Methyl-Cytosine-Based Immunoprecipitation for DNA Methylation Analysis

In mammalian cells, DNA methylation at the 5-position of cytosine leads to recruitment of proteins that selectively recognize and bind 5-methylcytosine (5mC). Taking advantage of the structural identity of 5mC, various affinity purification-based protocols have been developed to enrich for either DNA that is modified by 5mC or proteins that recognize 5mC. In this protocol, an antibody against 5mC is used to immunoprecipitate the methylated DNA. The method can be scaled up to perform genome-wide DNA methylation analysis. Because immunoprecipitation is a straightforward procedure that does not require any prior modification of genomic DNA, we also describe several commercial kits available to perform the immunoprecipitation-based detection of DNA methylation.