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One of the most important modifications of DNA involves the methylation of cytosines at CpG dinucleotides. When cytosines around the promoter are methylated, nucleosome density is great, and the DNA is not transcribed. Methylation can also prevent transcription factors from binding to their targets. Conversely, active genes are associated with unmethylated promoters and enhancers.
One of the most important modifications of DNA involves the methylation of cytosines at CpG dinucleotides. When cytosines around the promoter are methylated, nucleosome density is great, and the DNA is not transcribed. Methylation can also prevent transcription factors from binding to their targets. Conversely, active genes are associated with unmethylated promoters and enhancers.
One way to determine the methylation status of a region is through bisulfite mapping. Bisulfite converts cytosine residues to uracil (which codes like thymidine), but it leaves 5-methylcytosine 5-methylcytosine residues unchanged. In this way, bisulfite can change the DNA sequence from CG to UG. This alteration can be detected in several ways. One way is to use PCR primers that will only recognize the methylated (C) or the unmethylated (U/T) DNA. Thus, placing the CpG dimmer at the 3′ end of a primer can allow one to detect whether or not the CpG is methylated or not (Herman et al 1996; Fraga et al 2002).
Literature Cited
Fraga, M.F. and M. Esteller. 2002. DNA methylation: a profile of methods and applications. BioTechniques 33 (3): 632, 634, 636–649
Herman, J.G., J.R .Graff, S. Myöhänen, B.D. Nelkin and S.B. Baylin SB. 1996. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA. 93: 9821–9826. www.ncbi.nlm.nih.gov/pmc/articles/PMC38513/?tool=pmcentrez