title: High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells.
abstract: 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.
authors.affiliation: 1] Ministry 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 [2] National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Gang
authors.initials: G
authors.lastname: Chang
authors.affiliation: 1] Ministry 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 [2] National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Gao
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Xinfeng
authors.initials: X
authors.lastname: Hou
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Zijian
authors.initials: Z
authors.lastname: Xu
authors.affiliation: State 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.
authors.forename: Yanfeng
authors.initials: Y
authors.lastname: Liu
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Lan
authors.initials: L
authors.lastname: Kang
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Tao
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Wenqiang
authors.initials: W
authors.lastname: Liu
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Huang
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Kou
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Jiayu
authors.initials: J
authors.lastname: Chen
authors.affiliation: Ministry 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.
authors.forename: Lei
authors.initials: L
authors.lastname: An
authors.affiliation: Ministry 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.
authors.forename: Kai
authors.initials: K
authors.lastname: Miao
authors.affiliation: Ministry 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.
authors.forename: Keqian
authors.initials: K
authors.lastname: Di
authors.affiliation: Ministry 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.
authors.forename: Zhilong
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Ministry 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.
authors.forename: Kun
authors.initials: K
authors.lastname: Tan
authors.affiliation: State 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.
authors.forename: Tao
authors.initials: T
authors.lastname: Cheng
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Cai
authors.affiliation: National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China.
authors.forename: Shaorong
authors.initials: S
authors.lastname: Gao
authors.affiliation: Ministry 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.
authors.forename: Jianhui
authors.initials: J
authors.lastname: Tian
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D065150:Cellular Reprogramming; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D044127:Epigenesis, Genetic; D005260:Female; D015723:Gene Library; D018392:Genomic Imprinting; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D051379:Mice; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D017423:Sequence Analysis, RNA; D057891:Tetraploidy; D059467:Transcriptome
chemical_list: D002843:Chromatin; D006657:Histones; D009687:Nuclear Proteins; D012333:RNA, Messenger