Opposing chromatin remodelers control transcription initiation frequency and start site selection

Nature Structural & Molecular Biology
Slawomir KubikDavid Shore

Abstract

Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy following rapid remodeler depletion, we investigated the interplay between these enzymes and their impact on transcription in yeast. We show that many promoters are affected by multiple CRs that operate in concert or in opposition to position the key transcription start site (TSS)-associated +1 nucleosome. We also show that nucleosome movement after CR inactivation usually results from the activity of another CR and that in the absence of any remodeling activity, +1 nucleosomes largely maintain their positions. Finally, we present functional assays suggesting that +1 nucleosome positioning often reflects a trade-off between maximizing RNA polymerase recruitment and minimizing transcription initiation at incorrect sites. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to transcription initiation.

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Citations

Oct 31, 2019·Nucleic Acids Research·Christopher T ClarksonVladimir B Teif
Jun 4, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Sarah J Hainer, Craig D Kaplan
Feb 12, 2020·Nature Structural & Molecular Biology·Sandro BaldiPeter B Becker
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Feb 10, 2021·Nature Genetics·Mario IurlaroDirk Schübeler
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Feb 5, 2021·Journal of Molecular Biology·Ashish Kumar Singh, Felix Mueller-Planitz
Mar 13, 2021·Journal of Molecular Biology·Alexis A ReyesYuan He
May 30, 2021·Nature Communications·Elisa OberbeckmannPhilipp Korber
May 30, 2021·Nature Communications·Elisa OberbeckmannSebastian Eustermann
May 28, 2021·ELife·Christine E CucinottaToshio Tsukiyama
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Jul 5, 2021·Current Opinion in Structural Biology·Oliver Willhoft, Alessandro Costa
Dec 3, 2021·Nature Communications·Ashish Kumar SinghFelix Mueller-Planitz

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Methods Mentioned

BETA
ChEC-seq
MNase-seq
fluorescence microscopy
puller
ChIP-seq
PCR
ChIP
MNase assay

Software Mentioned

Bowtie2
FIMO
MEME Suite
HTSStation

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