ArticlePLoS biology2008
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
Article in PLoS biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 250 papers.
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Who cites it
250 citing papers in PubMed, 404 citations in OpenAlex.
- Chaperone condensates buffer the heat shock response against pleiotropic inputs.bioRxiv : the preprint server for biology · 2026Article
- Dynamic global acetylation remodeling during the yeast heat shock response.Genome biology · 2026Article
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- Comprehensive profiling of chromatin occupancy dynamics through the cell cycle.Nucleic acids research · 2026Article
- Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.Genome research · 2026Article
- The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells.Science advances · 2025Article
- Genome-Wide Detection of Leukemia Biomarkers from lincRNA-Protein-Coding Gene Interaction Networks in the Three-Dimensional Chromatin Structure.Current issues in molecular biology · 2025Article
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- Creating a bacterium that forms eukaryotic nucleosome core particles.Nature communications · 2024Article
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- A single fiber view of the nucleosome organization in eukaryotic chromatin.Nucleic acids research · 2024Article
- International Union of Basic and Clinical Pharmacology CXIII: Nuclear Receptor Superfamily-Update 2023.Pharmacological reviews · 2023Review
- Identification of mammalian transcription factors that bind to inaccessible chromatin.Nucleic acids research · 2023Article
- Functional analysis of structural variants in single cells using Strand-seq.Nature biotechnology · 2023Article
- Origins of DNA replication in eukaryotes.Molecular cell · 2023Review
- Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.Cell reports · 2022Article
- Control of Gene Expression via the Yeast CWI Pathway.International journal of molecular sciences · 2022Review
- The biogenesis and function of nucleosome arrays.Nature communications · 2021Article
- Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast.eLife · 2021Article
- Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin.International journal of molecular sciences · 2021Review
190 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit, but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome. We used ultra-high-throughput sequencing to map the remodeling of individual nucleosomes throughout the yeast genome before and after a physiological perturbation that causes genome-wide transcriptional changes. Nearly 80% of the genome is covered by positioned nucleosomes occurring in a limited number of stereotypical patterns in relation to transcribed regions and transcription factor binding sites. Chromatin remodeling in response to physiological perturbation was typically associated with the eviction, appearance, or repositioning of one or two nucleosomes in the promoter, rather than broader region-wide changes. Dynamic nucleosome remodeling tends to increase the accessibility of binding sites for transcription factors that mediate transcriptional changes. However, specific nucleosomal rearrangements were also evident at promoters even when there was no apparent transcriptional change, indicating that there is no simple, globally applicable relationship between chromatin remodeling and transcriptional activity. Our study provides a detailed, high-resolution, dynamic map of single-nucleosome remodeling across the yeast genome and its relation to global transcriptional changes.
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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.