Methylated DNA immunoprecipitation genome-wide analysis

DNA methylation is an important and potentially heritable component of the epigenetic machinery that has a major role in the control of gene expression and can be deregulated in many diseases. This modification of genomic DNA can be assessed using the methylated DNA immunoprecipitation (MeDIP) method, based on the quantification of methylated DNA fragments enriched using an antibody specific for methyl-cytosines. The relationship between the enrichment level and the real DNA methylation status is complex, and only a few methods have been developed to evaluate MeDIP enrichment measures to estimate the absolute or relative number of methyl-cytosines in a given sample. Two such methods are MEDME and BATMAN. This chapter focuses on the description and use of the former with a brief discussion of the latter.