Bisulfite methylation profiling of large genomes

Bisulfite conversion of genomic DNA differentiates cytosines from 5-methylcytosines and, thus, identifies DNA methylation patterns at the single-base level. Here, we review recent developments incorporating high-throughput sequencing of bisulfite-converted DNA for target-specific analyses and genome-wide mapping of plant and mammalian methylomes. These developments include the analysis of human embryonic stem cell and fetal fibroblast methylomes at single-base resolution, which supports the presence of non-CG DNA methylation in wild-type embryonic stem cells and induced pluripotent stem cells. New developments in nanopore sequencing technologies may lead to directly detecting 5-methylcytosine independently of bisulfite conversion, but the current accuracy of this approach remains a limitation. Furthermore, recent investigations detecting 5-hydroxymethylcytosine within mammalian DNA may add yet another level of complexity to the epigenetic code of the methylome.