Cytosine methylation is required for mammalian development and is often perturbed in human cancer. To determine how this epigenetic modification is distributed in the genomes of primary and transformed cells, we used an immunocapturing approach followed by DNA microarray analysis to generate methylation profiles of all human chromosomes at 80-kb resolution and for a large set of CpG islands. In primary cells we identified broad genomic regions of differential methylation with higher levels in gene-rich neighborhoods. Female and male cells had indistinguishable profiles for autosomes but differences on the X chromosome. The inactive X chromosome (Xi) was hypermethylated at only a subset of gene-rich regions and, unexpectedly, overall hypomethylated relative to its active counterpart. The chromosomal methylation profile of transformed cells was similar to that of primary cells. Nevertheless, we detected large genomic segments with hypomethylation in the transformed cell residing in gene-poor areas. Furthermore, analysis of 6,000 CpG islands showed that only a small set of promoters was methylated differentially, suggesting that aberrant methylation of CpG island promoters in malignancy might be less frequent than previously hypothesized.
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Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33 Suppl., 245–254 (2003).
Li, E., Bestor, T.H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).
Reik, W. & Walter, J. Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2, 21–32 (2001).
Jones, P.A. & Baylin, S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415–428 (2002).
Feinberg, A.P. & Vogelstein, B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301, 89–92 (1983).
Fazzari, M.J. & Greally, J.M. Epigenomics: beyond CpG islands. Nat. Rev. Genet. 5, 446–455 (2004).
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).
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).
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).
Ishkanian, A.S. et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 36, 299–303 (2004).
Migeon, B.R. X-chromosome inactivation: molecular mechanisms and genetic consequences. Trends Genet. 10, 230–235 (1994).
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).
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).
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).
Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
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).
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).
Yan, P.S. et al. Hypermethylation of ribosomal DNA in human breast carcinoma. Br. J. Cancer 82, 514–517 (2000).
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).
Salem, C.E. et al. PAX6 methylation and ectopic expression in human tumor cells. Int. J. Cancer 87, 179–185 (2000).
Yan, P.S. et al. CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer. Clin. Cancer Res. 6, 1432–1438 (2000).
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).
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).
Derynck, R., Akhurst, R.J. & Balmain, A. TGF-beta signaling in tumor suppression and cancer progression. Nat. Genet. 29, 117–129 (2001).
Toyota, M. et al. CpG island methylator phenotype in colorectal cancer. Proc. Natl. Acad. Sci. USA 96, 8681–8686 (1999).
Suter, C.M., Martin, D.I. & Ward, R.L. Germline epimutation of MLH1 in individuals with multiple cancers. Nat. Genet. 36, 497–501 (2004).
Adorjan, P. et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30, e21 (2002).
Rougier, N. et al. Chromosome methylation patterns during mammalian preimplantation development. Genes Dev. 12, 2108–2113 (1998).
Rabinowicz, P.D. et al. Genes and transposons are differentially methylated in plants, but not in mammals. Genome Res. 13, 2658–2664 (2003).
Bird, A.P. & Wolffe, A.P. Methylation-induced repression–belts, braces, and chromatin. Cell 99, 451–454 (1999).
Rountree, M.R. & Selker, E.U. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev. 11, 2383–2395 (1997).
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).
Bird, A.P. Gene number, noise reduction and biological complexity. Trends Genet. 11, 94–100 (1995).
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).
Woodfine, K. et al. Replication timing of the human genome. Hum. Mol. Genet. 13, 191–202 (2004).
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).
Gilbert, N. et al. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118, 555–566 (2004).
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).
Kohlmaier, A. et al. A chromosomal memory triggered by Xist regulates histone methylation in X inactivation. PLoS Biol. 2, E171 (2004).
Gaudet, F. et al. Induction of tumors in mice by genomic hypomethylation. Science 300, 489–492 (2003).
Xu, G.L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999).
Chen, R.Z., Pettersson, U., Beard, C., Jackson-Grusby, L. & Jaenisch, R. DNA hypomethylation leads to elevated mutation rates. Nature 395, 89–93 (1998).
Costello, J.F. et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat. Genet. 24, 132–138 (2000).
Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
Cam, H. et al. A common set of gene regulatory networks links metabolism and growth inhibition. Mol. Cell 16, 399–411 (2004).
Pollack, J.R. et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23, 41–46 (1999).
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).
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).
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).
We thank members of the laboratory of D.S. and W.L.L., C. Alvarez, C. MacAuly and U. Platzbecker for advice; C. Wirbelauer for technical assistance; P. Svoboda for advice on bisulfite genomic sequencing; A. Peters, M. Groudine, M. Lorincz and C. Brown for comments on the manuscript; T. Forné for sharing genomic DNA from hybrid mice; S. Der for access to CpG island sequence reads; B. van Steensel for help in gene annotation; and M. Rebhan for assistance in data analysis. This work was supported by funds from the Novartis Research foundation to D.S.; the Canadian Institute for Health Research, National Institute of Dental Cranial Research, and Genome Canada/British Columbia to W.L.L.; and National Sciences and Engineering Research Council of Canada and Michael Smith Foundation for Health Research Scholarships to J.J.D.
The authors declare no competing financial interests.
Profile of DNA methylation for the human genome. (PDF 264 kb)
Differences in methylation levels between male and female fibroblasts. (PDF 46 kb)
Genomic features of methylated DNA on the level of chromosomes and individual BAC probes. (PDF 119 kb)
Profile of DNA methylation in SW48 colon cancer cells. (PDF 246 kb)
Primer sequences. (PDF 12 kb)
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Weber, M., Davies, J., Wittig, D. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37, 853–862 (2005). https://doi.org/10.1038/ng1598
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