Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks (original) (raw)
Agius F, Kapoor A, Zhu JK (2006) Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci USA 103:11796–11801 ArticlePubMedCAS Google Scholar
Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657 ArticlePubMed Google Scholar
Bender J (2004) DNA methylation and epigenetics. Annu Rev Plant Physiol Plant Mol Biol 55:41–68 CAS Google Scholar
Boyko A, Kovalchuk I (2008) Epigenetic control of plant stress response. Environ Mol Mutagen 49:61–72 ArticlePubMedCAS Google Scholar
Casadesus J, Low D (2006) Epigenetic gene regulation in the bacterial world. Microbiol Mol Biol Rev 70:830–856 ArticlePubMedCAS Google Scholar
Chan SW, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351–360 ArticlePubMedCAS Google Scholar
Choi C, Sano H (2007) Identification of tobacco genes encoding proteins possessing removal activity of 5-methylcytosines. Plant Biotechnology 24:339–344 CAS Google Scholar
Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL (2002) DEMETER, a DNA glycosylase domain protein, Is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110:33–42 ArticlePubMedCAS Google Scholar
Colot V, Rossignol JL (1999) Eukaryotic DNA methylation as an evolutionary device. Bioessays 21:402–411 ArticlePubMedCAS Google Scholar
Esteller M (2005) Aberrant DNA methylation as a cancer-inducing mechanism. Annu Rev Pharmacol Toxicol 45:629–656 ArticlePubMedCAS Google Scholar
Finnegan EJ, Genger RK, Peacock WJ, Dennis ES (1998) DNA methylation in plants. Annu Rev Plant Physiol Plant Mol Biol 49:223–247 ArticlePubMedCAS Google Scholar
Frank D, Keshet I, Shani M, Levine A, Razin A, Cedar H (1991) Demethylation of CpG islands in embryonic cells. Nature 351:239–241 ArticlePubMedCAS Google Scholar
Gallais R, Demay F, Barath P, Finot L, Jurkowska R, Le Guevel R, Gay F, Jeltsch A, Metivier R, Salbert G (2007) Dnmt 3a and 3b associate with the nuclear orphan receptor COUP-TFI during gene activation. Mol Endocrinol 21:2085–2098 ArticlePubMedCAS Google Scholar
Garcia-Ortiz MV, Ariza RR, Roldan-Arjona T (2001) An OGG1 orthologue encoding a functional 8-oxoguanine DNA glycosylase/lyase in Arabidopsis thaliana. Plant Mol Biol 47:795–804 ArticlePubMedCAS Google Scholar
Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, Goldberg RB, Fischer RL (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124:495–506 ArticlePubMedCAS Google Scholar
Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481–514 ArticlePubMedCAS Google Scholar
Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK (2002) ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111:803–814 ArticlePubMedCAS Google Scholar
Hardeland U, Bentele M, Jiricny J, Schar P (2003) The versatile thymine DNA-glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs. Nucleic Acids Res 31:2261–2271 ArticlePubMedCAS Google Scholar
Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A (1999) The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401:301–304 ArticlePubMedCAS Google Scholar
Holliday R, Pugh JE (1975) DNA modification mechanisms and gene activity during development. Science 187:226–232 ArticlePubMedCAS Google Scholar
Jost JP, Siegmann M, Sun L, Leung R (1995) Mechanisms of DNA demethylation in chicken embryos. Purification and properties of a 5-methylcytosine-DNA glycosylase. J Biol Chem 270:9734–9739 ArticlePubMedCAS Google Scholar
Kieber JJ, Rothenberg M, Roman G, Feldmann KA, Ecker JR (1993) CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell 72:427–441 ArticlePubMedCAS Google Scholar
Kress C, Thomassin H, Grange T (2001) Local DNA demethylation in vertebrates: how could it be performed and targeted? FEBS Lett 494:135–140 ArticlePubMedCAS Google Scholar
Li E (2002) Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 3:662–673 ArticlePubMedCAS Google Scholar
Li YQ, Zhou PZ, Zheng XD, Walsh CP, Xu GL (2007) Association of Dnmt3a and thymine DNA glycosylase links DNA methylation with base-excision repair. Nucleic Acids Res 35:390–400 ArticlePubMedCAS Google Scholar
Lippman Z, May B, Yordan C, Singer T, Martienssen R (2003) Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol 1: E67 ArticlePubMed Google Scholar
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔC T method. Methods 25:402–408 ArticlePubMedCAS Google Scholar
Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marin MI, Martinez-Macias MI, Ariza RR, Roldan-Arjona T (2006) DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci USA 103:6853–6858 ArticlePubMedCAS Google Scholar
Neddermann P, Gallinari P, Lettieri T, Schmid D, Truong O, Hsuan JJ, Wiebauer K, Jiricny J (1996) Cloning and expression of human G/T mismatch-specific thymine-DNA glycosylase. J Biol Chem 271:12767–12774 ArticlePubMedCAS Google Scholar
Penterman J, Uzawa R, Fischer RL (2007a) Genetic interactions between DNA demethylation and methylation in Arabidopsis. Plant Physiol 145:1549–1557 ArticlePubMedCAS Google Scholar
Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (2007b) DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104:6752–6757 ArticlePubMedCAS Google Scholar
Riggs AD (1975) X inactivation, differentiation, and DNA methylation. Cytogenet Cell Genet 14:9–25 ArticlePubMedCAS Google Scholar
Roldan-Arjona T, Garcia-Ortiz MV, Ruiz-Rubio M, Ariza RR (2000) cDNA cloning, expression and functional characterization of an Arabidopsis thaliana homologue of the Escherichia coli DNA repair enzyme endonuclease III. Plant Mol Biol 44:43–52 ArticlePubMedCAS Google Scholar
Shi L, Kent R, Bence N, Britt AB (1997) Developmental expression of a DNA repair gene in Arabidopsis. Mutat Res 384:145–156 PubMedCAS Google Scholar
Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters AJ (2000) The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6:791–802 ArticlePubMedCAS Google Scholar
Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA (1995) Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J 14:4108–4120 PubMedCAS Google Scholar
Yoder JA, Walsh CP, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13:335–340 ArticlePubMedCAS Google Scholar
Zhu B, Zheng Y, Angliker H, Schwarz S, Thiry S, Siegmann M, Jost JP (2000a) 5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequence. Nucleic Acids Res 28:4157–4165 ArticlePubMedCAS Google Scholar
Zhu B, Zheng Y, Hess D, Angliker H, Schwarz S, Siegmann M, Thiry S, Jost JP (2000b) 5-methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complex. Proc Natl Acad Sci USA 97:5135–5139 ArticlePubMedCAS Google Scholar
Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK (2007) The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17:54–59 ArticlePubMedCAS Google Scholar