Abstract
DNA methylation is a key factor in epigenetic regulation, and contributes to the pathogenesis of many diseases, including various forms of cancers, and epigenetic events such X inactivation, cellular differentiation and proliferation, and embryonic development. The most conserved epigenetic modification in plants, animals, and fungi is 5-methylcytosine (5mC), which has been well characterized across a diverse range of species. Many technologies have been developed to measure modifications in methylation with respect to biological processes, and the most common method, long considered a gold standard for identifying regions of methylation, is bisulfite conversion. In this technique, DNA is treated with bisulfite, which converts cytosine residues to uracil, but does not affect cytosine residues that have been methylated, such as 5-methylcytosines. Following bisulfite conversion, the only cytosine residues remaining in the DNA, therefore, are those that have been methylated. Subsequent sequencing can then distinguish between unmethylated cytosines, which are displayed as thymines in the resulting amplified sequence of the sense strand, and 5-methylcytosines, which are displayed as cytosines in the resulting amplified sequence of the sense strand, at the single nucleotide level. In this chapter, we describe an array-based protocol for identifying methylated DNA regions. We discuss protocols for DNA quantification, bisulfite conversion, library preparation, and chip assembly, and present an overview of current methods for the analysis of methylation data.