Whole genome bisulfite sequencing of samples reprogramming to iPSC

During cellular reprogramming to induced pluripotent stem cells (iPSCs), somatic cells rebuild their epigenetic architecture to acquire a steady self-renewing state. The biological significance and mechanisms of this epigenetic remodeling have remained unclear. Here we characterize the epigenomic roadmap to pluripotency at base resolution by performing whole genome bisulfite sequencing of Project Grandiose samples. We investigated the changes in differentially methylated regions (DMRs) and integrated this with analysis of histone modifications. We observed that methylation gain in DMRs occurred gradually during reprogramming. In contrast, methylation loss in DMRs was achieved only at the transition to the ESC-like state. Supporting a prominent role for DNA methylation in reprogramming, DMRs were enriched for transcription factor binding sites (TFBSs) and histone mark H3K4me3. Cells exhibited focal DNA demethylation at the binding sites of activated reprogramming factors during high transgene expression leading to a pluripotent ‘F-class’ state. ESC-like pluripotent cells were distinguished by extension of demethylation to the wider neighborhood of these sites. Our data indicated contrasting modes of control for genes with CpG rich promoters, which demonstrated stable low DNA methylation and strong engagement of histone marks H3K4me3 and H3K27me3, and genes with CpG poor promoters whose repression was driven by DNA methylation. Such DNA methylation driven control is key to the expression of several ESC-pluripotency predictor genes, including Dppa4, Dppa5a and Esrrb. These results reveal the crucial role that DNA methylation plays in the epigenetic switch that drives somatic cells to pluripotency.