title: Intrachromosomal looping is required for activation of endogenous pluripotency genes during reprogramming.
abstract: Generation of induced pluripotent stem cells (iPSCs) by defined factors is an extremely inefficient process, because there is a strong epigenetic block preventing cells from achieving pluripotency. Here we report that virally expressed factors bound to the promoters of their target genes to the same extent in both iPSCs and unreprogrammed cells (URCs). However, expression of endogenous pluripotentcy genes was observed only in iPSCs. Comparison of local chromatin structure of the OCT4 locus revealed that there was a cohesin-complex-mediated intrachromosomal loop that juxtaposes a downstream enhancer to the gene's promoter, enabling activation of endogenous stemness genes. None of these long-range interactions were observed in URCs. Knockdown of the cohesin-complex gene SMC1 by RNAi abolished the intrachromosomal interaction and affected pluripotency. These findings highlight the importance of the SMC1-orchestrated intrachromosomal loop as a critical epigenetic barrier to the induction of pluripotency.
authors.affiliation: Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China.
authors.forename: He
authors.initials: H
authors.lastname: Zhang
authors.forename: Weiwei
authors.initials: W
authors.lastname: Jiao
authors.forename: Lin
authors.initials: L
authors.lastname: Sun
authors.forename: Jiayan
authors.initials: J
authors.lastname: Fan
authors.forename: Mengfei
authors.initials: M
authors.lastname: Chen
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Xu
authors.forename: Adong
authors.initials: A
authors.lastname: Shen
authors.forename: Tao
authors.initials: T
authors.lastname: Li
authors.forename: Beibei
authors.initials: B
authors.lastname: Niu
authors.forename: Shengfang
authors.initials: S
authors.lastname: Ge
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Jiuwei
authors.initials: J
authors.lastname: Cui
authors.forename: Guanjun
authors.initials: G
authors.lastname: Wang
authors.forename: Jingnan
authors.initials: J
authors.lastname: Sun
authors.forename: Xianqun
authors.initials: X
authors.lastname: Fan
authors.forename: Xiang
authors.initials: X
authors.lastname: Hu
authors.forename: Randall J
authors.initials: RJ
authors.lastname: Mrsny
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Hoffman
authors.forename: Ji-Fan
authors.initials: JF
authors.lastname: Hu
mesh_terms: D000818:Animals; D015153:Blotting, Western; D018797:Cell Cycle Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D049109:Cell Proliferation; D002478:Cells, Cultured; D065150:Cellular Reprogramming / Q000235:genetics*; D002843:Chromatin / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D002868:Chromosomal Proteins, Non-Histone / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D044127:Epigenesis, Genetic; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D005434:Flow Cytometry; D049452:Green Fluorescent Proteins / Q000378:metabolism; D057026:Induced Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism; D051379:Mice; D050814:Octamer Transcription Factor-3 / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D000098550:Structural Maintenance of Chromosome Protein 1
chemical_list: D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D050814:Octamer Transcription Factor-3; C494174:Pou5f1 protein, mouse; D012333:RNA, Messenger; D034741:RNA, Small Interfering; C485184:enhanced green fluorescent protein; D000098550:Structural Maintenance of Chromosome Protein 1; D049452:Green Fluorescent Proteins