Volume 24, No 3, Mar 2014

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 24 Issue 3, March 2014: 293-306

ORIGINAL ARTICLES

High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells

Gang Chang^1,2,*, Shuai Gao^1,2,*, Xinfeng Hou², Zijian Xu², Yanfeng Liu³, Lan Kang², Yu Tao², Wenqiang Liu², Bo Huang², Xiaochen Kou², Jiayu Chen², Lei An¹, Kai Miao¹, Keqian Di¹, Zhilong Wang¹, Kun Tan¹, Tao Cheng³, Tao Cai², Shaorong Gao² and Jianhui Tian¹

¹Ministry of Agriculture Key Laboratory of Animal Genetics, Breeding and Reproduction, National Engineering Laboratory for Animal Breeding, College of Animal Sciences and Technology, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China
²National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
³State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing Road, Tianjin 300020, China Correspondence: Jianhui Tian, Tel: 86-10-62896057; Fax: 86-10-62733856 E-mail: tianjh@cau.edu.cn; Shaorong Gao, Tel: 86-10-80728967; Fax: 86-10-80727535(gaoshaorong@nibs.ac.cn)

It remains controversial whether the abnormal epigenetic modifications accumulated in the induced pluripotent stem cells (iPSCs) can ultimately affect iPSC pluripotency. To probe this question, iPSC lines with the same genetic background and proviral integration sites were established, and the pluripotency state of each iPSC line was characterized using tetraploid (4N) complementation assay. Subsequently, gene expression and global epigenetic modifications of “4N-ON” and the corresponding “4N-OFF” iPSC lines were compared through deep sequencing analyses of mRNA expression, small RNA profile, histone modifications (H3K27me3, H3K4me3, and H3K4me2), and DNA methylation. We found that methylation of an imprinted gene, Zrsr1, was consistently disrupted in the iPSC lines with reduced pluripotency. Furthermore, the disrupted methylation could not be rescued by improving culture conditions or subcloning of iPSCs. Moreover, the relationship between hypomethylation of Zrsr1 and pluripotency state of iPSCs was further validated in independent iPSC lines derived from other reprogramming systems.

10.1038/cr.2013.173

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