Abstract
Methylation of the cytosine base in cytosine-guanine (CG) dinucleotides of genomic DNA is likely to be one of the primary epigenetic “imprints” that results in parental allele-specific expression of certain mammalian genes (1). Despite the increasing popularity of bisulphite sequencing (2), ligationmediated polymerase chain reaction (PCR) (3), the availability of antibodies to 5-methylcytosine (5mCG) (4), and more recent developments in DNA array technology (5), Southern analysis using methyl-sensitive DNA restriction enzymes remains one of the more popular methods for the detection and analysis of mammalian DNA methylation. However, it has two significant disadvantages. First, relatively large amounts of genomic DNA are required for Southern blotting, thereby reducing its usefulness in the study of DNA methylation in the female germline and preimplantation embryos. Second, the analysis is limited to CGs that occur in a DNA sequence context that is recognized by a methyl-sensitive restriction enzyme. However, despite these drawbacks, the fact that the technique is still widely used is testament to its robustness, reproducibility, and relative simplicity.
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References
Brannan, C. I. and Bartolomei, M. S. (1999) Mechanisms of genomic imprinting. Curr. Opin. Genet. Dev. 9, 164–170.
Olek, A., Oswald, J., and Walter, J. (1996) A modified and improved method for bisulphite based cytosine methylation analysis. Nucleic Acids Res. 24, 5064–50
Gillis, A. J., Verkerk, A. J., Dekker, M. C., van Gurp, R. J., Oosterhuis, J. W., and Looijenga, L. H. (1997) Methylation similarities of two CpG sites within exon 5 of human H19 between normal tissues and testicular germ cell tumours of adolescents and adults, without correlation with allelic and total level of expression. Br. J. Cancer 76, 725–7
Rougier, N., Bourchis, D., Gomes, D. M., Niveleau, A., Plachot, M., Paldi, A., and Viegas-Pequignot, E. (1998) Chromosome methylation patterns during mammalian preimplantation development. Genes Dev. 12, 2108–21
Huang, T. H., Perry, M. R., and Laux, D. E. (1999) Methylation profiling of CpG islands in human breast cancer cells. Hum. Mol. Genet. 8, 459–4
McDonald, L. E., Paterson, C. A., and Kay, G. F. (1998) Bisulphite genomic sequencing-derived methylation profile of the xist gene throughout early mouse development. Genomics 54, 279–2
Dean, W., Bowden, L., Aitchison, A., Klose, J., Moore, T., Meneses, J. J., Reik, W., and Feil, R. (1998) Altered imprinted gene methylation and expression in completely ES cell-derived mouse fetuses: association with aberrant phenotypes. Development 125, 2273–22
Moore, T., Constancia, M., Zubair, M., Bailleul, B., Feil, R., Sasaki, H., and Reik, W. (1997) Multiple sense and antisense transcripts, differential methylation and tandem repeats in a putative imprinting control region upstream of mouse Igf2. Proc. Natl. Acad. Sci. USA 94, 12,509–12,5
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Church, G. M. and Gilbert, W. (1984) Genomic sequencing. Proc. Natl. Acad. Sci. USA 81, 1991–19
Feinberg, A. P. and Vogelstein, B. (1983) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132, 6–
Feinberg, A. P. and Vogelstein, B. (1984) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Addendum. Anal. Biochem. 137, 266–2
Nelson, M. and McClelland, M. (1989) Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Res. 17(Suppl.), 389–4
McClelland, M., Nelson, M., and Raschke, E. (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 22, 3640–36
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© 2002 Humana Press Inc., Totowa, NJ
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Moore, T. (2002). Southern Analysis Using Methyl-Sensitive Restriction Enzymes. In: Ward, A. (eds) Genomic Imprinting. Methods in Molecular Biology™, vol 181. Humana Press. https://doi.org/10.1385/1-59259-211-2:193
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DOI: https://doi.org/10.1385/1-59259-211-2:193
Publisher Name: Humana Press
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