Reprogramming methods influence DNA methylation and expression patterns of mouse induced pluripotent stem cells [RNA-seq]

Induced pluripotent stem cells (iPSCs) can be derived from somatic cells through ectopic expression of transcriptional factors or chemical cocktails. Chemical reprogramming might be safe than transcriptional factors since there is no integration of exogenous genes. However, there is still little direct evidence to prove this hypothesis. In this study, we have performed whole genome profiling of the DNA methylomes of mouse chemical iPSCs (CiPSCs), transcriptional factors induced iPSCs (TF-iPSCs) and embryonic stem cells (ESCs). We find that the methylation levels of high-CpG-density promoters (HCPs) and intermediate- CpG-density promoters (ICPs) have no significant difference among them, but low-CpG-density promoters (LCP) and three retrotransposons (LINEs, LTRs and SINEs) show preference to different methylation levels. Surprisingly, CiPSCs are hypomethylated than TF-iPSCs and the major difference of methylation levels lies in the intergenic regions while two iPSCs lines are generally hypermethylated compared to ESCs. Moveover, we find the methylation states of imprinting control regions (ICRs) and the expression of imprinted genes of CiPSCs are more resemble ESCs than TF-iPSCs. Our data first provide the epigenetic states of chemical induced pluripotent stem cells and compare the difference of mouse CiPSCs, TF-iPSCs and ESCs. These observations might affect ongoing choices of reprogramming methods for disease modeling and give some guides for potential therapeutic applications. Overall design: Comparison of DNA methylation and genes expression patterns in 3 cell types