ArticleCell reports2022
Supercoiling-mediated feedback rapidly couples and tunes transcription.
Article in Cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Topoisomerase-mediated resolution of negative DNA supercoiling sustains human transcription and gene activation.bioRxiv : the preprint server for biology · 2026Article
- Programmable promoter editing for precise control of transgene expression.Nature biotechnology · 2026Article
- Sentinel plants enable quantitative monitoring of bioavailable nitrate in soils and microbial environments.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- STRAIGHT-IN Dual: a platform for dual single-copy integrations of DNA payloads and gene circuits into human induced pluripotent stem cells.Nature biomedical engineering · 2026Article
- Topoisomerases regulate alternative transcription start site selection in yeast.G3 (Bethesda, Md.) · 2026Article
- Programmable nanobody circuits for cell selection.bioRxiv : the preprint server for biology · 2026Article
- TORCphysics: a physical model of DNA-topology-controlled gene expression.Nucleic acids research · 2026Article
- The Roles of Topoisomerases in Transcriptional Regulation.International journal of molecular sciences · 2026Review
- Engineering plasmids with synthetic origins of replication.Nature communications · 2026Article
- STRAIGHT-IN: a platform for rapidly generating panels of genetically modified human pluripotent stem cell lines.Nature protocols · 2026Review
- Using peCHYRON to Record Mammalian Cells' History of Chemical Exposure into Their DNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Differential effect of supercoiling on bacterial transcription in topological domains.PLoS computational biology · 2025Article
- STRAIGHT-IN Dual: a platform for dual, single-copy integrations of DNA payloads and gene circuits into human induced pluripotent stem cell.bioRxiv : the preprint server for biology · 2025Article
- Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.PLoS computational biology · 2025Article
- High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes.Nucleic acids research · 2025Article
- U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation.Molecular cell · 2025Article
- Comparative single-cell analysis of transcriptional bursting reveals the role of genome organization in de novo transcript origination.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Termination sequence between an inducible promoter and ubiquitous chromatin opening element (UCOE) reduces gene expression leakage and silencing.Journal of biological engineering · 2025Article
- Gene syntaxes modulate gene expression and circuit behavior on plasmids.Journal of biological engineering · 2025Article
- Comparative single cell analysis of transcriptional bursting reveals the role of genome organization onbioRxiv : the preprint server for biology · 2025Article
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2 authors.
Funding
Abstract
Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. However, a theoretical framework is needed to integrate biophysical regulation with biochemical transcriptional regulation. To investigate the role of supercoiling-mediated feedback within multi-gene systems, we model transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, allowing us to identify patterns of expression that result from physical inter-gene coupling. We find that gene syntax-the relative ordering and orientation of genes-defines the expression profiles, variance, burst dynamics, and inter-gene correlation of two-gene systems. Furthermore, supercoiling can enhance or weaken biochemical regulation. Our results suggest that supercoiling couples behavior between neighboring genes, providing a regulatory mechanism that tunes transcriptional variance in engineered gene networks and explains the behavior of co-localized native circuits.
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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.