Background: DNA methylation plays an important role in the reprogramming process.
Understanding the underlying molecular mechanism of reprogramming is crucial for answering
fundamental questions regarding the transition of cell identity.
Method: In this study, based on the genome-wide DNA methylation data from different cell lines,
comparative methylation profiles were proposed to identify the epigenetic signature of cell
Results: The density profile of CpG methylation showed that pluripotent cells are more polarized
than human dermal fibroblasts (HDF) cells. The heterogeneity of iPS has a greater deviation in the
DNA hypermethylation pattern. The result of regional distribution showed that the differential
CpG sites between pluripotent cells and HDFs tend to accumulate in the gene body and CpG shelf
regions, whereas the internal differential methylation CpG sites (DMCs) of three types of
pluripotent cells tend to accumulate in the TSS1500 region. Furthermore, a series of endogenous
markers of cell reprogramming were identified based on the integrative analysis, including focal
adhesion, pluripotency maintenance and transcription regulation. The calcium signaling pathway
was detected as one of the signatures between NT cells and iPS cells. Finally, the regional bias of
DNA methylation for key pluripotency factors was discussed. Our studies provide new insight into
the barrier identification of cell reprogramming.
Conclusion: Taken together, our studies analyzed some epigenetic markers and barriers of nuclear
reprogramming, hoping to provide new insight into understanding the underlying molecular
mechanism of reprogramming.