In eukaryotes DNA generally is methylated on cytosines in the context of CpG dinucleotides – a modification called 5-methylcytosine (5-mC). More recently, researchers have discovered that cytosines can also be hydromethylated (5-hmC), formylated (5-fC) and carboxylated (5-caC). 

Researchers can purify methylated DNA using either antibodies or recombinant methyl-binding proteins (MBDs), methods that sometimes are called methyl-DNA immunoprecipitation (MeDIP) and the Methylated DNA Island Recover Assay (MIRA), respectively.