Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells

• DOI: 10.1371/journal.pcbi.1006034
• Publication Date: 2018-03-21T13:25:41Z
• Authors: Yanting Luo; Jianlin He; Xiguang Xu; Ming-an Sun; Xiaowei Wu; Xuemei Lu; Hehuang Xie
• Keywords: Epigenomics; CpG site; Differentially methylated regions

Embryonic stem cells (ESCs) consist of a population self-renewing displaying extensive phenotypic and functional heterogeneity. Research towards the understanding epigenetic mechanisms underlying heterogeneity among ESCs is still in its initial stage. Key issues, such as how to identify cell-subset specifically methylated loci interpret biological meanings methylation variations remain largely unexplored. To fill research gap, we implemented computational pipeline analyze single-cell methylome perform an integrative analysis with transcriptome data. According origins variation DNA methylation, determined genomic associated allelic-specific or asymmetric explored beta mixture model infer exhibiting specific (CSM). We observed that putative CSM are significantly enriched CpG island (CGI) shelves regions histone marks for promoter enhancer, genes hosting show wide-ranging expression ESCs. More interestingly, may be clustered into co-methylated modules enriching binding motifs distinct sets transcription factors. Taken together, our study provided novel tool explore reveal transcriptional regulatory networks