ArticleNucleic acids research2023
Assessing in vivo the impact of gene context on transcription through DNA supercoiling.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Genome-wide DNA supercoiling arises from transcription and SMC activity and mediates transcriptional negative feedback.bioRxiv : the preprint server for biology · 2026Article
- TORCphysics: a physical model of DNA-topology-controlled gene expression.Nucleic acids research · 2026Article
- Synthetic Biology Strategies for Activating Cryptic BGCs inACS omega · 2026Review
- Adaptive microevolution in CC17Frontiers in cellular and infection microbiology · 2026Article
- 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
- Gene syntaxes modulate gene expression and circuit behavior on plasmids.Journal of biological engineering · 2025Article
- DNA topology: A central dynamic coordinator in chromatin regulation.Current opinion in structural biology · 2024Review
- Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression.Molecular microbiology · 2024Review
- Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment.Nature communications · 2024Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
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Authors and funding
6 authors.
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Abstract
Gene context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest gene context consists of a single gene framed by two topological barriers, known as the twin transcriptional-loop model, which illustrates the interplay between transcription and DNA supercoiling. In vivo, DNA supercoiling is additionally modulated by topoisomerases, whose modus operandi remains to be quantified. Here, we bridge the gap between theory and in vivo properties by realizing in Escherichia coli the twin transcriptional-loop model and by measuring how gene expression varies with promoters and distances to the topological barriers. We find that gene expression depends on the distance to the upstream barrier but not to the downstream barrier, with a promoter-dependent intensity. We rationalize these findings with a first-principle biophysical model of DNA transcription. Our results are explained if TopoI and gyrase both act specifically, respectively upstream and downstream of the gene, with antagonistic effects of TopoI, which can repress initiation while facilitating elongation. Altogether, our work sets the foundations for a systematic and quantitative description of the impact of gene context on gene regulation.
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