1100–1103
Jacobsen SE, Sakai H, Finnegan EJ, Cao X, Meyerowitz EM (2000) Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr Biol 10:179–186
Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33:245–252
Janousek B, Matsunaga S, Kejnovsky E, Ziuvova J, Vyskot B (2002) DNA methylation analysis of a male reproductive organ specific gene (MROS1) during pollen development. Genome 45:930–938
Jeddeloh JA, Bender J, Richards EJ (1998) The DNA methylation locus DDM 1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev 12:1714–1725
Jeltsch A (2001) The cytosine N4-methyltransferase M.PvuII also modifies adenine residues. Biol Chem 382:707–710
Jones L, Hamilton AJ, Voinnet O, Thomas CL, Maule AJ, Baulcombe DC (1999) RNADNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell 11:2291–2301
Jones L, Ratcliff F, Baulcombe DC (2001) RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Curr Biol 11:747–757
Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19:187–191
Kakutani T (2002) Epi-alleles in plants: inheritance of epigenetic information over generations. Plant Cell Physiol 43:1106–1111
Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 93:12406–12411
Kakutani T, Munakata K, Richards EJ, Hirochika H (1999) Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151:831–838
Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163:1109–1122
Kanno T, Mette MF, Kreil DP, Aufsatz W, Matzke M, Matzke AJ (2004) Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14:801–805
Karrer KM, Van Nuland TA (1998) Position effect takes precedence over target sequence in determination of adenine methylation patterns in the nuclear genome of a eukaryote, Tetrahymena thermophila. Nucleic Acids Res 26:4566–4573
Karrer KM, Van Nuland TA (2002) Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1. Nucleic Acids Res 30:1364–1370
Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 13:421–426
Kay PH, Pereira E, Marlow SA, Turbett G, Mitchell CA, Jacobsen PF, Holliday R, Papadimitriou JM (1994) Evidence for adenine methylation within the mouse myogenic gene Myo-D1. Gene 151:89–95
Kimura H, Shiota K (2003) Methyl-CpG-binding protein, MeCP2, is a target molecule for maintenance DNA methyltransferase, Dnmtl. J Biol Chem 278:4806–4812
Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, Kakutani T (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303:521–523
Kirnos MD, Merkulova NA, Borkhsenius SN, Vanyushin BF (1980) Character of macronucleus DNA methylation in protozoan Tetrahymena pyriformis. Dokl Akad Nauk SSSR 255:225–227
Kirnos MD, Aleksandrushkina NI, Vanyushin BF (1981) 5-Methylcytosine in pyrimidine sequences of plant and animal DNA: specificity of DNA methylation. Biochemistry (Mosc) 46:1458–1474
Kirnos MD, Bakeeva LE, Volkova SA, Ganicheva NI, Vanyushin BF (1983a) Mitochondrial nature of newly formed DNA in aging coleoptiles of etiolated wheat seedlings. Biochemistry (Mosc) 48:1505–1512
Kirnos MD, Volkova SA, Ganicheva NI, Kudryashova IB, Vanyushin BF (1983b) Synchronous periodic DNA synthesis in coleoptile and initial leaf of etiolated wheat seedlings: nature and ratio between nuclear and mitochondrial DNA synthesis. Biochemistry (Mosc) 48:1587–1595
Kirnos MD, Ganicheva NI, Kutueva LI, Vanyushin BF (1984a) Non-replicative synthesis and methylation of DNA during cell cycle in cells of initial leaf of etiolated wheat seedlings. Biochemistry (Mosc) 49:1690–1702
Kirnos MD, Kutueva LI, Ganicheva NI, Vanyushin BF (1984b) Non-semiconservative character of replicative DNA methylation in meristem cells of wheat seedling initial leaf: formation of undermethylated sites and the different specificity of methylation of the DNA replication fragments. Biochemistry (Mosc) 49:1357–1366
Kirnos MD, Artyukovskaya NA, Alexandrushkina NI, Ashapkin VV, Vanyushin BF (1986) Effect of phytohormones on replicative and post-replicative methylation of nuclear DNA during S-phase of cell cycle in the initial leaf cells of the etiolated wheat seedlings. Biochemistry (Mosc) 51:1875–1885
Kirnos MD, Alexandrushkina NI, Kutueva LI, Artyukhovskaya NA, Vanyushin BF (1987) Post-replicative methylation is a discrete step of nuclear DNA methylation in the cell cycle of initial leaf cells of wheat seedlings. Influence of temperature, phytohormones, inhibitors of translation, transcription and DNA methylation. Biochemistry (Mosc) 52:625–637
Kirnos MD, Alexandrushkina NI, Kutueva LI, Vanyushin BF (1988) Replicative and post-replicative methylation of nuclear DNA modulates asymmetry of its complementary chains in respect of the 5-methylcytosine content during consequent cell cycles in the wheat seedling initial leaf cells. Biochemistry (Mosc) 53:355–367
Kirnos MD, Alexandrushkina NI, Goremykin VV, Kudryashova I B, Vanyushin BF (1992a) “Heavy” mitochondrial DNA in higher plants. Biochemistry (Mosc) 57:1566–157
Kirnos MD, Alexandrushkina NI, Zagorskaya GYa, Kireev II, Vanyushin BF (1992b) Superproduction of heavy minicircular mitochondrial DNA in aging wheat coleoptiles. FEBS Lett 298:109–112
Kiryanov GI, Isaeva LV, Kirnos MD, Ganicheva NI, Vanyushin BF (1982) Replicative DNA methylation in L-cells: influence of S-isobutyladenosine and cycloheximide and possible existence of two DNA-methylases. Biochemistry (Mosc) 47:153–161
Kishimoto N, Sakai H, Jackson J, Jacobsen SE, Meyerowitz EM, Dennis ES, Finnegan EJ (2001) Site specificity of the Arabidopsis METI DNA methyltransferase demonstrated through hypermethylation of the superman locus. Plant Mol Biol 46:171–183
Kitamura K, Hashida SN, Mikami T, Kishima Y (2001) Position effect of the excision frequency of the Antirrhinum transposon Tam3: implications for the degree of position-dependent methylation in the ends of the element. Plant Mol Biol 47:475–490
Klöti A, He X, Potrykus I, Hohn T, Fütterer J (2002) Tissue-specific silencing of a transgene in rice. Proc Natl Acad Sci USA 99:10881–10886
Komatsu M, Shimamoto K, Kyozuka J (2003) Two-step regulation and continuous retrotransposition of the rice LINE-type retrotransposon Karma. Plant Cell 15:1934–1944
Kooter JM, Matzke MA, Meyer P (1999) Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci 4:340–347
Kovalchuk O, Burke P, Arkhipov A, Kuchma N, James SJ, Kovalchuk I, Pogribny I (2003) Genome hypermethylation in Pinus silvestris of Chernobyl—a mechanism for radiation adaptation? Mutat Res 529:13–20
Kovarik A, Matyasek R, Leitch A, Gazdova B, Fulnecek J, Bezdek M (1997) Variability in CpNpG methylation in higher plant genomes. Gene 204:25–33
Kovarik A, Koukalova B, Lim KY, Matyasek R, Lichtenstein CP, Leitch AR, Bezdek M (2000a) Comparative analysis of DNA methylation in tobacco heterochromatic sequences. Chromosome Res 8:527–541
Kovarik A, Van Houdt H, Holy A, Depicker A (2000b) Drug-induced hypomethylation of a posttranscriptionally silenced transgene locus of tobacco leads to partial release of silencing. FEBS Lett 467:47–51
Kriaucionis S, Bird A (2004) The major form of MeCP2 has a novel N-terminus generated by alternative splicing. Nucleic Acids Res 32:1818–1823
Kudryashova IB, Vanyushin BF (1986) Incorporation of cytokinins in DNA of wheat seedlings. Biochemistry (Mosc) 51:321–327
Kumpatla SP, Hall TC (1998) Longevity of 5-azacytidine-mediated gene expression and re-establishment of silencing in transgenic rice. Plant Mol Biol 38:1113–1122
Kumpatla SP, Hall TC (1999) Organizational complexity of a rice transgene locus susceptible to methylation-based silencing. IUBMB Life 48:459–467
Kutueva LI, Ashapkin VV, Vanyushin BF (1996) The methylation pattern of a cytosine DNA-methyltransferase gene in Arabidopsis thaliana plants. Biochem Mol Biol Int 40:347–353
Lauria M, Rupe M, Guo M, Kranz E, Pirona R, Viotti A, Lund G (2004) Extensive maternal DNA hypomethylation in the endosperm of Zea mays. Plant Cell 16:510–522
Law RD, Suttle JC (2003) Transient decreases in methylation at 5′-CCGG-3′ sequences in potato (Solanum tuberosum L.) meristem DNA during progression of tubers through dormancy precede the resumption of sprout growth. Plant Mol Biol 51:437–447
Lawley PD, Crathorn AR, Shah SA, Smith BA (1972) Biomethylation of deoxyribonucleic acid in cultured human tumor cells (HeLa). Methylated bases other than 5-methylcytosine not detected. Biochem J 128:133–138
Lawrence RJ, Pikaard CS (2003) Transgene-induced RNA interference: a strategy for overcoming gene redundancy in polyploids to generate loss-of-function mutations. Plant J 36:114–121
Lawrence RJ, Earley K, Pontes O, Silva M, Chen ZJ, Neves N, Viegas W, Pikaard CS (2004) A concerted DNA methylation/histone methylation switch regulates rRNA gene dosage control and nucleolar dominance. Mol Cell 13:599–609
Li G, Hall TC, Holmes-Davis R (2002) Plant chromatin: development and gene control. Bioessays 24:234–243
Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of chromomethylase3 for maintenance of CpXpG methylation. Science 292:2077–2080
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471–476
Lisch D, Carey CC, Dorweiler JE, Chandler VL (2002) A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing. Proc Natl Acad Sci USA 99:6130–6135
Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol 29:365–379
Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak G, Hao S, Liu B (2004) Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theor Appl Genet 109:200–209
Lo Schiavo F, Pitto L, Giuliano G, Torti G, Nutti Ronchi V, Marazziti D, Vergara MR, Orselli S, Terzi M (1989) DNA methylation of embryonic carrot cell culture and its variations as caused by mutation, differentiation, hormones and hypomethylating drugs. Theor Appl Genet 77:325–331
Luchniak P, Maluszynska J, Olszewska MJ (2002) Different DNA methylation pattern in A and B chromosomes of Crepis capillaris detected by in situ nick-translation. Comparison with molecular methods. Folia Histochem Cytobiol 40:325–330
Lund G, Ciceri P, Viotti A (1995a) Maternal-specific demethylation and expression of specific alleles of zein genes in the endosperm of Zea mays L. Plant J 8:571–581
Lund G, Messing J, Viotti A (1995b) Endosperm-specific demethylation and activation of specific alleles of α-tubulin genes of Zea mays L. Mol Gen Genet 246:716–722
Lund G, Lauria M, Guldberg P, Zaina S (2003) Duplication-dependent CG suppression of the seed storage protein genes of maize. Genetics 165:835–848
Luo S, Preuss D (2003) Strand-biased DNA methylation associated with centromeric regions in Arabidopsis. Proc Natl Acad Sci USA 100:11133–11138
Lyko F (2001) DNA methylation learns to fly. Trends Genet 17:169–172
Lyko F, Ramsahoye BH, Jaenisch R (2000) DNA methylation in Drosophila melanogaster. Nature 408:538–540
Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129:733–746
Mallory AC, Ely L, Smith TH, Marathe R, Anandalakshmi R, Fagard M, Vaucheret H, Pruss G, Bowman L, Vance VB (2001) HC-Pro suppression of transgene silencing eliminates the small RNAs but not transgene methylation or the mobile signal. Plant Cell 13:571–583
Marinitch DV, Vorobyev IA, Holmes JA, Zakharchenko NS, Dyachenko OV, Buryanov YI, Shevchuk TV (2004) Hypermethylation of 5′-region of the human calcitonin gene in leukemias: structural features and diagnostic significance. Biochemistry (Mosc) 69:340–349
Martienssen RA, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293:1070–1074
Mathieu O, Picard G, Tourmente S (2002a) Methylation of a euchromatin-heterochromatin transition region in Arabidopsis thaliana chromosome 5 left arm. Chromosome Res 10:455–466
Mathieu O, Yukawa Y, Sugiura M, Picard G, Tourmente S (2002b) 5S rRNA genes expression is not inhibited by DNA methylation in Arabidopsis. Plant J 29:313–323
Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJM (2004) Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 1677:129–141
Matzke MA, Mette MF, Matzke AJ (2000) Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates. Plant Mol Biol 43:401–415
Mazin AL, Vanyushin BF (1986) Incorporation of cytokinin (6-benzylaminopurine) in DNA of Tetrahymena pyriformis. Izv Akad Nauk SSSR Biol 1:122–124
Mazin AL, Gimadutdinov OA, Turkin SI, Burtseva NN, Vanyushin BF (1985) Nonenzymatic DNA methylation by S-adenosylmethionine resulting in formation of minor 5-methylcytosine and thymine from cytosine residues. Mol Biol (Mosk) 19:903–914
McClintock B (1967) Genetic systems regulating gene expression during development. Dev Biol Suppl 1:84–112
Melquist S, Bender J (2003) Transcription from an upstream promoter controls methylation signaling from an inverted repeat of endogenous genes in Arabidopsis. Genes Dev 17:2036–2047
Meng L, Bregitzer P, Zhang S, Lemaux PG (2003) Methylation of the exon/intron region in the Ubi1 promoter complex correlates with transgene silencing in barley. Plant Mol Biol 53:327–340
Mette MF, Aufsatz W, van der Winden J, Matzke MA, Matzke AJ (2000) Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J 19:5194–5201
Meyer P (1995) DNA methylation and transgene silencing in Petunia hybrida. Curr Top Microbiol Immunol 197:15–28
Meyer P (1999) The role of chromatin remodeling in transgene silencing and plant development. In vitro Cell Dev Biol Plant 35:29–36
Meyer P, Niedenhof I, ten Lohuis M (1994) Evidence for cytosine methylation of nonsymmetrical sequences in transgenic Petunia hybrida. EMBO J 13:2084–2088
Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212–214
Montgomery MK (2004) RNA interference: historical overview and significance. Methods Mol Biol 265:3–21
Morel J-B, Mourrain P, Beclin C, Vaucheret H (2000) DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis. Curr Biol 10:1591–1594
Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA, Vaucheret H (2000) Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 101:533–542
Muller A, Marins M, Kamisugi Y, Meyer P (2002) Analysis of hypermethylation in the RPS element suggests a signal function for short inverted repeats in de novo methylation. Plant Mol Biol 48:383–399
Nakano Y, Steward N, Sekine M, Kusano T, Sano H (2000) A tobacco NtMET1 cDNA encoding a DNA methyltransferase: molecular characterization and abnormal phenotypes of transgenic tobacco plants. Plant Cell Physiol 41:448–457
Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–389
Nelson M, Burbank DE, Van Etten JL (1998) Chlorella viruses encode multiple DNA methyltransferases. Biol Chem 379:423–428
Ngernprasirtsiri J, Akazawa T (1990) Modulation of DNA methylation and gene expression in cultured sycamore cells treated by hypomethylating base analog. Eur J Biochem 194:513–520
Ngernprasirtsiri J, Kobayashi H, Akazawa T (1988) DNA methylation as a mechanism of transcriptional regulation in nonphotosynthetic plastids in plant cells. Proc Natl Acad Sci USA 85:4750–4754
Nyce J (1991) Gene silencing in mammalian cells by direct incorporation of electroporated 5-methyl-2′-deoxycytidine 5′-triphosphate. Somat Cell Mol Genet 17:543–550
Oakeley EJ, Jost JP (1996) Non-symmetrical cytosine methylation in tobacco pollen DNA. Plant Mol Biol 31:927–930
Oakeley EJ, Poresta A, Jost JP (1997) Developmental changes in DNA methylation of the two tobacco pollen nuclei during maturation. Proc Natl Acad Sci USA 94:11721–11725
Pakhomova MV (1974) N6-dimethylaminopurine in DNA of algae species. Dokl Akad Nauk SSSR 214:1202–1205
Pakhomova MV, Zaitseva GN, Belozerskii AN (1968) The presence of 5-methylcytosine and 6-methylaminopurine in the composition of DNA in some algae. Dokl Akad Nauk SSSR 182:712–714
Palmgren G, Mattson O, Okkels FT (1991) Specific levels of DNA methylations in various tissues, cell lines, and cell types of Daucus carota. Plant Physiol 95:174–178
Papa CM, Springer NM, Muszynski MG, Meeley R, Kaeppler SM (2001) Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13:1919–1928
Paszkowski J, Whitham SA (2001) Gene silencing and DNA methylation processes. Curr Opin Plant Biol 4:123–129
Pelissier T, Wassenegger M (2000) A DNA target of 30 bp is sufficient for RNA-directed DNA methylation. RNA 6:55–65
Pelissier T, Thalmeir S, Kempe D, Sanger H-L, Wassenegger M (1999) Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucleic Acids Res 27:1625–1634
Pintor-Toro JA (1987) Adenine methylation in zein genes. Biochem Biophys Res Commun 147:1082–1087
Pitto L, Cernilogar F, Evangelista M, Lombardi L, Miarelli C, Rocchi P (2000) Characterization of carrot nuclear proteins that exhibit specific binding affinity towards conventional and non-conventional DNA methylation. Plant Mol Biol 44:659–673
Pradhan S, Adams RL (1995) Distinct CG and CNG DNA methyltransferases in Pisum sativum. Plant J 7:471–481
Pradhan S, Cummings M, Roberts RJ, Adams RLP (1998) Isolation, characterization and baculovirus-mediated expression of the cDNA encoding cytosine DNA methyltransferase from Pisum sativum. Nucleic Acids Res 26:1214–1222
Prakash AP, Kush A, Lakshmanan P, Kumar PP (2003) Cytosine methylation occurs in a CDC48 homologue and a MADS-box gene during adventitious shoot induction in Petunia leaf explants. J Exp Bot 54:1361–1371
Pratt K, Hattman S (1981) Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila. Mol Cell Biol 1:600–608
Probst AV, Fagard M, Proux F, Mourrain P, Boutet S, Earley K, Lawrence RJ, Pikaard CS, Murfett J, Furner I, Vaucheret H, Scheid OM (2004) Arabidopsis histone deacetylase HDA6 is required for maintenance of transcriptional gene silencing and determines nuclear organization of rDNA repeats. Plant Cell 16:1021–1034
Que Q, Zhang Y, Nelson M, Ropp S, Burbank DE, Van Etten JL (1997) Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases. Gene 190:237–244
Rabinowicz PD, Palmer LE, May BP, Hemann MT, Lowe SW, McCombie WR, Martienssen RA (2003) Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res 13:2658–2664
Rae PM, Spear BB (1978) Macronuclear DNA of the hypotrichous ciliate Oxytricha fallax. Proc Natl Acad Sci USA 75:4992–4996
Ramsahoye B, Biniszkiewicz D, Lyko F, Clark V, Bird A, Jaenisch R (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 97:5237–5242
Ratel D, Boisseau S, Davidson SM, Ballester B, Mathieu J, Morange M, Adamski D, Berger F, Benabid AL, Wion D (2001) The bacterial nucleoside N(6)-methyl-deoxyadenosine induces the differentiation of mammalian tumor cells. Biochem Biophys Res Commun 285:800–805
Razin A (1998) CpG methylation, chromatin structure, and gene silencing—a threeway connection. EMBO J 17:4905–4908
Razin A, Riggs AD (1980) DNA methylation and gene function. Science 210:604–610
Reyes EM, Camacho-Arroyo I, Nava G, Cerbon MA (1997) Differential methylation in steroid 5 alpha-reductase isozyme genes in epididymis, testis, and liver of the adult rat. J Androl 18:372–377
Richards EJ (1997) DNA methylation and plant development. Trends Genet 319:319–323
Riddle NC, Richards EJ (2002) The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162:355–363
Riggs CD, Chrispeels MJ (1999) The expression of phytohemagglutinin genes in Phaseolus vulgaris is associated with organ-specific DNA methylation patterns. Plant Mol Biol 14:629–633
Rogers J, Rogers SW (1995) Comparison of the effects of N6-methyl-deoxyadenosine and N5-methyldeoxycytosine on transcription from nuclear gene promoters in barley. Plant J 7:221–233
Rogers SD, Rogers ME, Saunders G, Holt G (1986) Isolation of mutants sensitive to 2-aminopurine and alkylating agents and evidence for the role of DNA methylation in Penicillium chrysogenum. Curr Genet 10:557–560
Rogers SW, Rogers JC (1992) The importance of DNA methylation for stability of foreign DNA in barley. Plant Mol Biol 18:945–961
Rojas MV, Galanti N (1990) DNA methylation in Trypanosoma cruzi. FEBS Lett 263:113–116
Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273:654–657
Ros F, Kunze R (2001) Regulation of activator/dissociation transposition by replication and DNA methylation. Genetics 157:1723–1733
Rossi V, Motto M, Pellegrini L (1997) Analysis of the methylation pattern of the maize Opaque-2(02) promoter and in vitro binding studies indicate that the O2 B-Zip protein and other endosperm factors can bind to methylated target sequences. J Biol Chem 272:13758–13765
Salomon R, Kaye AM (1970) Methylation of mouse DNA in vivo: di-and tripyrimidine sequences containing 5-methylcytosine. Biochim Biophys Acta 204:340–351
Sano H (2002) DNA methylation and Lamarckian inheritance. Proc Jpn Acad 78 Ser B:293–298
Saze H, Scheid OM, Paszkowski J (2003) Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34:65–69
Scebba F, Bernacchia G, De Bastiani M, Evangelista M, Cantoni RM, Cella R, Locci MT, Pitto L (2003) Arabidopsis MBD proteins show different binding specificities and nuclear localization. Plant Mol Biol 53:715–731
Schlappi M, Raina R, Fedoroff N (1994) Epigenetic regulation of the maize Spm transposable element: novel activation of a methylated promoter by TnpA. Cell 77:427–437
Scott RJ, Spielman M (2004) Epigenetics: imprinting in plants and mammals—the same but different? Curr Biol 14:R201–R203
Sheldon CC, Burn JE, Perez PP, Metzger J, Edwards JA, Peacock WJ, Dennis ES (1999) The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11:445–458
Sheldon CC, Finnegan EJ, Rouse DT, Tadege M, Bagnall DJ, Helliwell CA, Peacock WJ, Dennis ES (2000) The control of flowering by vernalization. Curr Opin Plant Biol 3:418–422
Sherman JD, Talbert LE (2002) Vernalization-induced changes of the DNA methylation pattern in winter wheat. Genome 45:253–260
Shorning BYu, Vanyushin BF (2001) Putative DNA-(amino)methyltransferases in eukaryotes. Biochemistry (Mosc) 66:753–762
Singer T, Yordan C, Martienssen RA (2001) Robertson’s mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene decrease in DNA methylation (DDM 1). Genes Dev 15:591–602
Siroky J, Castiglione MR, Vyskot B (1998) DNA methylation patterns of Melandrium album chromosomes. Chromosome Res 6:441–446
Sneider TW (1972) Methylation of mammalian deoxyribonucleic acid. III. Terminal versus internal location of 5-methylcytosine in oligodeoxyribonucleotides from Novikoff hepatoma cell deoxyribonucleic acid. J Biol Chem 247:2872–2875
Soppe WJJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21:6549–6559
Spielman M, Vinkenoog R, Scott RJ (2003) Genetic mechanisms of apomixis. Philos Trans R Soc Lond B Biol Sci 358:1095–1103
Staiger D, Kaulen H, Schell J (1989) A CACGTG motif of the Antirrhinum majus chalcone synthase promoter is recognized by an evolutionarily conserved nuclear protein. Proc Natl Acad Sci USA 86:6930–6934
Steimer A, Schob H, Grossniklaus U (2004) Epigenetic control of plant development: new layers of complexity. Curr Opin Plant Biol 7:11–19
Steward N, Kusano T, Sano H (2000) Expression of ZmMETI, a gene encoding a DNA methyltransferase from maize, is associated not only with DNA replication in actively proliferating cells, but also with altered DNA methylation status in cold-stressed quiescent cells. Nucleic Acids Res 28:3250–3259
Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H (2002) Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 277:37741–37746
Stokes T (2003) DNA-RNA-protein gang together in silence. Trends Plant Sci 8:53–55
Sturaro M, Viotti A (2001) Methylation of the Opaque2 box in zein genes is parent-dependent and affects O2 DNA binding activity in vitro. Plant Mol Biol 46:549–560
Sugimoto K, Takeda S, Hirochika H (2003) Transcriptional activation mediated by binding of a plant GATA-type zinc finger protein AGP1 to the AG-motif (AGATCCAA) of the wound-inducible Myb gene NtMyb2. Plant J 36:550–564
Sulimova GE, Vanyushin BF, Chvojka L, Fridrich A, Bulgakov R, Cherny B (1978) On the impossibility of the 5-methylcytosine and its nucleosides incorporation into DNA of higher plants. Biochemistry (Mosc) 43:240–245
Tamaru H, Selker EU (2001) Ahistone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414:277–283
Tang W, Leisner S (1998) Methylation of nonintegrated multiple copy DNA in plants. Biochem Biophys Res Commun 245:403–406
Tariq M, Paszkowski J (2004) DNA and histone methylation in plants. Trends Genet 20:244–251
Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci USA 100:8823–8827
ten Lohuis M, Galliano H, Heidmann I, Meyer P (1995a) Treatment with propionic and butyric acid enhances expression variegation and promoter methylation in plant transgenes. Biol Chem Hoppe Seyler 376:311–320
ten Lohuis M, Muller A, Heidmann I, Niedenhof I, Meyer P (1995b) A repetitive DNA fragment carrying a hot spot for de novo DNA methylation enhances expression variegation in tobacco and petunia. Plant J 8:919–932
Theiss G, Schleicher R, Schimpff-Weiland G, Follmann H (1987) DNA methylation in wheat. Purification and properties of DNA methyltransferase. Eur J Biochem 167:89–96
Tian L, Chen ZJ (2001) Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc Natl Acad Sci USA 98:200–205
Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S (2002) Genome-wide profiling of DNA methylation reveals transposon targets of chromomethylase3. Curr Biol 12:65–68
Toth M, Müller U, Doerfler W (1990) Establishment of de novo DNA methylation patterns. Transcription factor binding and deoxycytidine methylation at CpG and non-CpG sequences in an integrated adenovirus promoter. J Mol Biol 214:673–683
Unger G, Venner H (1966) Nachweis von Minoritätsbasen in Sperma Desoxyribonucleinsäure. Hoppe Seylers Z Physiol Chem 344:280–282
Vaistij FE, Jones L, Baulcombe DC (2002) Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase. Plant Cell 14:857–867
Van Blokland R, Ross S, Corrado G, Scollan C, Meyer P (1998) Developmental abnormalities associated with deoxyadenosine methylation in transgenic tobacco. Plant J 15:543–551
Vanyushin BF (1984) Replicative DNA methylation in animals and higher plants. Curr Top Microbiol Immunol 108:99–114
Vanyushin BF, Belozersky AN (1959) Nucleotide composition of deoxyribonucleic acids in higher plants. Dokl Akad Nauk SSSR 129:944–947
Vanyushin BF, Kirnos MD (1974) The nucleotide composition and pyrimidine clusters in DNA from beef heart mitochondria. FEBS Lett 39:195–199
Vanyushin BF, Kirnos MD (1988) DNA methylation in plants. Gene 74:117–121
Vanyushin BF, Belozersky AN, Kokurina NA, Kadirova DX (1968) 5-Methylcytosine and 6-methylaminopurine in bacterial DNA. Nature 218:1066–1067
Vanyushin BF, Tkacheva SG, Belozersky AN (1970) Rare bases in animal DNA. Nature 225:948–949
Vanyushin BF, Kadyrova DK, Karimov KK, Belozersky AN (1971)Minor bases in DNA of higher plants. Biochemistry (Mosc) 36:1251–1258
Vanyushin BF, Nemirovsky LE, Klimenko VV, Vasiliev VK, Belozersky AN (1973) The 5-methylcytosine in DNA of rats. Tissue and age specificity and the changes-induced by hydrocortisone and other agents. Gerontologia 19:138–152
Vanyushin BF, Singkh SS, Sonvol G (1979) Changes in DNA methylation in alfalfa plants infected with Cuscuta and tissue differences in DNA methylation of the parasite plants. Biochemistry (Mosc) 44:864–867
Vanyushin BF, Aleksandrushkina NI, Kirnos MD (1988) N6-methyladenine in mitochondrial DNA of higher plants. FEBS Lett 223:397–399
Vanyushin BF, Sevostyanova SS, Kirnos MD, Saidova NS (1990) An increase in the protein content in wheat seeds induced by inhibitor of DNA methylation, 5-azacytidine. Izv Akad Nauk SSSR Biol 1:75–83
Vanyushin BF, Shorning BYu, Seredina AV, Aleksandrushkina NI (2002) The effects of phytohormones and 5-azacytidine on apoptosis in etiolated wheat seedlings. Russ J Plant Physiol 49:501–506
Vanyushin BF, Bakeeva LE, Zamyatnina VA, Aleksandrushkina NI (2004) Apoptosis in plants: specific features of plant apoptotic cells and effect of various factors and agents. Int Rev Cytol 233:135–179
Vaucheret H, Fagard M (2001) Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet 17:29–35
Vielle-Calzada J-P, Thomas J, Spillane C, Coluccio A, Hoeppner MA, Grossniklaus U (1999) Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM 1 activity. Genes Dev 13:2971–2982
Vinkenoog R, Bushell C, Spielman M, Adams S, Dickinson HG, Scott RJ (2003) Genomic imprinting and endosperm development in flowering plants. Mol Biotechnol 25:149–184
Vlasova TI, Demidenko TI, Kirnos MD, Vanyushin BF (1995) In vitro DNA methylation by wheat nuclear cytosine DNA-methyltransferase: effect of phytohormones. Gene 157:279–281
Vlasova TI, Kirnos MD, Vanyushin BF (1996) Cytosine DNA methyltransferase from wheat seedlings. Biochemistry (Mosc) 61:774–780
Vogt U, Pelissier T, Putz A, Razvi F, Fischer R, Wassenegger M (2004) Viroid-induced RNA silencing of GFP-viroid fusion transgenes does not induce extensive spreading of methylation or transitive silencing. Plant J 38:107–118
Wada Y, Ohya H, Yamaguchi Y, Koizumi N, Sano H (2003) Preferential de novo methylation of cytosine residues in non-CpG sequences by a domains rearranged DNA methyltransferase from tobacco plants. J Biol Chem 278:42386–42393
Wang L, Heinlein M, Kunze R (1996) Methylation pattern of Activator transposase binding sites in maize endosperm. Plant Cell 8:747–758
Wang MB, Wesley SV, Finnegan EJ, Smith NA, Waterhouse PM (2001) Replicating satellite RNA induces sequence-specific DNA methylation and truncated transcripts in plants. RNA 7:16–28
Wassenegger M (2000) RNA-directed DNA methylation. Plant Mol Biol 43:203–220
Wassenegger M (2002) Gene silencing. Int Rev Cytol 219:61–113
Wassenegger M, Heimes S, Riedel L, Sanger HL (1994) RNA directed de novo methylation of genomic sequences in plants. Cell 76:567–576
Woodcock DM, Crowther PJ, Diver WP (1987) The majority of methylated deoxycytidines in human DNA are not in the CpG dinucleotide. Biochem Biophys Res Commun 145:888–894
Xiao W, Gehring M, Choi Y, Margossian L, Pu H, Harada JJ, Goldberg RB, Pennell RI, Fischer RL (2003) Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev Cell 5:891–901
Xiong LZ, Xu CG, Saghai Maroof MA, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Gen Genet 261:439–446
Yuan Y, SanMiguel PJ, Bennetzen JL (2002) Methylation-spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays. Genome Res 12:1345–1349
Zaitseva GN, Kolesnikov AA, Iatsenko IA, Kirnos MD, Vaniushin BF (1974) Primary structure of DNA from Crithidia oncopelti kinetoplasts. Dokl Akad Nauk SSSR 219:243–245
Zemach A, Grafi G (2003) Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins. Plant J 34:565–572
Zhang D, Ehrilch KC, Supakar PC, Ehrlich M (1989) A plant DNA-binding protein that recognizes 5-methylcytosine residues. Mol Cell Biol 9:1351–1356
Zhang Z, Chen CQ, Manev H (2004) DNA methylation as an epigenetic regulator of neural 5-lipoxygenase expression: evidence in human NT2 and NT2-N cells. J Neurochem 88:1424–1430
Zhu CM, Henney HR Jr (1990) DNA methylation pattern during the encystment of Physarum flavicomum. Biochem Cell Biol 68:944–948
Zilberman D, Cao X, Jacobsen SE (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science 299:716–719
Zluvova J, Janousek B, Vyskot B (2001) Immunohistochemical study of DNA methylation dynamics during plant development. J Exp Bot 52:2265–2273
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Vanyushin, B.F. (2006). DNA Methylation in Plants. In: Doerfler, W., Böhm, P. (eds) DNA Methylation: Basic Mechanisms. Current Topics in Microbiology and Immunology, vol 301. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-31390-7_4
Download citation
DOI: https://doi.org/10.1007/3-540-31390-7_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29114-5
Online ISBN: 978-3-540-31390-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)