ArticlePLoS biology2013
Linking stochastic fluctuations in chromatin structure and gene expression.
Article in PLoS biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
72 citing papers in PubMed.
- Cell heterogeneity contributes to the variable response of HIV-1 to latency-reversing agents.Science advances · 2026Article
- Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.Nature communications · 2026Article
- SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.Nucleic acids research · 2025Article
- SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.bioRxiv : the preprint server for biology · 2025Article
- MONITTR allows real-time imaging of transcription and endogenous proteins in C. elegans.The Journal of cell biology · 2025Article
- Transcriptional silencing in Saccharomyces cerevisiae: known unknowns.Epigenetics & chromatin · 2024Review
- 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network.Science advances · 2024Article
- The method in the madness: Transcriptional control from stochastic action at the single-molecule scale.Current opinion in structural biology · 2024Review
- Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription.Nature communications · 2024Article
- Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming.Life science alliance · 2024Article
- Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency.Nucleic acids research · 2023Article
- Quantifying how promoter-associated nucleosomes regulate transcriptional bursting.Nature structural & molecular biology · 2023Article
- Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting.Nature structural & molecular biology · 2023Article
- Quantifying stimulus-response specificity to probe the functional state of macrophages.Cell systems · 2023Article
- Regulatory Mechanisms for Transcriptional Bursting Revealed by an Event-Based Model.Research (Washington, D.C.) · 2023Article
- Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses.Plants (Basel, Switzerland) · 2022Review
- Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses.Genetics · 2021Article
- Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.Nature communications · 2021Article
- Microbial metabolic noise.WIREs mechanisms of disease · 2021Review
12 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
The number of mRNA and protein molecules expressed from a single gene molecule fluctuates over time. These fluctuations have been attributed, in part, to the random transitioning of promoters between transcriptionally active and inactive states, causing transcription to occur in bursts. However, the molecular basis of transcriptional bursting remains poorly understood. By electron microscopy of single PHO5 gene molecules from yeast, we show that the "activated" promoter assumes alternative nucleosome configurations at steady state, including the maximally repressive, fully nucleosomal, and the maximally non-repressive, nucleosome-free, configuration. We demonstrate that the observed probabilities of promoter nucleosome configurations are obtained from a simple, intrinsically stochastic process of nucleosome assembly, disassembly, and position-specific sliding; and we show that gene expression and promoter nucleosome configuration can be mechanistically coupled, relating promoter nucleosome dynamics and gene expression fluctuations. Together, our findings suggest a structural basis for transcriptional bursting, and offer new insights into the mechanism of transcriptional regulation and the kinetics of promoter nucleosome transitions.
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Registered trials
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.