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Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Author

Listed:
  • Elisa Oberbeckmann

    (LMU Munich
    Max Planck Institute for Biophysical Chemistry)

  • Vanessa Niebauer

    (Ludwig-Maximilians-Universität München
    Ludwig-Maximilians-Universität München)

  • Shinya Watanabe

    (University of Massachusetts)

  • Lucas Farnung

    (Max Planck Institute for Biophysical Chemistry
    Harvard Medical School)

  • Manuela Moldt

    (Ludwig-Maximilians-Universität München
    Ludwig-Maximilians-Universität München)

  • Andrea Schmid

    (LMU Munich)

  • Patrick Cramer

    (Max Planck Institute for Biophysical Chemistry)

  • Craig L. Peterson

    (University of Massachusetts)

  • Sebastian Eustermann

    (Ludwig-Maximilians-Universität München
    Ludwig-Maximilians-Universität München
    European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit)

  • Karl-Peter Hopfner

    (Ludwig-Maximilians-Universität München
    Ludwig-Maximilians-Universität München)

  • Philipp Korber

    (LMU Munich)

Abstract

Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the ‘ruler’ that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.

Suggested Citation

  • Elisa Oberbeckmann & Vanessa Niebauer & Shinya Watanabe & Lucas Farnung & Manuela Moldt & Andrea Schmid & Patrick Cramer & Craig L. Peterson & Sebastian Eustermann & Karl-Peter Hopfner & Philipp Korbe, 2021. "Ruler elements in chromatin remodelers set nucleosome array spacing and phasing," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23015-0
    DOI: 10.1038/s41467-021-23015-0
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    Cited by:

    1. Ashish Kumar Singh & Tamás Schauer & Lena Pfaller & Tobias Straub & Felix Mueller-Planitz, 2021. "The biogenesis and function of nucleosome arrays," Nature Communications, Nature, vol. 12(1), pages 1-15, December.

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