ArticlePLoS computational biology2022
A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- TORCphysics: a physical model of DNA-topology-controlled gene expression.Nucleic acids research · 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
- Nucleosomes play a dual role in regulating transcription dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Differential roles of positive and negative supercoiling in organizing the E. coli genome.Nucleic acids research · 2024Article
- spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.Nucleic acids research · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Women's contribution in understanding how topoisomerases, supercoiling, and transcription control genome organization.Frontiers in molecular biosciences · 2023Article
- Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations.Molecular microbiology · 2023Review
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- Collective polymerase dynamics emerge from DNA supercoiling during transcription.Biophysical journal · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
In Escherichia coli, translocation of RNA polymerase (RNAP) during transcription introduces supercoiling to DNA, which influences the initiation and elongation behaviors of RNAP. To quantify the role of supercoiling in transcription regulation, we developed a spatially resolved supercoiling model of transcription. The integrated model describes how RNAP activity feeds back with the local DNA supercoiling and how this mechanochemical feedback controls transcription, subject to topoisomerase activities and stochastic topological domain formation. This model establishes that transcription-induced supercoiling mediates the cooperation of co-transcribing RNAP molecules in highly expressed genes, and this cooperation is achieved under moderate supercoiling diffusion and high topoisomerase unbinding rates. It predicts that a topological domain could serve as a transcription regulator, generating substantial transcriptional noise. It also shows the relative orientation of two closely arranged genes plays an important role in regulating their transcription. The model provides a quantitative platform for investigating how genome organization impacts transcription.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.