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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
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    Citations

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    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. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    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.

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