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Systems-level dynamic analyses of fate change in murine embryonic stem cells

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  • Rong Lu

    (Department of Molecular Biology,
    Present addresses: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Beckman Center B261, 279 Campus Drive, Stanford, California 94305, USA (R.L.); Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK (F.M.); Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics 615 North Wolfe Street, Baltimore, Maryland 21205, USA (J.T.L.); Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02128, USA (E.M.A.); Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel (R.R.).)

  • Florian Markowetz

    (Princeton University, Princeton, New Jersey 08544, USA
    Present addresses: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Beckman Center B261, 279 Campus Drive, Stanford, California 94305, USA (R.L.); Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK (F.M.); Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics 615 North Wolfe Street, Baltimore, Maryland 21205, USA (J.T.L.); Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02128, USA (E.M.A.); Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel (R.R.).)

  • Richard D. Unwin

    (Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Imaging Sciences, Manchester Academic Health Science Centre, University of Manchester, Wolfson Molecular Imaging Centre)

  • Jeffrey T. Leek

    (Department of Gene and Cell Medicine and The Black Family Stem Cell Institute,
    Present addresses: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Beckman Center B261, 279 Campus Drive, Stanford, California 94305, USA (R.L.); Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK (F.M.); Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics 615 North Wolfe Street, Baltimore, Maryland 21205, USA (J.T.L.); Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02128, USA (E.M.A.); Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel (R.R.).)

  • Edoardo M. Airoldi

    (Princeton University, Princeton, New Jersey 08544, USA
    Present addresses: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Beckman Center B261, 279 Campus Drive, Stanford, California 94305, USA (R.L.); Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK (F.M.); Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics 615 North Wolfe Street, Baltimore, Maryland 21205, USA (J.T.L.); Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02128, USA (E.M.A.); Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel (R.R.).)

  • Ben D. MacArthur

    (Department of Gene and Cell Medicine and The Black Family Stem Cell Institute,
    Mount Sinai School of Medicine, New York, New York 10029, USA)

  • Alexander Lachmann

    (Mount Sinai School of Medicine, New York, New York 10029, USA)

  • Roye Rozov

    (Department of Gene and Cell Medicine and The Black Family Stem Cell Institute,
    Present addresses: Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Beckman Center B261, 279 Campus Drive, Stanford, California 94305, USA (R.L.); Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK (F.M.); Johns Hopkins Bloomberg School of Public Health, Department of Biostatistics 615 North Wolfe Street, Baltimore, Maryland 21205, USA (J.T.L.); Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02128, USA (E.M.A.); Blavatnik School of Computer Science, Tel Aviv University, 69978 Tel Aviv, Israel (R.R.).)

  • Avi Ma’ayan

    (Mount Sinai School of Medicine, New York, New York 10029, USA)

  • Laurie A. Boyer

    (Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA)

  • Olga G. Troyanskaya

    (Princeton University, Princeton, New Jersey 08544, USA)

  • Anthony D. Whetton

    (Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Imaging Sciences, Manchester Academic Health Science Centre, University of Manchester, Wolfson Molecular Imaging Centre)

  • Ihor R. Lemischka

    (Department of Molecular Biology,
    Department of Gene and Cell Medicine and The Black Family Stem Cell Institute,)

Abstract

Cell fate at the systems level Rong Lu et al. present a dynamic systems-level study of cell fate changes in mouse embryonic stem cells following a single well-defined perturbation by downregulating the pluripotency factor Nanog. They measure global changes in histone acetylation, chromatin-bound RNA polymerase II, mRNA and nuclear protein levels for five days, and find progressive widespread changes in multiple molecular regulatory layers and provide a dynamic view of information flow in the epigenome, transcriptome and proteome.

Suggested Citation

  • Rong Lu & Florian Markowetz & Richard D. Unwin & Jeffrey T. Leek & Edoardo M. Airoldi & Ben D. MacArthur & Alexander Lachmann & Roye Rozov & Avi Ma’ayan & Laurie A. Boyer & Olga G. Troyanskaya & Antho, 2009. "Systems-level dynamic analyses of fate change in murine embryonic stem cells," Nature, Nature, vol. 462(7271), pages 358-362, November.
    • Handle: RePEc:nat:nature:v:462:y:2009:i:7271:d:10.1038_nature08575
    DOI: 10.1038/nature08575
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    Cited by:

    1. Xinyu Hu & Bob van Sluijs & Óscar García-Blay & Yury Stepanov & Koen Rietrae & Wilhelm T. S. Huck & Maike M. K. Hansen, 2024. "ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Angela Re & Levi Waldron & Alessandro Quattrone, 2016. "Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites," PLOS Computational Biology, Public Library of Science, vol. 12(12), pages 1-25, December.
    3. Sébastien Durand & Marion Bruelle & Fleur Bourdelais & Bigitha Bennychen & Juliana Blin-Gonthier & Caroline Isaac & Aurélia Huyghe & Sylvie Martel & Antoine Seyve & Christophe Vanbelle & Annie Adrait , 2023. "RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    4. Melody K Morris & Julio Saez-Rodriguez & David C Clarke & Peter K Sorger & Douglas A Lauffenburger, 2011. "Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli," PLOS Computational Biology, Public Library of Science, vol. 7(3), pages 1-20, March.

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