Abstract
DNA methylation is a mechanism for regulation of gene expression in animals (1-3). The addition of a methyl group at the 5-position of cytosine bases occurs exclusively at CpG dinucleotides. CpG dinucleotides in the vertebrate genome are underrepresented and amount to 1% of the genome (4). However, in some regions of the genome, CpG residues amount to 6% or more of the dinucleotides in the genome. These regions, known as CpG islands, are usually associated with the promoter regions of housekeeping genes and, in contrast to CpGs throughout the genome, are unmethylated (5,6). Methylation of CpG islands occurs only in silenced genes on the inactive X chromosome and in parentally imprinted genes (7). In addition, CpG islands may become methylated upon oncogenic transformation. These alterations in the methylation profile are correlated with silencing of tumor suppressor genes such as p15, p16, Rb, VHL, e-cadherin, ER, and HIC1 (8).
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References
Cedar, H. (1988) DNA methylation and gene activity. Cell 53, 3–4.
Doerfler, W. (1983) DNA methylation and gene activity. Annu. Rev. Biochem. 52, 93–124.
Siegfried, Z. and Cedar, H. (1997) DNA methylation: a molecular lock. Curr. Biol. 7, 305–307.
Schorderer, D. F. and Gartler, S. M. (1992) Analysis of CpG suppression in methylated and nonmethylated species. Proc. Natl. Acad. Sci. USA 89, 957–961.
Bird, A. P. (1986) CpG-rich islands and the function of DNA methylation. Nature 321, 209–213.
Eden, S. and Cedar, H. (1994) Role of DNA methylation in the regulation of transcription. Curr. Opin. Genet. Dev. 4, 255–259.
Li, E., Beard, C., and Jaenisch, R. (1993) Role for DNA methylation in genomic imprinting. Nature 366, 362–365.
Baylin, S. B., Herman, J. G., Graff, J. R., Vertino, P. M., and Issa, J. P. (1998) Alterations in DNA methylation: a fundamental aspect of neoplasia, in Advances In Cancer Research (Vandewoude, G. and Klein, G., eds.), Academic, San Diego, CA, pp. 141–196.
Brandeis, M., Kafri, T., Ariel, M., Chaillet, J. R., McCarrey, J., Razin, A., and Cedar, H. (1993) The ontogeny of allele-specific methylation associated with imprinted genes in the mouse. EMBO J. 12, 3669–3677.
Razin, A. and Cedar, H. (1994) DNA methylation and genomic imprinting. Cell 77, 473–476.
Ariel, M., Robinson, E., McCarrey, J. R., and Cedar, H. (1995) Gamete-specific methylation imprints on the Xist gene. Nature Genet. 9, 312–315.
Monk, M., Boubelik, M., and Lehnert, S. (1987) Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99, 371–382.
Kafri, T., Ariel, M., Brandeis, M., Shemer, R., Urven, L., McCarrey, J., Cedar, H., and Razin, A. (1992) Developmental pattern of gene-specific DNA methylation in the mouse embryo and germline. Genes Dev. 6, 705–714.
Brandeis, M., Ariel, M., and Cedar, H. (1993) Dynamics of DNA methylation during development. BioEssays 15, 1–5.
Shemer, R., Kafri, T., O’Connell, A., Eisenberg, S., Breslow, J. L., and A., R. (1991) Methylation changes in the apo AI gene during embryonic development of the mouse. Proc. Natl. Acad. Sci. USA 88, 10,300–10,304.
Kubota, T., Nonoyama, S., Tonoki, H., Masuno, M., Imaizumi, K., Kojima, M., Wakui, K., Shimadzu, M., and Fukushima, Y. (1999) A new assay for the analysis of X-chromosome inactivation based on methylation-specific PCR. Hum. Genet. 104, 49–55.
Willard, H. F. (1995) The sex chromosomes and X chromosome inactivation, in The Metabolic and Molecular Bases of Inherited Diseases (Scriver, C. R., Beaudet, A. L., Sly, W. S., and Valle, D., eds.), McGraw-Hill, New York, pp. 718–737.
Southern, E. M. (1975) Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503–517.
Bird, A. P. (1978) Use of restriction enzyme to study eukaryotic DNA methylation. II. The symmetry of methylation sites supports semiconservative copying of the methylation pattern. J. Mol. Biol. 118, 49–60.
Maxam, A. M. and Gilbert, W. (1980) Sequencing and labeling DNA with basespecific chemical cleavages. Meth. Enzymol. 65, 499.
Saluz, H. P. and Jost, J. P. (1993) Major techniques to study DNA methylation, in DNA Methylation: Molecular Biology and Biological Signfi cance (Jost, J. P. and Saluz, H. P., eds.), Burkhausen-Verlag, Basil, pp. 11–26.
Frommer, M., McDonald, L. E., Millar, D. S., Collis, C. M., Watt, F., Grigg, G. W., Molloy, P. L., and Paul, C. L. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89, 1827–1831.
Clark, S. J., Harrison, J., Paul, C. L., and Frommer, M. (1994) High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990–2997.
Singer-Sam, J., LeBon, J. M., Tanguay, R. L., and Riggs, A. D. (1990) A quantitative HpaII-PCR assay to measure methylation of DNA from a small number of cells. Nucl. Acids Res. 18, 687–692.
Singer-Sam, J., Yang, T. P., Mori, N., Tanguay, R. L., Le Bon, J. M., Flores, J. C., and Riggs, A. D. (1990) DNA methylation in the 5′ region of the mouse PGK-1 gene and a quantitative PCR assay for methylation, in Nucleic Acid Methylation (Clawson, G., Willis, D., Weissbach, A., and Jones, P., eds.), Liss, New York, pp. 285–298.
Herman, J. G., Graff, J. R., Myohanen, S., Nelkin, B. D., and Baylin, S. B. (1996) Methylation specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93, 9821–9826.
Herman, J. G., Umar, A., Polyak, K., Graff, J. R., Ahuja, N., Issa, J.-P., J., Markowitz, S., Willson, J. K. V., Hamilton, S. R., Kinzler, K. W., Kane, M. F., Kolodner, R. D., Vogelstein, B., Kunkel, T. A., and Baylin, S. T. (1998) Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectral carcinoma. Proc. Natl. Acad. Sci. USA 95, 6870–6875.
Kubota, T., Das, S., Christian, S. L., Bayling, S. B., Herman, J. G., and Ledbetter, D. H. (1997) Methylation-specific PCR simplifies imprinting analysis. Nature Genet. 16, 16–17.
Shibata, H., Ueda, T., Kamiya, M., Yoshiki, A., Kusakabe, M., Plass, C., Held, W. A., Sunahara, S., Katsuki, M., Muramatsu, M., and Hayashizaki, Y. (1997) An oocyte-specific methylation imprint center in the mouse U2afbp-rs/U2af1-rs1 gene marks the establishment of allele-specific methylation during preimplantation development. Genomics 44, 171–17
Stoger, R., Kubicka, P., Liu, C.-G., Kafri, T., Razin, A., Cedar, H., and Barlow, D. P. (1993) Maternal-specific methylation of the imprinted mouse Igf2r locus identifies the expressed locus as carrying the imprinting signal. Cell 73, 61–71.
Glenn, C. C., Porter, K. A., Jong, M. T. C., Nicholls, R. D., and Driscoll, D. J. (1993) Functional imprinting and epigenetic modification of the human SNRPN gene. Hum. Mol. Genet. 2, 2001–2002.
Reis, A., Dittrich, B., Greger, V., Buiting, K., Lalande, M., Gillessen-Kaesbach, G., Anvret, M., and Horsthemke, B. (1994) Imprinting mutations suggested by abnormal DNA methylation patterns in familial Angelman and Prader-Willi syndromes. Am. J. Hum. Genet. 54, 741–747.
Chotai, K. A. and Payne, S. J. (1998) A rapid, PCR based test for differential molecular diagnosis of Prader-Willi Angelman syndromes. J. Med. Genet. 35, 472–475.
Yu, Y., Xu, F., Peng, H., Fang, X., Zhao, S., Li, Y., Cuevas, B., Kuo, W.-L., Gray, J. W., Siciliano, M., Mills, G. B., and Bast, R. C., Jr. (1999) NOEY2 (ARhi), an imprinted putative tumor suppressor gene in ovarian and breast carcinomas. Proc. Natl. Acad. Sci. USA 96, 214–219.
Allen, R. C., Zogbi, H. Y., Moseley, A. B., Rosenblatt, H. M., and Belmont, J. W. (1992) Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation. Am. J. Hum. Genet. 51, 1229–1239.
Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18, 7213–7218.
Kohno, T., Kawanishi, M., Inazawa, J., and Yokota, J. (1998) Identification of CpG islands hypermethylated in human lung cancer by the arbitrarily primed-PCR method. Hum. Genet. 102, 258–264.
Gonzalgo, M. L., Liang, G., Spruck III, C. H., Zingg, J.-M., Rideout, W. M. III, and Jones, P. A. (1997) Identification and characterization of differentially methylated regions of genomic DNA by methylation-sensitive arbitrarily primed PCR. Cancer Res. 57, 594–599.
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Ariel, M. (2002). A PCR-Based Method for Studying DNA Methylation. In: Ward, A. (eds) Genomic Imprinting. Methods in Molecular Biology™, vol 181. Humana Press. https://doi.org/10.1385/1-59259-211-2:205
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DOI: https://doi.org/10.1385/1-59259-211-2:205
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