Molecular distributions in gene regulatory dynamics

DOI10.1016/J.JTBI.2011.01.020zbMATH Open1331.92046arXiv1009.5810OpenAlexW1987109029WikidataQ83265176 ScholiaQ83265176MaRDI QIDQ5963480FDOQ5963480

M. Tyran-Kamińska, R. Yvinec, M. C. Mackey

Publication date: 22 February 2016

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: We show how one may analytically compute the stationary density of the distribution of molecular constituents in populations of cells in the presence of noise arising from either bursting transcription or translation, or noise in degradation rates arising from low numbers of molecules. We have compared our results with an analysis of the same model systems (either inducible or repressible operons) in the absence of any stochastic effects, and shown the correspondence between behaviour in the deterministic system and the stochastic analogs. We have identified key dimensionless parameters that control the appearance of one or two steady states in the deterministic case, or unimodal and bimodal densities in the stochastic systems, and detailed the analytic requirements for the occurrence of different behaviours. This approach provides, in some situations, an alternative to computationally intensive stochastic simulations. Our results indicate that, within the context of the simple models we have examined, bursting and degradation noise cannot be distinguished analytically when present alone.

Full work available at URL: https://arxiv.org/abs/1009.5810

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zbMATH Keywords

stochastic modellingbursting transcriptioninducible/repressible operon

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

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Cited In (18)

• A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks
• Exponential equilibration of genetic circuits using entropy methods
• Existence of a unique invariant measure for a class of equicontinuous Markov operators with application to a stochastic model for an autoregulated gene
• The combined effects of Feller diffusion and transcriptional/translational bursting in simple gene networks
• Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting
• Gene expression noise is affected differentially by feedback in burst frequency and burst size
• Adiabatic reduction of a model of stochastic gene expression with jump Markov process
• Influence of gene copy number on self-regulated gene expression
• The limiting dynamics of a bistable molecular switch with and without noise
• Transcriptional bursting diversifies the behaviour of a toggle switch: hybrid simulation of stochastic gene expression
• Existence of invariant densities for semiflows with jumps
• Application of the Goodwin model to autoregulatory feedback for stochastic gene expression
• Asymptotic behavior of a delayed stochastic logistic model with impulsive perturbations
• Stationary distributions and metastable behaviour for self-regulating proteins with general lifetime distributions
• Regulatory Signals in Genomic Sequences
• Mathematical model of GAL regulon dynamics in \textit{Saccharomyces cerevisiae}
• Ergodicity and stability of a dynamical system perturbed by impulsive random interventions
• Analytical results for a non-Markovian process of gene expression with positive and negative feedbacks

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