Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Elisa Oberbeckmann, Vanessa Niebauer, Shinya Watanabe, Lucas Farnung, Manuela Moldt, Andrea Schmid, Patrick Cramer, Craig L. Peterson, Sebastian Eustermann (), Karl-Peter Hopfner () and Philipp Korber ()
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Elisa Oberbeckmann: LMU Munich
Vanessa Niebauer: Ludwig-Maximilians-Universität München
Shinya Watanabe: University of Massachusetts
Lucas Farnung: Max Planck Institute for Biophysical Chemistry
Manuela Moldt: 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
Karl-Peter Hopfner: Ludwig-Maximilians-Universität München
Philipp Korber: LMU Munich

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-23015-0

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