Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators.

Molecular and Cellular Biology
Dana J HuebertAudrey P Gasch

Abstract

The response to stressful stimuli requires rapid, precise, and dynamic gene expression changes that must be coordinated across the genome. To gain insight into the temporal ordering of genome reorganization, we investigated dynamic relationships between changing nucleosome occupancy, transcription factor binding, and gene expression in Saccharomyces cerevisiae yeast responding to oxidative stress. We applied deep sequencing to nucleosomal DNA at six time points before and after hydrogen peroxide treatment and revealed many distinct dynamic patterns of nucleosome gain and loss. The timing of nucleosome repositioning was not predictive of the dynamics of downstream gene expression change but instead was linked to nucleosome position relative to transcription start sites and specific cis-regulatory elements. We measured genome-wide binding of the stress-activated transcription factor Msn2p over time and found that Msn2p binds different loci with different dynamics. Nucleosome eviction from Msn2p binding sites was common across the genome; however, we show that, contrary to expectation, nucleosome loss occurred after Msn2p binding and in fact required Msn2p. This negates the prevailing model that nucleosomes obscuring Msn2p sites r...Continue Reading

Associated Datasets

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Citations

Sep 29, 2012·Genome Biology and Evolution·Andrea Hodgins-DavisJeffrey P Townsend
Mar 14, 2013·Nucleic Acids Research·Kyoung-Jae WonWei Wang
Aug 4, 2012·PLoS Biology·Karen T Smith, Jerry L Workman
Aug 2, 2012·Genetics·Qiaoning GuanAudrey P Gasch
Jun 15, 2013·Neurology Research International·Mitchell J OdomJ Mocco
Mar 4, 2014·Nucleic Acids Research·Oscar FloresModesto Orozco
Feb 5, 2016·Scientific Reports·Hungyo KharerinRanjith Padinhateeri
Sep 29, 2015·Briefings in Bioinformatics·Vladimir B Teif
Dec 23, 2014·Chromosoma·Corinna LielegPhilipp Korber
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Nov 12, 2013·Current Biology : CB·Jacob Stewart-OrnsteinHana El-Samad
Oct 31, 2016·Nucleic Acids Research·Alireza F Siahpirani, Sushmita Roy
Aug 10, 2016·PLoS Genetics·Pål O Westermark
Jan 1, 2013·G3 : Genes - Genomes - Genetics·Jeffrey A Lewis, Audrey P Gasch
Nov 21, 2014·Molecular Systems Biology·Deborah ChasmanAudrey P Gasch
Feb 13, 2021·NAR Genomics and Bioinformatics·Christina B AzodiShin-Han Shiu
Apr 10, 2018·Biophysical Journal·Răzvan V Chereji, David J Clark

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