An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator

TLDR

Reprogramming of somatic cells to induced pluripotent stem cells involves a dynamic rearrangement of the epigenetic landscape. The study aims to characterize the epigenomic roadmap of murine secondary reprogramming. This was achieved by performing MethylC‑seq, ChIP‑seq for H3K4/K27/K36me3, and RNA‑Seq on samples collected at multiple time points during reprogramming. DNA methylation gain during reprogramming is gradual, loss occurs only at the ESC‑like state, and demethylation patterns differ between activated factor binding sites and ESC‑like cells; CpG‑rich promoters remain lowly methylated with strong histone marks while CpG‑poor promoters are protected by methylation, underscoring DNA methylation as a key epigenetic switch regulating pluripotency genes such as Dppa4, Dppa5a, and Esrrb.

Abstract

Abstract Reprogramming of somatic cells to induced pluripotent stem cells involves a dynamic rearrangement of the epigenetic landscape. To characterize this epigenomic roadmap, we have performed MethylC-seq, ChIP-seq (H3K4/K27/K36me3) and RNA-Seq on samples taken at several time points during murine secondary reprogramming as part of Project Grandiose. We find that DNA methylation gain during reprogramming occurs gradually, while loss is achieved only at the ESC-like state. Binding sites of activated factors exhibit focal demethylation during reprogramming, while ESC-like pluripotent cells are distinguished by extension of demethylation to the wider neighbourhood. We observed that genes with CpG-rich promoters demonstrate stable low methylation and strong engagement of histone marks, whereas genes with CpG-poor promoters are safeguarded by methylation. Such DNA methylation-driven control is the key to the regulation of ESC-pluripotency genes, including Dppa4, Dppa5a and Esrrb . These results reveal the crucial role that DNA methylation plays as an epigenetic switch driving somatic cells to pluripotency.