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Analysis on epigenetic signature of cell reprogramming by computational DNA methylation profiles

Author(s):

Yongchun Zuo*, Mingmin Song, Hanshuang Li, Xing Chen, Pengbo Cao, Lei Zheng and Guifang Cao  

Abstract:


Background: DNA methylation plays an important role in reprogramming process. Understanding the underlying molecular mechanism of reprogramming is crucial for answering fundamental questions regarding transition of cell identity.

Method: In this study, based on the genome-wide DNA methylation data from different cell lines, the comparative methylation profiles were proposed to identify epigenetic signature of cell reprogramming.

Results: The density profile of CpG methylation showed that pluripotent cells perform more polarized than human dermal fibroblasts (HDF) cells. The heterogeneity of iPS has a greater deviation in DNA hypermethylation pattern. The result of regional distribution showed that the differential CpG sites between pluripotent cells and HDFs tend to accumulate in gene body and CpG shelf regions, whereas the internal differential methylation CpG sites (DMCs) of three types of pluripotent cells prefer to accumulate in TSS1500 region. Furthermore, a series of endogenous markers of cell reprogramming were identified based on integrative analysis, including focal adhesion, pluripotency maintenance and transcription regulation. Calcium signaling pathway was detected as one of signatures between NT cells and iPS cells. At last, 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 have analyzed some epigenetic markers and barriers of nuclear reprogramming, hoping to provide a new insight into understanding the underlying molecular mechanism of reprogramming.

Keywords:

DNA methylation profile, Bioinformatics, Epigenetic signature, Regional distribution, Cell reprogramming.

Affiliation:

The College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, The College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018



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