ArticlePLoS computational biology2010
Effects of transcriptional pausing on gene expression dynamics.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 67 citations in OpenAlex.
- Transcriptional Bursting in Pluripotent Stem Cells.Biology · 2026Review
- Unifying non-Markovian dynamics and agent heterogeneity in scalable stochastic networks.Nature communications · 2026Article
- Fast TV-PRO-seq: Accelerated and Streamlined Protocol for Timing RNA Polymerase Pausing.Bio-protocol · 2025Article
- Efficient approximations of transcriptional bursting effects on the dynamics of a gene regulatory network.Journal of the Royal Society, Interface · 2025Article
- Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters.Science advances · 2025Article
- spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.Nucleic acids research · 2023Article
- Bayesian inference of polymerase dynamics over the exclusion process.Royal Society open science · 2023Article
- Timing RNA polymerase pausing with TV-PRO-seq.Cell reports methods · 2021Article
- Statistics of Nascent and Mature RNA Fluctuations in a Stochastic Model of Transcriptional Initiation, Elongation, Pausing, and Termination.Bulletin of mathematical biology · 2020Article
- Probing Mechanisms of Transcription Elongation Through Cell-to-Cell Variability of RNA Polymerase.Biophysical journal · 2020Article
- Added value of autoregulation and multi-step kinetics of transcription initiation.Royal Society open science · 2018Article
- Bayesian inference on stochastic gene transcription from flow cytometry data.Bioinformatics (Oxford, England) · 2018Article
- Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise.Biophysical journal · 2018Article
- Dissecting the stochastic transcription initiation process in live Escherichia coli.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Collective Properties of a Transcription Initiation Model Under Varying Environment.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
- The utility of simple mathematical models in understanding gene regulatory dynamics.In silico biology · 2015Review
- Article
- Cooperative RNA polymerase molecules behavior on a stochastic sequence-dependent model for transcription elongation.PloS one · 2013Article
- Effects of multimerization on the temporal variability of protein complex abundance.BMC systems biology · 2013Article
- Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes.Genome biology and evolution · 2013Article
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Stochasticity in gene expression affects many cellular processes and is a source of phenotypic diversity between genetically identical individuals. Events in elongation, particularly RNA polymerase pausing, are a source of this noise. Since the rate and duration of pausing are sequence-dependent, this regulatory mechanism of transcriptional dynamics is evolvable. The dependency of pause propensity on regulatory molecules makes pausing a response mechanism to external stress. Using a delayed stochastic model of bacterial transcription at the single nucleotide level that includes the promoter open complex formation, pausing, arrest, misincorporation and editing, pyrophosphorolysis, and premature termination, we investigate how RNA polymerase pausing affects a gene's transcriptional dynamics and gene networks. We show that pauses' duration and rate of occurrence affect the bursting in RNA production, transcriptional and translational noise, and the transient to reach mean RNA and protein levels. In a genetic repressilator, increasing the pausing rate and the duration of pausing events increases the period length but does not affect the robustness of the periodicity. We conclude that RNA polymerase pausing might be an important evolvable feature of genetic networks.
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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.