- Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
Article CAS Google Scholar
- Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33 Suppl., 245–254 (2003).
Article CAS Google Scholar
- Li, E., Bestor, T.H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).
Article CAS Google Scholar
- Reik, W. & Walter, J. Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2, 21–32 (2001).
Article CAS Google Scholar
- Jones, P.A. & Baylin, S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415–428 (2002).
Article CAS Google Scholar
- Feinberg, A.P. & Vogelstein, B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301, 89–92 (1983).
Article CAS Google Scholar
- Fazzari, M.J. & Greally, J.M. Epigenomics: beyond CpG islands. Nat. Rev. Genet. 5, 446–455 (2004).
Article CAS Google Scholar
- Rakyan, V.K. et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol. 2, e405 (2004).
Article Google Scholar
- Weber, M. et al. Extensive tissue-specific variation of allelic methylation in the Igf2 gene during mouse fetal development: relation to expression and imprinting. Mech. Dev. 101, 133–141 (2001).
Article CAS Google Scholar
- Tremblay, K.D., Duran, K.L. & Bartolomei, M.S. A 5′ 2-kilobase-pair region of the imprinted mouse H19 gene exhibits exclusive paternal methylation throughout development. Mol. Cell. Biol. 17, 4322–4329 (1997).
Article CAS Google Scholar
- Ishkanian, A.S. et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 36, 299–303 (2004).
Article CAS Google Scholar
- Migeon, B.R. X-chromosome inactivation: molecular mechanisms and genetic consequences. Trends Genet. 10, 230–235 (1994).
Article CAS Google Scholar
- Bernardino, J., Lombard, M., Niveleau, A. & Dutrillaux, B. Common methylation characteristics of sex chromosomes in somatic and germ cells from mouse, lemur and human. Chromosome Res. 8, 513–525 (2000).
Article CAS Google Scholar
- Viegas-Pequignot, E., Dutrillaux, B. & Thomas, G. Inactive X chromosome has the highest concentration of unmethylated Hha I sites. Proc. Natl. Acad. Sci. USA 85, 7657–7660 (1988).
Article CAS Google Scholar
- Giacalone, J., Friedes, J. & Francke, U. A novel GC-rich human macrosatellite VNTR in Xq24 is differentially methylated on active and inactive X chromosomes. Nat. Genet. 1, 137–143 (1992).
Article CAS Google Scholar
- Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
Article CAS Google Scholar
- Cross, S.H., Charlton, J.A., Nan, X. & Bird, A.P. Purification of CpG islands using a methylated DNA binding column. Nat. Genet. 6, 236–244 (1994).
Article CAS Google Scholar
- Groot, G.S. & Kroon, A.M. Mitochondrial DNA from various organisms does not contain internally methylated cytosine in -CCGG- sequences. Biochim. Biophys. Acta 564, 355–357 (1979).
Article CAS Google Scholar
- Yan, P.S. et al. Hypermethylation of ribosomal DNA in human breast carcinoma. Br. J. Cancer 82, 514–517 (2000).
Article CAS Google Scholar
- Oakes, C.C., Smiraglia, D.J., Plass, C., Trasler, J.M. & Robaire, B. Aging results in hypermethylation of ribosomal DNA in sperm and liver of male rats. Proc. Natl. Acad. Sci. USA 100, 1775–1780 (2003).
Article CAS Google Scholar
- Salem, C.E. et al. PAX6 methylation and ectopic expression in human tumor cells. Int. J. Cancer 87, 179–185 (2000).
Article CAS Google Scholar
- Yan, P.S. et al. CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer. Clin. Cancer Res. 6, 1432–1438 (2000).
CAS PubMed Google Scholar
- Louro, R. et al. RASL11A, member of a novel small monomeric GTPase gene family, is down-regulated in prostate tumors. Biochem. Biophys. Res. Commun. 316, 618–627 (2004).
Article CAS Google Scholar
- Watson, J.E. et al. Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer. Oncogene 23, 3487–3494 (2004).
Article CAS Google Scholar
- Derynck, R., Akhurst, R.J. & Balmain, A. TGF-beta signaling in tumor suppression and cancer progression. Nat. Genet. 29, 117–129 (2001).
Article CAS Google Scholar
- Toyota, M. et al. CpG island methylator phenotype in colorectal cancer. Proc. Natl. Acad. Sci. USA 96, 8681–8686 (1999).
Article CAS Google Scholar
- Suter, C.M., Martin, D.I. & Ward, R.L. Germline epimutation of MLH1 in individuals with multiple cancers. Nat. Genet. 36, 497–501 (2004).
Article CAS Google Scholar
- Adorjan, P. et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30, e21 (2002).
Article Google Scholar
- Rougier, N. et al. Chromosome methylation patterns during mammalian preimplantation development. Genes Dev. 12, 2108–2113 (1998).
Article CAS Google Scholar
- Rabinowicz, P.D. et al. Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res. 13, 2658–2664 (2003).
Article CAS Google Scholar
- Bird, A.P. & Wolffe, A.P. Methylation-induced repression–belts, braces, and chromatin. Cell 99, 451–454 (1999).
Article CAS Google Scholar
- Rountree, M.R. & Selker, E.U. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev. 11, 2383–2395 (1997).
Article CAS Google Scholar
- Lorincz, M.C., Dickerson, D.R., Schmitt, M. & Groudine, M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat. Struct. Mol. Biol. 11, 1068–1075 (2004).
Article CAS Google Scholar
- Bird, A.P. Gene number, noise reduction and biological complexity. Trends Genet. 11, 94–100 (1995).
Article CAS Google Scholar
- Walsh, C.P., Chaillet, J.R. & Bestor, T.H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116–117 (1998).
Article CAS Google Scholar
- Woodfine, K. et al. Replication timing of the human genome. Hum. Mol. Genet. 13, 191–202 (2004).
Article CAS Google Scholar
- White, E.J. et al. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc. Natl. Acad. Sci. USA 101, 17771–17776 (2004).
Article CAS Google Scholar
- Gilbert, N. et al. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118, 555–566 (2004).
Article CAS Google Scholar
- Chadwick, B.P. & Willard, H.F. Multiple spatially distinct types of facultative heterochromatin on the human inactive X chromosome. Proc. Natl. Acad. Sci. USA 101, 17450–17455 (2004).
Article CAS Google Scholar
- Kohlmaier, A. et al. A chromosomal memory triggered by Xist regulates histone methylation in X inactivation. PLoS Biol. 2, E171 (2004).
Article Google Scholar
- Gaudet, F. et al. Induction of tumors in mice by genomic hypomethylation. Science 300, 489–492 (2003).
Article CAS Google Scholar
- Xu, G.L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999).
Article CAS Google Scholar
- Chen, R.Z., Pettersson, U., Beard, C., Jackson-Grusby, L. & Jaenisch, R. DNA hypomethylation leads to elevated mutation rates. Nature 395, 89–93 (1998).
Article CAS Google Scholar
- Costello, J.F. et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet. 24, 132–138 (2000).
Article CAS Google Scholar
- Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
Article CAS Google Scholar
- Cam, H. et al. A common set of gene regulatory networks links metabolism and growth inhibition. Mol. Cell 16, 399–411 (2004).
Article CAS Google Scholar
- Pollack, J.R. et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23, 41–46 (1999).
Article CAS Google Scholar
- Schubeler, D. et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263–1271 (2004).
Article Google Scholar
- Schubeler, D. et al. Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat. Genet. 32, 438–442 (2002).
Article Google Scholar
- Svoboda, P., Stein, P., Filipowicz, W. & Schultz, R.M. Lack of homologous sequence-specific DNA methylation in response to stable dsRNA expression in mouse oocytes. Nucleic Acids Res. 32, 3601–3606 (2004).
Article CAS Google Scholar