IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v458y2009i7236d10.1038_nature07667.html
   My bibliography  Save this article

The DNA-encoded nucleosome organization of a eukaryotic genome

Author

Listed:
  • Noam Kaplan

    (Department of Computer Science and Applied Mathematics,)

  • Irene K. Moore

    (Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, Illinois 60208, USA)

  • Yvonne Fondufe-Mittendorf

    (Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, Illinois 60208, USA)

  • Andrea J. Gossett

    (Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA)

  • Desiree Tillo

    (University of Toronto, Toronto, Ontario M5S 1A8, Canada)

  • Yair Field

    (Department of Computer Science and Applied Mathematics,)

  • Emily M. LeProust

    (Agilent Technologies Inc., Genomics—LSSU, 5301 Stevens Creek Boulevard, MS 3L/MT Santa Clara, California 95051, USA)

  • Timothy R. Hughes

    (University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Terrence Donnelly Centre for Cellular & Biomolecular Research,
    160 College Street, Toronto, Ontario M5S 3E1, Canada)

  • Jason D. Lieb

    (Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA)

  • Jonathan Widom

    (Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, Illinois 60208, USA)

  • Eran Segal

    (Department of Computer Science and Applied Mathematics,
    Weizmann Institute of Science, Rehovot 76100, Israel)

Abstract

Organizing nucleosomes The nucleosomes are the basic repeating units of eukaryotic chromatin, and nucleosome organization is critically important for gene regulation. Kaplan et al. tested the importance of the intrinsic DNA sequence preferences of nucleosomes by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map is remarkably similar to in vivo nucleosome maps, indicating that the organization of nucleosomes in vivo is largely governed by the underlying genomic DNA sequence.

Suggested Citation

  • Noam Kaplan & Irene K. Moore & Yvonne Fondufe-Mittendorf & Andrea J. Gossett & Desiree Tillo & Yair Field & Emily M. LeProust & Timothy R. Hughes & Jason D. Lieb & Jonathan Widom & Eran Segal, 2009. "The DNA-encoded nucleosome organization of a eukaryotic genome," Nature, Nature, vol. 458(7236), pages 362-366, March.
    • Handle: RePEc:nat:nature:v:458:y:2009:i:7236:d:10.1038_nature07667
    DOI: 10.1038/nature07667
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature07667
    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/nature07667?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. Jean Francois Lefebvre & Emilio Vello & Bing Ge & Stephen B Montgomery & Emmanouil T Dermitzakis & Tomi Pastinen & Damian Labuda, 2012. "Genotype-Based Test in Mapping Cis-Regulatory Variants from Allele-Specific Expression Data," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-15, June.
    2. Aileen Julia Riesle & Meijiang Gao & Marcus Rosenblatt & Jacques Hermes & Helge Hass & Anna Gebhard & Marina Veil & Björn Grüning & Jens Timmer & Daria Onichtchouk, 2023. "Activator-blocker model of transcriptional regulation by pioneer-like factors," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Meijiang Gao & Marina Veil & Marcus Rosenblatt & Aileen Julia Riesle & Anna Gebhard & Helge Hass & Lenka Buryanova & Lev Y. Yampolsky & Björn Grüning & Sergey V. Ulianov & Jens Timmer & Daria Onichtch, 2022. "Pluripotency factors determine gene expression repertoire at zygotic genome activation," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    4. Behrouz Eslami-Mossallam & Raoul D Schram & Marco Tompitak & John van Noort & Helmut Schiessel, 2016. "Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-14, June.
    5. Vivekanandan Ramalingam & Xinyang Yu & Brian D. Slaughter & Jay R. Unruh & Kaelan J. Brennan & Anastasiia Onyshchenko & Jeffrey J. Lange & Malini Natarajan & Michael Buck & Julia Zeitlinger, 2023. "Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Kate E. Stanley & Tatjana Jatsenko & Stefania Tuveri & Dhanya Sudhakaran & Lore Lannoo & Kristel Calsteren & Marie Borre & Ilse Parijs & Leen Coillie & Kris Bogaert & Rodrigo Almeida Toledo & Liesbeth, 2024. "Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Wolfram Möbius & Ulrich Gerland, 2010. "Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites," PLOS Computational Biology, Public Library of Science, vol. 6(8), pages 1-11, August.
    8. Xinyun Jing & Niubing Zhang & Xiaojuan Zhou & Ping Chen & Jie Gong & Kaixiang Zhang & Xueting Wu & Wenjuan Cai & Bang-Ce Ye & Pei Hao & Guo-ping Zhao & Sheng Yang & Xuan Li, 2024. "Creating a bacterium that forms eukaryotic nucleosome core particles," Nature Communications, Nature, vol. 15(1), pages 1-16, 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:458:y:2009:i:7236:d:10.1038_nature07667. 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.