Cytosine methylation in genomic DNA is a common epigenetic mechanism, which occurs through the addition of a methyl group by DNA methyltransferases to cytosine residues in cytosine:guanine (CpG) dinucleotides. CpG dinucleotides are often localized in clusters referred to as “CpG islands” (Antequera and Bird, 1993). There are approximately 45,000 CpG islands in the human genome, with many found in the promoter region of some genes, generally from upstream of the transcription start site to within the first exon (Gardiner-Garden and Frommer, 1987). DNA methylation in promoter regions is associated with decreased gene expression [e.g., (Alikhani-Koopaei et al, 2004; Andria and Simon, 1999; Douet et al, 2007; Iguchi-Ariga and Schaffner, 1989; Jaenisch and Bird, 2003; Michelotti et al, 2007)]. Many transcription factor binding sites, such as those for Sp1, have CpG dinucleotides, and when these are methylated, they display altered binding to their cognate transcription factors [e.g. (Alikhani-Koopaei et al, 2004; Douet et al, 2007; Michelotti et al, 2007)].
