Abstract
Modern approaches for studies on genome functioning include investigation of its epigenetic regulation. Methylation of cytosines in CpG dinucleotides is an inherited epigenetic modification that is responsible for both functional activity of certain genomic loci and total chromosomal stability. This review describes the main approaches for studies on DNA methylation. Under consideration are site specific approaches based on bisulfite sequencing and methyl-sensitive PCR, whole-genome approaches aimed at searching for new methylation hot spots, and also mapping of unmethylated CpG sites in extended genomic loci.
Similar content being viewed by others
REFERENCES
Bird, A. P., and Wolffe, A. P. (1999) Cell, 99, 451–454.
Ng, H. H., Zhang, Y., Hendrich, B., Johnson, C. A., Turner, B. M., Erdjument-Bromage, H., Tempst, P., Reinberg, D., and Bird, A. (1999) Nat. Genet., 23, 58–61.
Bird, A. (2002) Genes Dev., 16, 6–21.
Avner, P., and Heard, E. (2001) Nat. Rev. Genet., 2, 59–67.
Reik, W., and Walter, J. (2001) Nat. Rev. Genet., 2, 21–32.
Hsieh, J., and Fire, A. (2000) Annu. Rev. Genet., 34, 187–204.
Thomassin, H., Flavin, M., Espinas, M. L., and Grange, T. (2001) EMBO J., 20, 1974–1983.
Li, E. (2002) Nat. Rev. Genet., 3, 662–673.
Jones, P. A., and Baylin, S. B. (2002) Nat. Rev. Genet., 3, 415–428.
Amir, R. E., van den Veyver, I. B., Wan, M., Tran, C. Q., Francke, U., and Zoghbi, H. Y. (1999) Nat. Genet., 23, 185–188.
Xin, Z., Tachibana, M., Guggiari, M., Heard, E., Shinkai, Y., and Wagstaff, J. (2003) J. Biol. Chem., 278, 14996–15000.
Hotchkiss, R. D. (1948) J. Biol. Chem., 175, 315–332.
Visher, E., and Chargaff, E. (1948) J. Biol. Chem., 176, 703–714.
Vanyushin, B. F., Belozersky, A. N., Kokurina, N. A., and Kadirova, D. X. (1968) Nature, 218, 1066–1067.
Rubery, E. D., and Newton, A. A. (1971) Analyt. Biochem., 42, 149–154.
Razin, A., and Sedat, J. (1977) Analyt. Biochem., 77, 370–377.
Burtis, C. A. (1970) J. Chromatogr., 51, 183–194.
Kuo, K. C., McCune, R. A., Gehrke, C. W., Midgett, R., and Ehrlich, M. (1980) Nucleic Acids Res., 8, 4763–4776.
Patel, C. V., and Gopinathan, K. P. (1987) Biochem. Biophys. Res. Commun., 142, 334–340.
Razin, A., and Cedar, H. (1977) Proc. Natl. Acad. Sci. USA, 74, 2725–2728.
Singer, J., Schnute, W. C., Jr., Shively, J. E., Todd, C. W., and Riggs, A. D. (1979) Analyt. Biochem., 94, 297–301.
Vanyushin, B. F., Tkacheva, A. N., and Belozersky, A. N. (1970) Nature, 225, 948–949.
Oakeley, E. J., Schmitt, F., and Jost, J. P. (1999) Biotechniques, 27, 744–746, 748–750, 752.
Sheid, B., Srinivasan, P. R., and Borek, E. (1968) Biochemistry, 7, 280–285.
Wu, J., Issa, J. P., Herman, J., Bassett, D. E., Jr., Nelkin, B. D., and Baylin, S. B. (1993) Proc. Natl. Acad. Sci. USA, 90, 8891–8895.
Miller, O. J., Schnedl, W., Allen, J., and Erlanger, B. F. (1974) Nature, 251, 636–637.
Cross, S. H., Charlton, J. A., Nan, X., and Bird, A. P. (1994) Nat. Genet., 6, 236–244.
Huang, T. H., Perry, M. R., and Laux, D. E. (1999) Hum. Mol. Genet., 8, 459–470.
Maxam, A. M., and Gilbert, W. (1977) Proc. Natl. Acad. Sci. USA, 74, 560–564.
Church, G. M., and Gilbert, W. (1984) Proc. Natl. Acad. Sci. USA, 81, 1991–1995.
Rein, T., Natale, D. A., Gartner, U., Niggemann, M., DePamphilis, M. L., and Zorbas, H. (1997) J. Biol. Chem., 272, 10021–10029.
Frommer, M., McDonald, L. E., Millar, D. S., Collis, C. M., Watt, F., Grigg, G. W., Molloy, P. L., and Paul, C. L. (1992) Proc. Natl. Acad. Sci. USA, 89, 1827–1831.
Paul, C. L., and Clark, S. J. (1996) Biotechniques, 21, 126–133.
Clark, S. J., Harrison, J., Paul, C. L., and Frommer, M. (1994) Nucleic Acids Res., 22, 2990–2997.
Raizis, A. M., Schmitt, F., and Jost, J. P. (1995) Analyt. Biochem., 226, 161–166.
Rein, T., DePamphilis, M. L., and Zorbas, H. (1998) Nucleic Acids Res., 26, 2255–2264.
Olek, A., Oswald, J., and Walter, J. (1996) Nucleic Acids Res., 24, 5064–5066.
Rein, T., Zorbas, H., and DePamphilis, M. L. (1997) Mol. Cell. Biol., 17, 416–426.
Cedar, H., Solage, A., Glaser, G., and Razin, A. (1979) Nucleic Acids Res., 6, 2125–2132.
Singer, J., Roberts-Ems, J., and Riggs, A. D. (1979) Science, 203, 1019–1021.
Antequera, F., Tamame, M., Villanueva, J. R., and Santos, T. (1984) J. Biol. Chem., 259, 8033–8036.
McClelland, M., Nelson, M., and Raschke, E. (1994) Nucleic Acids Res., 22, 3640–3659.
Bird, A. P., and Southern, E. M. (1978) J. Mol. Biol., 118, 27–47.
Singer-Sam, J., Grant, M., LeBon, J. M., Okuyama, K., Chapman, V., Monk, M., and Riggs, A. D. (1990) Mol. Cell. Biol., 10, 4987–4989.
Singer-Sam, J., LeBon, J. M., Tanguay, R. L., and Riggs, A. D. (1990) Nucleic Acids Res., 18, 687.
Steigerwald, S. D., Pfeifer, G. P., and Riggs, A. D. (1990) Nucleic Acids Res., 18, 1435–1439.
Herman, J. G., Graff, J. R., Myohanen, S., Nelkin, B. D., and Baylin, S. B. (1996) Proc. Natl. Acad. Sci. USA, 93, 9821–9826.
Gonzalgo, M. L., and Jones, P. A. (1997) Nucleic Acids Res., 25, 2529–2531.
Sadri, R., and Hornsby, P. J. (1996) Nucleic Acids Res., 24, 5058–5059.
Xiong, Z., and Laird, P. W. (1997) Nucleic Acids Res., 25, 2532–2534.
Bianco, T., Hussey, D., and Dobrovic, A. (1999) Hum. Mutat., 14, 289–293.
Reyna-Lopez, G. E., Simpson, J., and Ruiz-Herrera, J. (1997) Mol. Gen. Genet., 253, 703–710.
Huang, T. H., Laux, D. E., Hamlin, B. C., Tran, P., Tran, H., and Lubahn, D. B. (1997) Cancer Res., 57, 1030–1034.
Costello, J. F., Fruhwald, M. C., Smiraglia, D. J., Rush, L. J., Robertson, G. P., Gao, X., Wright, F. A., Feramisco, J. D., Peltomaki, P., Lang, J. C., Schuller, D. E., Yu, L., Bloomfield, C. D., Caligiuri, M. A., Yates, A., Nishikawa, R., Su Huang, H., Petrelli, N. J., Zhang, X., O’Dorisio, M. S., Held, W. A., Cavenee, W. K., and Plass, C. (2000) Nat. Genet., 24, 132–138.
Lindsay, S., and Bird, A. P. (1987) Nature, 327, 336–338.
Rouillard, J. M., Erson, A. E., Kuick, R., Asakawa, J., Wimmer, K., Muleris, M., Petty, E. M., and Hanash, S. (2001) Genome Res., 11, 1453–1459.
Takahashi, K., Nakazawa, M., and Watanabe, Y. (2001) Genome Inform. Ser. Workshop Genome Inform., 12, 212–221.
Plass, C., Weichenhan, D., Catanese, J., Costello, J. F., Yu, F., Yu, L., Smiraglia, D., Cavenee, W. K., Caligiuri, M. A., deJong, P., and Held, W. A. (1997) DNA Res., 4, 253–255.
Ushijima, T., Morimura, K., Hosoya, Y., Okonogi, H., Tatematsu, M., Sugimura, T., and Nagao, M. (1997) Proc. Natl. Acad. Sci. USA, 94, 2284–2289.
Kaneda, A., Takai, D., Kaminishi, M., Okochi, E., and Ushijima, T. (2003) Ann. N. Y. Acad. Sci., 983, 131–141.
Peters, J., Wroe, S. F., Wells, C. A., Miller, H. J., Bodle, D., Beechey, C. V., Williamson, C. M., and Kelsey, G. (1999) Proc. Natl. Acad. Sci. USA, 96, 3830–3835.
Yuan, L., Shan, J., De Risi, D., Broome, J., Lovecchio, J., Gal, D., Vinciguerra, V., and Xu, H. P. (1999) Cancer Res., 59, 3215–3221.
Muller, K., Heller, H., and Doerfler, W. (2001) J. Biol. Chem., 276, 14271–14278.
Azhikina, T., Gainetdinov, I., Skvortsova, Y., Batrak, A., Dmitrieva, N., and Sverdlov, E. (2004) Mol. Genet. Genomics, 271, 22–32.
Diatchenko, L., Lau, Y. F., Campbell, A. P., Chenchik, A., Moqadam, F., Huang, B., Lukyanov, S., Lukyanov, K., Gurskaya, N., Sverdlov, E. D., and Siebert, P. D. (1996) Proc. Natl. Acad. Sci. USA, 93, 6025–6030.
Author information
Authors and Affiliations
Corresponding author
Additional information
__________
Translated from Biokhimiya, Vol. 70, No. 5, 2005, pp. 722–730.
Original Russian Text Copyright © 2005 by Azhikina, Sverdlov.
Rights and permissions
About this article
Cite this article
Azhikina, T.L., Sverdlov, E.D. Study of Tissue-Specific CpG Methylation of DNA in Extended Genomic Loci. Biochemistry (Moscow) 70, 596–603 (2005). https://doi.org/10.1007/s10541-005-0153-9
Received:
Issue Date:
DOI: https://doi.org/10.1007/s10541-005-0153-9