ArticleNucleic acids research2018
Properties of gene expression and chromatin structure with mechanically regulated elongation.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 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
- Nucleosomes play a dual role in regulating transcription dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- 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
- Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments.Nature communications · 2022Article
- Collective polymerase dynamics emerge from DNA supercoiling during transcription.Biophysical journal · 2022Article
- Supercoiling-mediated feedback rapidly couples and tunes transcription.Cell reports · 2022Article
- A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation.PLoS computational biology · 2022Article
- DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases.Nucleic acids research · 2022Article
- Context-aware synthetic biology by controller design: Engineering the mammalian cell.Cell systems · 2021Review
- Reconciling kinetic and thermodynamic models of bacterial transcription.PLoS computational biology · 2021Article
- A Mechanochemical Model of Transcriptional Bursting.Biophysical journal · 2020Article
- Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling.Biophysical journal · 2019Article
- Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling.Nucleic acids research · 2019Article
- DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?Computational and structural biotechnology journal · 2019Review
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Authors and funding
2 authors.
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Abstract
In recent years, physical elements of transcription have emerged as central in our understanding of gene expression. Recent work has been done introducing a simple description of the basic physical elements of transcription where RNA elongation, RNA polymerase (RNAP) rotation and DNA supercoiling are coupled (1). Here we generalize this framework to accommodate the behavior of many RNAPs operating on multiple genes on a shared piece of DNA. The resulting framework is combined with well-established stochastic processes of transcription resulting in a model which characterizes the impact of the mechanical properties of transcription on gene expression and DNA structure. Transcriptional bursting readily emerges as a common phenomenon with origins in the geometric nature of the genetic system and results in the bounding of gene expression statistics. Properties of a multiple gene system are examined with special attention paid to the role that genome composition (gene orientation, size and intergenic distance) plays in the ability of genes to transcribe. The role of transcription in shaping DNA structure is examined and the possibility of transcription driven domain formation is discussed.
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