IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v448y2007i7153d10.1038_nature06008.html
   My bibliography  Save this article

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Author

Listed:
  • Tarjei S. Mikkelsen

    (Broad Institute of Harvard and MIT,
    MIT, and)

  • Manching Ku

    (Broad Institute of Harvard and MIT,
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA)

  • David B. Jaffe

    (Broad Institute of Harvard and MIT,)

  • Biju Issac

    (Broad Institute of Harvard and MIT,
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA)

  • Erez Lieberman

    (Broad Institute of Harvard and MIT,
    MIT, and)

  • Georgia Giannoukos

    (Broad Institute of Harvard and MIT,)

  • Pablo Alvarez

    (Broad Institute of Harvard and MIT,)

  • William Brockman

    (Broad Institute of Harvard and MIT,)

  • Tae-Kyung Kim

    (Children’s Hospital, and)

  • Richard P. Koche

    (Broad Institute of Harvard and MIT,
    MIT, and
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA)

  • William Lee

    (Broad Institute of Harvard and MIT,)

  • Eric Mendenhall

    (Broad Institute of Harvard and MIT,
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA)

  • Aisling O’Donovan

    (Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA)

  • Aviva Presser

    (Broad Institute of Harvard and MIT,)

  • Carsten Russ

    (Broad Institute of Harvard and MIT,)

  • Xiaohui Xie

    (Broad Institute of Harvard and MIT,)

  • Alexander Meissner

    (Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA)

  • Marius Wernig

    (Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA)

  • Rudolf Jaenisch

    (Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA)

  • Chad Nusbaum

    (Broad Institute of Harvard and MIT,)

  • Eric S. Lander

    (Broad Institute of Harvard and MIT,
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA)

  • Bradley E. Bernstein

    (Broad Institute of Harvard and MIT,
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
    Harvard Medical School, Boston, Massachusetts 02115, USA)

Abstract

We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

Suggested Citation

  • Tarjei S. Mikkelsen & Manching Ku & David B. Jaffe & Biju Issac & Erez Lieberman & Georgia Giannoukos & Pablo Alvarez & William Brockman & Tae-Kyung Kim & Richard P. Koche & William Lee & Eric Mendenh, 2007. "Genome-wide maps of chromatin state in pluripotent and lineage-committed cells," Nature, Nature, vol. 448(7153), pages 553-560, August.
    • Handle: RePEc:nat:nature:v:448:y:2007:i:7153:d:10.1038_nature06008
    DOI: 10.1038/nature06008
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature06008
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature06008?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Yan Jiang & Siqi Sun & Yuan Quan & Xin Wang & Yuling You & Xiao Zhang & Yue Zhang & Yin Liu & Bingjing Wang & Henan Xu & Xuetao Cao, 2023. "Nuclear RPSA senses viral nucleic acids to promote the innate inflammatory response," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Mohammad Jaber & Ahmed Radwan & Netanel Loyfer & Mufeed Abdeen & Shulamit Sebban & Areej Khatib & Hazar Yassen & Thorsten Kolb & Marc Zapatka & Kirill Makedonski & Aurelie Ernst & Tommy Kaplan & Yosef, 2022. "Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    3. Liang-Yu Fu & Tao Zhu & Xinkai Zhou & Ranran Yu & Zhaohui He & Peijing Zhang & Zhigui Wu & Ming Chen & Kerstin Kaufmann & Dijun Chen, 2022. "ChIP-Hub provides an integrative platform for exploring plant regulome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Dongjun Chung & Dan Park & Kevin Myers & Jeffrey Grass & Patricia Kiley & Robert Landick & Sündüz Keleş, 2013. "dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(10), pages 1-13, October.
    5. Phoebe Lut Fei Tam & Ming Fung Cheung & Lu Yan Chan & Danny Leung, 2024. "Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Federica Baccini & Monica Bianchini & Filippo Geraci, 2022. "Graph-Based Integration of Histone Modification Profiles," Mathematics, MDPI, vol. 10(11), pages 1-15, May.
    7. Chet H. Loh & Siebe Genesen & Matteo Perino & Magnus R. Bark & Gert Jan C. Veenstra, 2021. "Loss of PRC2 subunits primes lineage choice during exit of pluripotency," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    8. Emely Möller & Viviane Praz & Sanalkumar Rajendran & Rui Dong & Alexandra Cauderay & Yu-Hang Xing & Lukuo Lee & Carlo Fusco & Liliane C. Broye & Luisa Cironi & Sowmya Iyer & Shruthi Rengarajan & Mary , 2022. "EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    9. Gaylor Boulay & Liliane C. Broye & Rui Dong & Sowmya Iyer & Rajendran Sanalkumar & Yu-Hang Xing & Rémi Buisson & Shruthi Rengarajan & Beverly Naigles & Benoît Duc & Angela Volorio & Mary E. Awad & Raf, 2024. "EWS-WT1 fusion isoforms establish oncogenic programs and therapeutic vulnerabilities in desmoplastic small round cell tumors," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    10. Daniel Sánchez-Taltavull & Parameswaran Ramachandran & Nelson Lau & Theodore J Perkins, 2016. "Bayesian Correlation Analysis for Sequence Count Data," PLOS ONE, Public Library of Science, vol. 11(10), pages 1-24, October.
    11. Linghua Zhou & Yong Shen & Libo Jiang & Danni Yin & Jingxin Guo & Hui Zheng & Hao Sun & Rongling Wu & Yunqian Guo, 2015. "Systems Mapping for Hematopoietic Progenitor Cell Heterogeneity," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-18, May.
    12. Yayoi Natsume-Kitatani & Hiroshi Mamitsuka, 2016. "Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-18, March.
    13. Yurika Matsui & Mohamed Nadhir Djekidel & Katherine Lindsay & Parimal Samir & Nina Connolly & Gang Wu & Xiaoyang Yang & Yiping Fan & Beisi Xu & Jamy C. Peng, 2023. "SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:448:y:2007:i:7153:d:10.1038_nature06008. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.