DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [PBAT Bisfulfite-seq]

Mouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that affect particularly CpG poor regions including distal enhancers. These oscillations are dependent on DNA methylation turnover by Dnmt3 and Tet enzymes and influence the probability of transcriptional state switching. Our observations suggest that regulated DNA methylation heterogeneity may contribute to lineage priming in cells poised for differentiation. Overall design: 2i_release: A long-term culture of 2i/Lif mouse embryonic stem cells were transferred to serum/Lif culture conditions and triplicate samples were collected over a time course of 30 time points. NanogGFP: NanogGFP (TNGA) mouse embryonic stem cells were sorted into Nanog-high and Nanog-low subpopulations. After 2 days of recapturing, a second cell sort was performed yielding 4 populations of cells. Data are from triplicate experiments.