ArticleGenes & development2016
Nucleosome repositioning underlies dynamic gene expression.
Article in Genes & development, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 90 citations in OpenAlex.
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- Comprehensive profiling of chromatin occupancy dynamics through the cell cycle.Nucleic acids research · 2026Article
- Refined mechanism of promoter nucleosome-depleted regions resetting after replication.Nucleic acids research · 2025Article
- Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC.Nature communications · 2025Article
- Inferring differential protein binding from time-series chromatin accessibility data.Bioinformatics advances · 2025Article
- The transcriptional coordination of functional gene clusters is dependent on multiple chromatin remodelers in a haploid strain of the budding yeast,Frontiers in fungal biology · 2025Article
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- The SWI/SNF chromatin remodeling complex: a critical regulator of metabolism.Biochemical Society transactions · 2024Review
- Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection.Communications biology · 2024Article
- Differential requirements for Gcn5 and NuA4 HAT activities in the starvation-induced versus basal transcriptomes.Nucleic acids research · 2023Article
- Global early replication disrupts gene expression and chromatin conformation in a single cell cycle.Genome biology · 2022Article
- In Vitro Mapping of Nucleosome Positions at Base-Pair Resolution Using Ortho-Phenanthroline.Current protocols · 2022Article
- Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq.Stem cell reports · 2022Article
- Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly.PLoS genetics · 2022Article
- Article
- Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells.eLife · 2021Article
- Comparative analysis and prediction of nucleosome positioning using integrative feature representation and machine learning algorithms.BMC bioinformatics · 2021Article
- Linking the dynamics of chromatin occupancy and transcription with predictive models.Genome research · 2021Article
- Impact of DNA methylation on 3D genome structure.Nature communications · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Nucleosome repositioning at gene promoters is a fundamental aspect of the regulation of gene expression. However, the extent to which nucleosome repositioning is used within eukaryotic genomes is poorly understood. Here we report a comprehensive analysis of nucleosome positions as budding yeast transit through an ultradian cycle in which expression of >50% of all genes is highly synchronized. We present evidence of extensive nucleosome repositioning at thousands of gene promoters as genes are activated and repressed. During activation, nucleosomes are relocated to allow sites of general transcription factor binding and transcription initiation to become accessible. The extent of nucleosome shifting is closely related to the dynamic range of gene transcription and generally related to DNA sequence properties and use of the coactivators TFIID or SAGA. However, dynamic gene expression is not limited to SAGA-regulated promoters and is an inherent feature of most genes. While nucleosome repositioning occurs pervasively, we found that a class of genes required for growth experience acute nucleosome shifting as cells enter the cell cycle. Significantly, our data identify that the ATP-dependent chromatin-remodeling enzyme Snf2 plays a fundamental role in nucleosome repositioning and the expression of growth genes. We also reveal that nucleosome organization changes extensively in concert with phases of the cell cycle, with large, regularly spaced nucleosome arrays being established in mitosis. Collectively, our data and analysis provide a framework for understanding nucleosome dynamics in relation to fundamental DNA-dependent transactions.
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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.