Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

We applied sequential ChIP-bisulfite-sequencing for H3K4me1 and H3K27ac in mouse embryonic stem cells (ESCs). By obtaining over ~4*10^9 bases of sequence from chromatin immunoprecipitated DNA which was bisulfite treated, we identified enhancers that were differentially methylated between these two marks. We found a global gain of CpG methylation, primarily in H3K4me1-marked nucleosomes during mouse ESC differentiation. This gain occurred largely in enhancer regions that regulate genes critical for differentiation. We showed that higher levels of DNA methylation in H3K4me1 comparing to H3K27ac indicates cellular heterogeneity of enhancer states. We then used single-cell RNA-seq profiles to show that this heterogeneity correlates with gene expression during ESC differentiation. Furthermore, we showed that heterogeneity of enhancer methylation correlates with transcription start site methylation. Our results provide insights into enhancer-based functional variation in complex biological systems. Examination of H3K4me1 and H3K27ac DNA that was sequentially bisulfite treated in embryonic stem cells and differentiated cells