DNA methylation plays a critical role in the regulation of gene expression. It is known to be an essential mechanism for guiding normal cellular development and maintaining of tissue identities. DNA methylation is the first discovered epigenetic mark, and remains the most studied. In animals, it predominantly involves the addition of a methyl group to the carbon-5 position of cytosine residues of the dinucleotide CpG. Many techniques have been developed to analyze DNA methylation. These methods can be divided into three groups: (1) chemical modification with bisulfite, (2) affinity- based isolation of methylated DNA and (3) treatment with methylation-sensitive restriction enzymes. Of these, bisulfite modification of DNA is a method most frequently used. Treatment of DNA with bisulfite converts cytosine residues to uracil, but leaves 5-methylcytosine residues unaffected (Figure 1). Thus, bisulfite treatment introduces specific changes in the DNA sequence that depends on the methylation status of individual cytosine residues, yielding single nucleotide resolution information about the methylation status. Various analyses can be performed on the altered sequence to retrieve this information: bisulfite sequencing, methylation-specific PCR, high resolution melting curve analysis, microarray-based approaches, next-generation sequencing.
