A Novel Method for Detection and Quantification of Genome-Wide Methylation

Epigenetic marks are heritable, reversible DNA modifications that modulate gene expression. Alterations in a relatively well-characterized epigenetic modification, DNA methylation have been linked to cell differentiation, imprinting, and numerous diseases. Current assays for identification of methylated genomic regions are costly and time consuming. We develop an efficient method for detection of genome-wide methylation by employing the Arabidopsis thaliana glycosylase DEMETER (DME) to specifically cleave methylated cytosines from the genome. Limited digestion of the genome by DME produces small DNA fragments that originate from methylation sites. Purification and end-sequencing of these fragments results in the identification and digital quantification of methylation patterns genome-wide.  This assay will facilitate in studying methylation patterns in multiple cell types and will provide insight into the process of cellular differentiation.