Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods

Item Type:	Article
Title:	Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods
Creators Name:	Churko, J.M. and Lee, J. and Ameen, M. and Gu, M. and Venkatasubramanian, M. and Diecke, S. and Sallam, K. and Im, H. and Wang, G. and Gold, J.D. and Salomonis, N. and Snyder, M.P. and Wu, J.C.
Abstract:	Many reprogramming methods can generate human induced pluripotent stem cells (hiPSCs) that closely resemble human embryonic stem cells (hESCs). This has led to assessments of how similar hiPSCs are to hESCs, by evaluating differences in gene expression, epigenetic marks and differentiation potential. However, all previous studies were performed using hiPSCs acquired from different laboratories, passage numbers, culturing conditions, genetic backgrounds and reprogramming methods, all of which may contribute to the reported differences. Here, by using high-throughput sequencing under standardized cell culturing conditions and passage number, we compare the epigenetic signatures (H3K4me3, H3K27me3 and HDAC2 ChIP-seq profiles) and transcriptome differences (by RNA-seq) of hiPSCs generated from the same primary fibroblast population by using six different reprogramming methods. We found that the reprogramming method impacts the resulting transcriptome and that all hiPSC lines could terminally differentiate, regardless of the reprogramming method. Moreover, by comparing the differences between the hiPSC and hESC lines, we observed a significant proportion of differentially expressed genes that could be attributed to polycomb repressive complex targets.
Source:	Nature Biomedical Engineering
ISSN:	2157-846X
Publisher:	Springer Nature
Volume:	1
Number:	10
Page Range:	826-837
Date:	October 2017
Official Publication:	https://doi.org/10.1038/s41551-017-0141-6
PubMed:	View item in PubMed

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