Genome information processing by the INO80 chromatin remodeler positions nucleosomes

Elisa Oberbeckmann, Nils Krietenstein, Vanessa Niebauer, Yingfei Wang, Kevin Schall, Manuela Moldt, Tobias Straub, Remo Rohs, Karl-Peter Hopfner (), Philipp Korber () and Sebastian Eustermann ()
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Elisa Oberbeckmann: Ludwig-Maximilians-Universität München
Nils Krietenstein: Ludwig-Maximilians-Universität München
Vanessa Niebauer: Ludwig-Maximilians-Universität München
Yingfei Wang: University of Southern California
Kevin Schall: Ludwig-Maximilians-Universität München
Manuela Moldt: Ludwig-Maximilians-Universität München
Tobias Straub: Ludwig-Maximilians-Universität München
Remo Rohs: University of Southern California
Karl-Peter Hopfner: Ludwig-Maximilians-Universität München
Philipp Korber: Ludwig-Maximilians-Universität München
Sebastian Eustermann: Ludwig-Maximilians-Universität München

Nature Communications, 2021, vol. 12, issue 1, 1-19

Abstract: Abstract The fundamental molecular determinants by which ATP-dependent chromatin remodelers organize nucleosomes across eukaryotic genomes remain largely elusive. Here, chromatin reconstitutions on physiological, whole-genome templates reveal how remodelers read and translate genomic information into nucleosome positions. Using the yeast genome and the multi-subunit INO80 remodeler as a paradigm, we identify DNA shape/mechanics encoded signature motifs as sufficient for nucleosome positioning and distinct from known DNA sequence preferences of histones. INO80 processes such information through an allosteric interplay between its core- and Arp8-modules that probes mechanical properties of nucleosomal and linker DNA. At promoters, INO80 integrates this readout of DNA shape/mechanics with a readout of co-evolved sequence motifs via interaction with general regulatory factors bound to these motifs. Our findings establish a molecular mechanism for robust and yet adjustable +1 nucleosome positioning and, more generally, remodelers as information processing hubs that enable active organization and allosteric regulation of the first level of chromatin.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23016-z

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DOI: 10.1038/s41467-021-23016-z

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