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  Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Oberbeckmann, E., Niebauer, V., Watanabe, S., Farnung, L., Moldt, M., Schmid, A., et al. (2021). Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nature Communications, 12: 3232. doi:10.1038/s41467-021-23015-0.

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 Creators:
Oberbeckmann, E.1, Author              
Niebauer, V., Author
Watanabe, S., Author
Farnung, L.1, Author              
Moldt, M., Author
Schmid, A., Author
Cramer, P.1, Author              
Peterson, C. L., Author
Eustermann, S., Author
Hopfner, K.-P., Author
Korber, P., Author
Affiliations:
1Department of Molecular Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1863498              

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Free keywords: Chromatin remodelling; Chromatin structure; DNA; Enzyme mechanisms; Nucleosomes
 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.

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Language(s): eng - English
 Dates: 2021-05-28
 Publication Status: Published online
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41467-021-23015-0
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Title: Nature Communications
Source Genre: Journal
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Pages: 17 Volume / Issue: 12 Sequence Number: 3232 Start / End Page: - Identifier: -