title: Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers.
abstract: BACKGROUND
  Nucleosome organization determines the chromatin state, which in turn controls gene expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it is still unclear to what degree the re-established nucleosome organization of induced pluripotent stem cells (iPSCs) resembles embryonic stem cells (ESCs), and whether the iPSCs inherit some residual gene expression from the parental fibroblast cells.
  
  
  RESULTS
  We generated genome-wide nucleosome maps in mouse ESCs and in iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system. Pairwise comparisons showed that the nucleosome organizations in the iPSCs, regardless of the iPSCs' tissue of origin, were nearly identical to the ESCs, but distinct from mouse embryonic fibroblasts (MEF). There is a canonical nucleosome arrangement of -1, nucleosome depletion region, +1, +2, +3, and so on nucleosomes around the transcription start sites of active genes whereas only a nucleosome occupies silent transcriptional units. Transcription factor binding sites possessed characteristic nucleosomal architecture, such that their access was governed by the rotational and translational settings of the nucleosome. Interestingly, the tissue-specific genes were highly expressed only in the parental somatic cells of the corresponding iPS cell line before reprogramming, but had a similar expression level in all the resultant iPSCs and ESCs.
  
  
  CONCLUSIONS
  The re-established nucleosome landscape during nuclear reprogramming provides a conserved setting for accessibility of DNA sequences in mouse pluripotent stem cells. No persistent residual expression program or nucleosome positioning of the parental somatic cells that reflected their tissue of origin was passed on to the resulting mouse iPSCs.
authors.affiliation: College of Life Science, Beijing Normal University, Beijing, 100875, China. taoyu@nibs.ac.cn.|National Institute of Biological Sciences, NIBS, Beijing, 102206, China. taoyu@nibs.ac.cn.
authors.forename: Yu
authors.initials: Y
authors.lastname: Tao
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. wisense@2008.sina.com.
authors.forename: Weisheng
authors.initials: W
authors.lastname: Zheng
authors.affiliation: National Institute of Biological Sciences, NIBS, Beijing, 102206, China. jiangyonghua@126.com.
authors.forename: Yonghua
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. dingguitao@gmail.com.
authors.forename: Guitao
authors.initials: G
authors.lastname: Ding
authors.affiliation: National Institute of Biological Sciences, NIBS, Beijing, 102206, China. houxinfeng@nibs.ac.cn.
authors.forename: Xinfeng
authors.initials: X
authors.lastname: Hou
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. tyt49an@sina.com.
authors.forename: Yitao
authors.initials: Y
authors.lastname: Tang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Beijing, 100101, China. yueyinglee2010@hotmail.com.
authors.forename: Yueying
authors.initials: Y
authors.lastname: Li
authors.affiliation: National Institute of Biological Sciences, NIBS, Beijing, 102206, China. gaoshuai1959@163.com.
authors.forename: Shuai
authors.initials: S
authors.lastname: Gao
authors.affiliation: National Institute of Biological Sciences, NIBS, Beijing, 102206, China. gangki2004@163.com.
authors.forename: Gang
authors.initials: G
authors.lastname: Chang
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. zhangxb@tongji.edu.cn.
authors.forename: Xiaobai
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. liuwenqiang@nibs.ac.cn.
authors.forename: Wenqiang
authors.initials: W
authors.lastname: Liu
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. kouxiaochen@tongji.edu.cn.
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Kou
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. wanghong1008@tongji.edu.cn.
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. czjiang@tongji.edu.cn.
authors.forename: Cizhong
authors.initials: C
authors.lastname: Jiang
authors.affiliation: Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, The School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, 1239 Siping Road, Shanghai, 200092, China. gaoshaorong@tongji.edu.cn.
authors.forename: Shaorong
authors.initials: S
authors.lastname: Gao
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D065150:Cellular Reprogramming; D053595:Embryonic Stem Cells / Q000378:metabolism; D005347:Fibroblasts; D015870:Gene Expression; D005855:Germ Layers / Q000378:metabolism*; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D051379:Mice; D009707:Nucleosomes / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D009707:Nucleosomes