DNA methylation in health and disease (original) (raw)
Lei, H. et al. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Development122, 3195 –3205 (1996). CASPubMed Google Scholar
Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell69, 915–926 (1992). ArticleCASPubMed Google Scholar
Okano, M., Bell, D. W., Haber, D. A. & Li, W. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell99, 247–257 (1999). References 2 and 3 describe the effects of loss ofDnmt1, Dnmt3aandDnmt3bon mouse development. CASPubMed Google Scholar
Bird, A. P. Gene number, noise reduction and biological complexity. Trends Genet.11, 94–99 ( 1995). CASPubMed Google Scholar
Steinbach, O. C., Wolffe, A. P. & Rupp, R. A. Somatic linker histones cause loss of mesodermal competence in Xenopus. Nature389, 395–399 (1997). CASPubMed Google Scholar
Mannervik, M., Nibu, Y., Zhang, H. & Levine, M. Transcriptional coregulators in development. Science284, 606–609 (1999). CASPubMed Google Scholar
Baylin, S. B., Herman, J. G., Herman, J. R., Vertino, P. M. & Issa, J.-P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer Res.72, 141–196 (1998). CASPubMed Google Scholar
Jones, P. A. & Laird, P. W. Cancer epigenetics comes of age . Nature Genet.21, 163– 166 (1999).References 7 and 8 are good reviews on the roles of DNA methylation in cancer. CASPubMed Google Scholar
Jaenisch, R. DNA methylation and imprinting: why bother? Trends Genet.13, 323–329 (1997). CASPubMed Google Scholar
Jirtle, J. L., Sander, M. & Barrett, J. C. Genomic imprinting and environmental disease susceptibility . Environ. Health Perspect.108, 271– 278 (2000). CASPubMedPubMed Central Google Scholar
Tyko, B. & Ashkenas, J. Epigenetics and its role in disease . J. Clin. Invest.105, 245– 246 (2000). Google Scholar
Post, W. S. et al. Methylation of the estrogen receptor gene is associated with aging and atherosclerosis in the cardiovascular system. Cardiovasc. Res.43, 985–991 ( 1999). CASPubMed Google Scholar
Cooper, D. N. & Krawczak, M. Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum. Genet.83, 181–188 (1989). CASPubMed Google Scholar
Bird, A., Taggart, M., Frommer, M., Miller, O. J. & Macleod, D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell10, 91–99 (1985). Google Scholar
Antequera, F. & Bird, A. Number of CpG islands and genes in human and mouse. Proc. Natl Acad. Sci. USA90, 11995–11999 (1993). CASPubMedPubMed Central Google Scholar
Tazi, J. & Bird, A. Alternative chromatin structure at CpG islands. Cell60, 909– 920 (1990). CASPubMed Google Scholar
Jiricny, J. in Cancer Surveys: Genetic Instability in Cancer Vol. 28 47–68 (Imperial Cancer Research Fund, 1996). Google Scholar
Cooper, D. N. & Youssoufian, H. The CpG dinucleotide and human genetic disease. Hum. Genet.78, 151– 155 (1988). CASPubMed Google Scholar
Rideout, W. M. I., Coetzee, G. A., Olumi, A. F. & Jones, P. A. 5-methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science249, 1288– 1290 (1990). CASPubMed Google Scholar
Greenblatt, M. S., Bennett, W. P., Hollstein, M. & Harris, C. C. Mutations in the p53 tumor suppressor gene: Clues to cancer etiology and molecular pathogenesis. Cancer Res.54, 4855– 4878 (1994). CASPubMed Google Scholar
Bestor, T., Laudano, A., Mattaliano, R. & Ingram, V. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells . J. Mol. Biol.203, 971– 983 (1988). CASPubMed Google Scholar
Pradhan, S., Bacolla, A., Wells, R. D. & Roberts, R. J. Recombinant human DNA (cytosine-5) methyltransferase I. Expression, purification, and comparison of de novo and maintenance methylation. J. Biol. Chem.274, 33002–33010 (1999). CASPubMed Google Scholar
Pradhan, S. et al. Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase. Nucleic Acids Res.25, 4666–4673 (1997). CASPubMedPubMed Central Google Scholar
Robertson, K. D. et al. The human DNA methyltransferases (DNMTs) 1, 3a, and 3b: Coordinate mRNA expression in normal tissues and overexpression in tumors. Nucleic Acids Res.27, 2291–2298 (1999). ArticleCASPubMedPubMed Central Google Scholar
Leonhardt, H., Page, A. W., Weier, H. & Bestor, T. H. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell71, 865–873 (1992). CASPubMed Google Scholar
Chuang, L. S.-H. et al. Human DNA-(cytosine-5) methyltransferase-PCNA complex is a target for p21_Waf1_. Science277 , 1996–2000 (1997). CASPubMed Google Scholar
Li, E., Beard, C. & Jaenisch, R. Role for DNA methylation in genomic imprinting. Nature366, 362–365 ( 1993). CASPubMed Google Scholar
Beard, C., Li, E. & Jaenisch, R. Loss of methylation activates Xist in somatic but not in embryonic cells. Genes Dev.9, 2325– 2334 (1995). CASPubMed Google Scholar
Hung, M.-S. et al. Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases. Proc. Natl Acad. Sci. USA96, 11940–11945 (1999). CASPubMedPubMed Central Google Scholar
Tweedie, S. et al. Vestiges of DNA methylation system in Drosophila melanogaster . Nature Genet.23, 389– 390 (1999). CASPubMed Google Scholar
Okano, M., Xie, S. & Li, E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nature Genet.19, 219 –220 (1998). CASPubMed Google Scholar
Cao, X. et al. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl Acad. Sci. USA97 , 4979–4984 (2000). CASPubMedPubMed Central Google Scholar
Lyko, L. et al. Mammalian (cytosine-5) methyltransferases cause genomic DNA methylation and lethality in Drosophila. Nature Genet.23, 363–366 (1999). CASPubMed Google Scholar
Vertino, P. M., Yen, R.-W. C., Gao, J. & Baylin, S. B. De novo methylation of CpG island sequences in human fibroblasts overexpressing DNA (cytosine-5)-methyltransferase . Mol. Cell. Biol.16, 4555– 4565 (1996).This paper uniquely describes the use of somatic cell knockout technology to delete theDNMT1gene in a cancer cell line. CASPubMedPubMed Central Google Scholar
Rhee, I. et al. CpG methylation is maintained in human cancer cells lacking DNMT1 . Nature404, 1003–1007 (2000). CASPubMed Google Scholar
Robertson, K. D. et al. DNMT1 forms a complex with Rb, E2F1, and HDAC1 and represses transcription from E2F-responsive promoters. Nature Genet.25, 338–342 (2000). CASPubMed Google Scholar
Roundtree, M. R., Bachman, K. E. & Baylin, S. B. DNMT1 binds HDAC2 and a new co-repressor DMAP1, to form a complex at replication foci. Nature Genet.25 , 269–277 (2000). Google Scholar
Yoder, J. A., Walsh, C. P. & Bestor, T. H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet.13, 335– 340 (1997). CASPubMed Google Scholar
Colot, V. & Rossignol, J.-L. Eukaryotic DNA methylation as an evolutionary device. BioEssays21, 402–411 (1999). CASPubMed Google Scholar
Montagna, M. et al. Identification of a 3 kb Alu-mediated BRCA1 gene rearrangement in two breast/ovarian cancer families. Oncogene18, 4160–4165 (1999). CASPubMed Google Scholar
Kazazian, J. H. H. & Moran, J. V. The impact of L1 retrotransposons on the human genome. Nature Genet.19, 19–24 (1998). CASPubMed Google Scholar
Kochanek, S., Renz, D. & Doerfler, W. Transcriptional silencing of human Alu sequences and inhibition of protein binding in the B box regulatory elements by 5′-CG-3′ methylation. FEBS Lett.360, 115– 120 (1995). CASPubMed Google Scholar
Chen, R. Z., Pettersson, U., Beard, C., Jackson-Grusby, L. & Jaenisch, R. DNA hypomethylation leads to elevated mutation rates. Nature395, 89– 93 (1998). ArticleCASPubMed Google Scholar
Walsh, C. P., Chaillet, J. R. & Bestor, T. H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nature Genet.20, 116–117 (1998). CASPubMed Google Scholar
Waugh-O'Neill, R. J., O'Neill, M. J. & Marshall-Graves, J. A. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid . Nature393, 68–72 (1988). Google Scholar
Flori, A. R., Lower, R., Schmitz-Drager, B. J. & Schulz, W. A. DNA methylation and expression of LINE-1 and HERV-K provirus sequences in urothelial and renal cell carcinomas. Br. J. Cancer80, 1312–1321 (1999). Google Scholar
Grassi, M., Girault, J. M., Wang, W. P., Thiery, J. P. & Jouanneau, J. Metastatic rat carcinoma cells express a new retrotransposon. Gene233, 59–66 (1999). CASPubMed Google Scholar
Puget, N. et al. A 1-kb Alu-mediated germ-line deletion removing BRCA1 exon 17. Cancer Res.57, 828– 831 (1997). CASPubMed Google Scholar
Rouyer, F., Simmler, M. C., Page, D. & Weissenbach, J. A sex chromosome rearrangement in a human XX male caused by Alu-Alu recombination. Cell51, 417–425 ( 1987). CASPubMed Google Scholar
Small, K., Iber, J. & Warren, S. T. Emerin deletion reveals a common X chromosome inversion mediated by inverted repeats. Nature Genet.16, 96–99 (1997). CASPubMed Google Scholar
Maloisel, L. & Rossignol, J.-L. Suppression of crossing-over by DNA methylation in Ascobolus. Genes Dev.12, 1381–1389 (1998). CASPubMedPubMed Central Google Scholar
Hsieh, C.-L. & Lieber, M. R. CpG methylated minichromosomes become inaccessible for V(D)J recombination after undergoing replication. EMBO J.11, 3115–325 ( 1992). Google Scholar
Paldi, A., Gyapay, G. & Jami, J. Imprinted chromosomal regions of the human genome display sex-specific meiotic recombination frequencies. Curr. Biol.5, 1030–1035 (1995). CASPubMed Google Scholar
Miniou, P. et al. Abnormal methylation pattern in constitutive and facultative (X inactive chromosome) heterochromatin of ICF patients. Hum. Mol. Genet.3, 2093–2102 ( 1994). CASPubMed Google Scholar
Ji, W. et al. DNA demethylation and pericentromeric rearrangements of chromosome 1. Mutat. Res.379, 33– 41 (1997). CASPubMed Google Scholar
Jones, P. L. et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nature Genet.19, 187– 191 (1998). CASPubMed Google Scholar
Nan, X. et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 invloves a histone deacetylase complex. Nature393, 386–389 (1998).References 56 and 57 were the first reports to link DNA methylation to methyl-CpG binding proteins and chromatin-remodelling factors, such as histone deacetylase. CASPubMed Google Scholar
Tate, P. H. & Bird, A. P. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev.3, 226–231 (1993). CASPubMed Google Scholar
Lewis, J. D. et al. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell69, 905–914 (1992). CASPubMed Google Scholar
Wakefield, R. I. D. et al. The solution structure of the domain from MeCP2 that binds to methylated DNA. J. Mol. Biol.291, 1055 –1065 (1999). CASPubMed Google Scholar
Nan, X., Campoy, F. J. & Bird, A. MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell88, 471 –481 (1997).This paper was the first to report that Rett syndrome was associated with mutations in theMeCP2gene. CASPubMed Google Scholar
Amir, R. E. et al. Rett syndrome is caused by mutations in X-linked MECP2 , encoding methyl-CpG-binding protein. Nature Genet.23, 185–188 (1999). CASPubMed Google Scholar
Kaludov, N. & Wolffe, A. P. MeCP2 driven transcriptional repression in vitro: selectivity for methylated DNA, action at a distance and contacts with the basal transcription machinery. Nucleic Acids Res.28, 1921–1928 (2000). CASPubMedPubMed Central Google Scholar
Nan, X., Tate, P., Li, E. & Bird, A. DNA methylation specifies chromosomal localization of MeCP2. Mol. Cell. Biol.10, 414–421 (1996). Google Scholar
Chandler, S. P., Guschin, D., Landsberger, N. & Wolffe, A. P. The methyl CpG binding transcriptional repressor MeCP2 stably associates with nucleosomal DNA. Biochemistry38, 7008– 7018 (1999). CASPubMed Google Scholar
Buschhausen, G., Wittig, B., Graessmann, M. & Graessmann, A. Chromatin structure is required to block transcription from the methylated herpes simplex virus thymidine kinase gene. Proc. Natl Acad. Sci. USA84, 1177–1181 ( 1986). Google Scholar
Kass, S. U., Landsberger, N. & Wolffe, A. P. DNA methylation directs a time-dependent repression of transcription initiation. Curr. Biol.7, 157–165 (1997). CASPubMed Google Scholar
Wade, P. A. et al. The Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nature Genet.23, 62–66 (1999). CASPubMed Google Scholar
Ng, H.-H. et al. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nature Genet.23, 58 –61 (1999). CASPubMed Google Scholar
Tse, C., Sera, T., Wolffe, A. P. & Hansen, J. C. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol. Cell. Biol.18, 4629–4638 (1998). CASPubMedPubMed Central Google Scholar
Ng, H.-H., Jeppesen, P. & Bird, A. Active repression of methylated genes by the chromosomal protein MBD1. Mol. Cell. Biol.20, 1394– 1406 (2000). CASPubMedPubMed Central Google Scholar
Fujita, N. et al. Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms. Mol. Cell. Biol.19, 6415–6426 (1999). CASPubMedPubMed Central Google Scholar
Fuks, F., Bergers, W. A., Brehm, A., Hughes-Davies, L. & Kouzarides, T. DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nature Genet.24 , 88–91 (2000). CASPubMed Google Scholar
Gibbons, R. J. et al. Mutations in ATRX, encoding a SWI/SNF-like protein, cause diverse changes in the patterns of DNA methylation. Nature Genet.24, 368–371 ( 2000). CASPubMed Google Scholar
Jeddeloh, J. A., Stokes, T. L. & Richards, E. J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nature Genet.22, 94– 97 (1999). CASPubMed Google Scholar
Goto, K. et al. Expression of DNA methyltransferase gene in mature and immature neurons as well as proliferating cells in mice. Differentiation56, 39–44 ( 1993). Google Scholar
Endres, M. et al. DNA methyltransferase contributes to delayed ischemic brain injury. J. Neurosci.20, 3175– 3181 (2000). CASPubMedPubMed Central Google Scholar
Smeets, D. F. C. M. et al. ICF syndrome: a new case and review of the literature. Hum. Genet.94, 240–246 (1994). CASPubMed Google Scholar
Franceschini, P. et al. Variability of clinical and immunological phenotype in immunodeficiency-centromeric instability-facial anamolies syndrome. Eur. J. Pediatr.154, 840–846 (1995). CASPubMed Google Scholar
Tagarro, I., Fernandez-Peralta, A. M. & Gonzales-Aguilera, J. J. Chromosomal localization of human satellites 2 and 3 by FISH method using oligonucleotides as probes. Hum. Genet.93, 383–388 ( 1994). CASPubMed Google Scholar
Jeanpierre, M. et al. An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome. Hum. Mol. Genet.2 , 731–735 (1993). CASPubMed Google Scholar
Kondo, T. et al. Whole-genome methylation scan in ICF syndrome: hypomethylation of non-satellite DNA repeats D4Z4 and NBL2. Hum. Mol. Genet.9, 597–604 ( 2000). CASPubMed Google Scholar
Xu, G.-L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature402 , 187–191 (1999). CASPubMed Google Scholar
Hansen, R. S. et al. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc. Natl Acad. Sci. USA96, 14412–14417 (1999). CASPubMedPubMed Central Google Scholar
Xie, S. et al. Cloning, expression and chromosome locations of the human DNMT3 gene family. Gene236, 87– 95 (1999).References 83–85 were the first to report that ICF syndrome is associated with mutations in theDNMT3Bgene. CASPubMed Google Scholar
Wijmenga, C. et al. Localization of the ICF syndrome to chromosome 20 by heterozygosity mapping. Am. J. Hum. Genet.63, 803– 809 (1998). CASPubMedPubMed Central Google Scholar
Hagberg, B., Aicardi, J., Dias, K. & Ramos, O. A progressive syndrome of autism, dementia, ataxia, and loss of purposeful hand use in girls: Rett's syndrome: report of 35 cases. Ann. Neurol.14, 471–479 (1983). CASPubMed Google Scholar
Wan, M. et al. Rett syndrome and beyond: recurrent spontaneous familial MECP2 mutations at CpG hotspots. Am. J. Hum. Genet.65, 1520–1529 (2000). Google Scholar
Ballestar, E., Yusufzai, T. M. & Wolffe, A. P. The effects of Rett syndrome mutations of the methyl-CpG binding domain of the transcriptional repressor MeCP2 on selectivity for association with methylated DNA. Biochemistry39, 7100 –7106 (2000). CASPubMed Google Scholar
Tate, P., Skarnes, W. & Bird, A. The methyl-CpG binding protein MeCP2 is essential for embryonic development in the mouse. Nature Genet.12 , 205–208 (1996). CASPubMed Google Scholar
Willard, H. F. & Hendrich, B. D. Breaking the silence in Rett syndrome. Nature Genet.23, 127–128 (1999). CASPubMed Google Scholar
Bird, A. & Tweedie, S. Transcriptional noise and the evolution of gene number. Phil. Trans. R. Soc. Lond.349, 249–253 (1995). CAS Google Scholar
Warren, S. T. & Nelson, D. L. Trinucleotide repeat expansions in neurological disease. Curr. Opin. Neurobiol.3, 752–759 (1993). CASPubMed Google Scholar
Kremer, E. J. et al. Mapping of DNA instability at the fragile X to a trinucleotide repeat sequence p(CCG)n. Science252, 1711 –1714 (1991). CASPubMed Google Scholar
Oberle, I. et al. Instability of a 550-base pair segment and abnormal methylation in Fragile X Syndrome. Science252, 1097 –1102 (1991).References 94 and 95 were among the first to show that lack of expression of theFMR1gene was associated with abnormal expansion and methylation of a trinucleotide repeat. CASPubMed Google Scholar
Coffee, B., Zhang, F., Warren, S. T. & Reines, D. Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells . Nature Genet.22, 98– 101 (1999). CASPubMed Google Scholar
Fu, Y. H. et al. Variation of the CGG repeat at the Fragile X site results in genetic instability: Resolution of the Sherman paradox. Cell67, 1047–1058 (1991). CASPubMed Google Scholar
Smith, S. S., Laayoun, A., Lingeman, R. G., Baker, D. J. & Riley, J. Hypermethylation of telomere-like foldbacks at codon 12 of the human c-Ha ras gene and the trinucleotide repeat of the FMR-1 gene of fragile X. J. Mol. Biol.243, 143–151 (1994). CASPubMed Google Scholar
Feng, Y. et al. FMRP associates with polyribosomes as an mRNP, and the 1304N mutation of severe fragile X syndrome abolishes this association. Mol. Cell1, 109–118 ( 1997). CASPubMed Google Scholar
Hendrich, B. & Bird, A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol.10, 6538–6547 ( 1998). Google Scholar
Hornstra, I. K., Nelson, D. L., Warren, S. T. & Yang, T. P. High resolution methylation analysis of the FMR1 gene trinucleotide repeat region in fragile X syndrome. Hum. Mol. Genet.2, 1659–1665 (1993). CASPubMed Google Scholar