ArticleNucleic acids research2022
DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 36 citations in OpenAlex.
- A continuum-based reaction-diffusion model for spread of gene silencing in chromosomal inactivation.RNA (New York, N.Y.) · 2026Article
- Topology Resetting During Transcription-Coupled Nucleotide Excision Repair.International journal of molecular sciences · 2026Review
- Apical localization of RNA polymerases modulates transcription dynamics and supercoiling domains revealed by cryo-ET.Molecular cell · 2026Article
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails.Nucleic acids research · 2026Article
- Slow RNAPII elongation enhances naive pluripotency rewiring while maintaining high replication fork speed.Science advances · 2026Article
- Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET.bioRxiv : the preprint server for biology · 2026Article
- Exploring the energy landscape of bacterial chromosome segregation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- TORCphysics: a physical model of DNA-topology-controlled gene expression.Nucleic acids research · 2026Article
- A data-driven chromatin model reveals spatial and dynamic features of genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Differential effect of supercoiling on bacterial transcription in topological domains.PLoS computational biology · 2025Article
- U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation.Molecular cell · 2025Article
- DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase.Nature communications · 2025Article
- KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid.Nature microbiology · 2025Article
- DNA Gene's Basic Structure as a Nonperturbative Circuit Quantum Electrodynamics: Is RNA Polymerase II the Quantum Bus of Transcription?Current issues in molecular biology · 2024Article
- Nucleosomes play a dual role in regulating transcription dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.Nature communications · 2024Article
- Single-molecule visualization of twin-supercoiled domains generated during transcription.Nucleic acids research · 2024Article
- Assessing in vivo the impact of gene context on transcription through DNA supercoiling.Nucleic acids research · 2023Article
- spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or 'push' between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.
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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.