Analysis of Global Genome Methylation Using the Cytosine-Extension Assay

DNA methylation is a reversible covalent chemical modification of DNA intended to regulate chromatin structure and gene expression in a cell- and tissue-specific manner and in response to the environment. Cytosine methylation is predominantly occurring in plants, and cytosine nucleotides in plants can be methylated at symmetrical (CpG and CpHpG) and nonsymmetrical sites. Although there exists a number of various methods for the detection of cytosine methylation, most of them are either laborious or expensive or both. Here, we describe a quick inexpensive method for the analysis of global genome methylation using a cytosine-extension assay. The assay can be used for the analysis of the total level of CpG, CpHpG, and CpHpH methylation in a given sample of plant DNA.