Through generation of the first unbiased, whole-genome, single-base-resolution DNA methylomes for a variety of human iPSCs and ES cells we have gained several new insights into the epigenomic reprogramming process. Reprogramming induces a remarkable reconfiguration of the DNA methylation patterns throughout the somatic cell genome, returning PMDs to a fully methylated state, reinstating non-CG methylation, and reprogramming most unmethylated and methylated CG islands to an ES-cell-like state. Overall, this process generates an iPSC methylome that, in general, is very similar to that of ES cells.
