ArticlePLoS computational biology2014
Torsion-mediated interaction between adjacent genes.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Topoisomerase-mediated resolution of negative DNA supercoiling sustains human transcription and gene activation.bioRxiv : the preprint server for biology · 2026Article
- DNA topological regulation in RNA polymerase II transcription.Cellular & molecular biology letters · 2026Review
- TORCphysics: a physical model of DNA-topology-controlled gene expression.Nucleic acids research · 2026Article
- Alternative nucleic acid structures in microbial biology: regulatory functions and antimicrobial opportunities.Frontiers in cellular and infection microbiology · 2026Review
- Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.PLoS computational biology · 2025Article
- DNA supercoiling modulates eukaryotic transcription in a gene-orientation dependent manner.bioRxiv : the preprint server for biology · 2025Article
- Assessing in vivo the impact of gene context on transcription through DNA supercoiling.Nucleic acids research · 2023Article
- Single-Cell Heterogeneity in Snake Venom Expression Is Hardwired by Co-Option of Regulators from Progressively Activated Pathways.Genome biology and evolution · 2023Article
- DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes.Molecular cell · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Supercoiling-mediated feedback rapidly couples and tunes transcription.Cell reports · 2022Article
- Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle?Biomolecules · 2022Review
- Relationship between the Chromosome Structural Dynamics and Gene Expression-A Chicken and Egg Dilemma?Microorganisms · 2022Review
- Transcriptional neighborhoods regulate transcript isoform lengths and expression levels.Science (New York, N.Y.) · 2022Article
- DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases.Nucleic acids research · 2022Article
- The bacterial promoter spacer modulates promoter strength and timing by length, TG-motifs and DNA supercoiling sensitivity.Scientific reports · 2021Article
- DNA Supercoiling Drives a Transition between Collective Modes of Gene Synthesis.Physical review letters · 2021Article
- The regulation of DNA supercoiling across evolution.Protein science : a publication of the Protein Society · 2021Review
- Chromosomal Organization and Regulation of Genetic Function inEcoSal Plus · 2020Article
- Coherent Domains of Transcription Coordinate Gene Expression During Bacterial Growth and Adaptation.Microorganisms · 2019Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA torsional stress is generated by virtually all biomolecular processes involving the double helix, in particular transcription where a significant level of stress propagates over several kilobases. If another promoter is located in this range, this stress may strongly modify its opening properties, and hence facilitate or hinder its transcription. This mechanism implies that transcribed genes distant of a few kilobases are not independent, but coupled by torsional stress, an effect for which we propose the first quantitative and systematic model. In contrast to previously proposed mechanisms of transcriptional interference, the suggested coupling is not mediated by the transcription machineries, but results from the universal mechanical features of the double-helix. The model shows that the effect likely affects prokaryotes as well as eukaryotes, but with different consequences owing to their different basal levels of torsion. It also depends crucially on the relative orientation of the genes, enhancing the expression of eukaryotic divergent pairs while reducing that of prokaryotic convergent ones. To test the in vivo influence of the torsional coupling, we analyze the expression of isolated gene pairs in the Drosophila melanogaster genome. Their orientation and distance dependence is fully consistent with the model, suggesting that torsional gene coupling may constitute a widespread mechanism of (co)regulation in eukaryotes.
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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.