ArticleMolecular and cellular biology2012
Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators.
Article in Molecular and cellular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 65 citations in OpenAlex.
- Twenty-Five Years of the Environmental Stress Response and the Enduring Power of Yeast in Stress Biology.Yeast (Chichester, England) · 2026Review
- The importance of regulated resource reallocation during dynamic environmental shifts in yeast.The EMBO journal · 2026Article
- Comprehensive profiling of chromatin occupancy dynamics through the cell cycle.Nucleic acids research · 2026Article
- Molecular circuit between Aspergillus nidulans transcription factors MsnA and VelB to coordinate fungal stress and developmental responses.PLoS genetics · 2025Article
- Regulated resource reallocation is transcriptionally hard wired into the yeast stress response.bioRxiv : the preprint server for biology · 2024Article
- A study of strong nucleosomes in the human genome.iScience · 2022Article
- TheNAR genomics and bioinformatics · 2020Article
- The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis.The Plant journal : for cell and molecular biology · 2019Article
- The in vitro functional analysis of single-nucleotide polymorphisms associated with growth hormone (GH) response in children with GH deficiency.The pharmacogenomics journal · 2019Article
- Article
- Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters.PloS one · 2019Article
- Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize.Genome research · 2018Article
- Major Determinants of Nucleosome Positioning.Biophysical journal · 2018Review
- Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression.BMC genomics · 2018Article
- Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress.PLoS biology · 2017Article
- The coupled effect of nucleosome organization on gene transcription level and transcriptional plasticity.Nucleus (Austin, Tex.) · 2017Review
- Regulation of Rab5 isoforms by transcriptional and post-transcriptional mechanisms in yeast.FEBS letters · 2017Article
- A prior-based integrative framework for functional transcriptional regulatory network inference.Nucleic acids research · 2017Article
- Changes in nucleosome formation at gene promoters in the archiascomycetous yeastAIMS microbiology · 2017Article
- Linking Core Promoter Classes to Circadian Transcription.PLoS genetics · 2016Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
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 regulate DNA access and must be lost before Msn2p can bind DNA. Together, these results highlight the complexities of stress-dependent chromatin changes and their effects on gene expression.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.