A PCR-based method for studying DNA methylation

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).