ArticleNucleic acids research2019
Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- The adaptive landscapes of three globaleLife · 2026Article
- TORCphysics: a physical model of DNA-topology-controlled gene expression.Nucleic acids research · 2026Article
- Structural Mutations Set an Equilibrium Noncoding Genome Fraction.Molecular biology and evolution · 2025Article
- Analysis of Teg41 and PSMα promoter activity using a divergent fluorescent reporter plasmid.mSphere · 2025Article
- Differential effect of supercoiling on bacterial transcription in topological domains.PLoS computational biology · 2025Article
- Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.PLoS computational biology · 2025Article
- Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution.Nucleic acids research · 2025Article
- Targeting bacterial transcription factors for infection control: opportunities and challenges.Transcription · 2025Review
- DNA supercoiling modulates eukaryotic transcription in a gene-orientation dependent manner.bioRxiv : the preprint server for biology · 2025Article
- Prokaryotic homeostasis - a solution to thrive and survive.Frontiers in molecular biosciences · 2025Review
- Genome and transcriptomic analysis of the adaptation ofComputational and structural biotechnology journal · 2024Review
- DNA supercoiling enhances DNA condensation by ParB proteins.Nucleic acids research · 2024Article
- Article
- Single-molecule visualization of twin-supercoiled domains generated during transcription.Nucleic acids research · 2024Article
- DNA supercoiling and regulation of intrinsic β-lactamase in pathogenic Escherichia coli.Archives of microbiology · 2023Review
- 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
- DNA supercoiling restricts the transcriptional bursting of neighboring eukaryotic genes.Molecular cell · 2023Article
- Recollections of a Helmstetter Disciple.Life (Basel, Switzerland) · 2023Review
- The role of replication-induced chromosomal copy numbers in spatio-temporal gene regulation and evolutionary chromosome plasticity.Frontiers in microbiology · 2023Article
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role in adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial supercoiling heterogeneities caused by the transcription process itself, which strongly contribute to this regulation mode. We propose a new mechanistic modeling of the transcription-supercoiling dynamical coupling along a genome, which allows simulating and quantitatively reproducing in vitro and in vivo transcription assays, and highlights the role of genes' local orientation in their supercoiling sensitivity. Consistently with predictions, we show that chromosomal relaxation artificially induced by gyrase inhibitors selectively activates convergent genes in several enterobacteria, while conversely, an increase in DNA supercoiling naturally selected in a long-term evolution experiment with Escherichia coli favours divergent genes. Simulations show that these global expression responses to changes in DNA supercoiling result from fundamental mechanical constraints imposed by transcription, independently from more specific regulation of each promoter. These constraints underpin a significant and predictable contribution to the complex rules by which bacteria use DNA supercoiling as a global but fine-tuned transcriptional regulator.
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