ArticlePLoS computational biology2021
Reconciling kinetic and thermodynamic models of bacterial transcription.
Article in PLoS computational biology, 2021. 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.
- Exchange dynamics and kinetic control of gene regulation complexes.Nature reviews. Molecular cell biology · 2026Review
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- A unified computational framework for quantitative design and optimization of transcriptional regulation across bacterial species.Nucleic acids research · 2026Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Biophysical modeling reveals the transcriptional regulatory mechanism of Spo0A, the master regulator in starvingmSystems · 2025Article
- Anti-correlation of LacI association and dissociation rates observed in living cells.Nature communications · 2025Article
- Flexibility and sensitivity in gene regulation out of equilibrium.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Energy Aware Technology Mapping of Genetic Logic Circuits.ACS synthetic biology · 2024Article
- Energy Aware Technology Mapping of Genetic Logic Circuits.bioRxiv : the preprint server for biology · 2024Article
- New and notable: Revisiting the "two cultures" through extrinsic noise.Biophysical journal · 2024Article
- Synergising single-cell resolution and 4sU labelling boosts inference of transcriptional bursting.Genome biology · 2023Article
- Collective polymerase dynamics emerge from DNA supercoiling during transcription.Biophysical journal · 2022Article
- Eukaryotic gene regulation at equilibrium, or non?Current opinion in systems biology · 2022Article
- Review
- A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting.Current opinion in cell biology · 2020Review
- Actin Filament Barbed-End Depolymerization by Combined Action of Profilin, Cofilin, and Twinfilin.PRX lifeArticle
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Authors and funding
3 authors.
Funding
Abstract
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including fluorescence and sequencing readouts have raised the bar for what it means to quantitatively understand transcriptional regulation. In particular our understanding of the simplest genetic circuit is sufficiently refined both experimentally and theoretically that it has become possible to carefully discriminate between different conceptual pictures of how this regulatory system works. This regulatory motif, originally posited by Jacob and Monod in the 1960s, consists of a single transcriptional repressor binding to a promoter site and inhibiting transcription. In this paper, we show how seven distinct models of this so-called simple-repression motif, based both on thermodynamic and kinetic thinking, can be used to derive the predicted levels of gene expression and shed light on the often surprising past success of the thermodynamic models. These different models are then invoked to confront a variety of different data on mean, variance and full gene expression distributions, illustrating the extent to which such models can and cannot be distinguished, and suggesting a two-state model with a distribution of burst sizes as the most potent of the seven for describing the simple-repression motif.
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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.