11.1. Introduction

Methylation of chromosomal DNA is a flexible epigenetic mechanism that plays a critical role in gene regulation, and patterns of methylation across the genome are often surrogates for interesting sets of proteins that are regulated in concert with each other and with biological traits.  In order to detect methylated bases in genomic DNA (essentially only cytosines are methylated), DNA has to be treated with bisulfite to convert non-methylated cytosines to uracil and subsequently to thymine during the PCR amplification step.