Methylation of DNA, the most experimentally accessible epigenetic alteration of eukaryotic cells, has generated an extensive literature and an abundance of analytical tools. The term “methylome” (referring to the complete set of cytosine modifications in a genome) is appearing with greater frequency in the literature, reflecting the growing number of researchers in the field. Here we introduce a set of robust protocols for methods that can be performed routinely for the elucidation of DNA chemical modifications involving methylation of cytosine. The strengths and limitations of each approach are also discussed.
