Nano-MeDIP-seq Methylome Analysis Using Low DNA Concentrations

Abstract

DNA methylation is an epigenetic mark that is indispensable for mammalian development and occurs at cytosine residues throughout the genome (the “methylome”). Approximately 70 % of all CpG dinucleotides are affected by DNA methylation, which serve to “lock in” chromatin states and thus transcriptional programs. The systemic and pervasive occurrence of DNA methylation throughout the genome defines cellular identity and therefore requires genome-wide assays to fully appreciate and discern differential patterns of methylation that influence aspects of phenotypic plasticity including susceptibility to common complex disease.

One method that permits methylome analysis is methylated DNA immunoprecipitation (MeDIP) combined with next-generation sequencing (MeDIP-seq). MeDIP uses an antibody raised against 5-methylcytosine to capture methylated fragments of DNA, which are subsequently sequenced to envisage the methylome landscape. The advantageous cost versus coverage balance of MeDIP-seq has made it the method of choice to replace or complement array-based methods for population epigenetic studies. Here we detail nano-MeDIP-seq, which allows methylome analysis using nanogram quantities of starting material.