Distribution profiles and their dynamic transition in stochastic gene transcription

DOI10.1016/J.JDE.2013.01.019MaRDI QIDQ1945857zbMATH OpenOpenAlexFDO

Authors Feng Jiao, Moxun Tang, Jianshe Yu

Publication date 17 April 2013

Published in Journal of Differential Equations (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jde.2013.01.019

zbMATH Keywords

bimodal distributiondistribution profilesgene transcriptiongenerating functionsmaster equationmethod of characteristicsprobability mass functionsspectral solutions

Mathematics Subject Classification ID

Ordinary differential equations and systems with randomness (34F05) Generation, random and stochastic difference and differential equations (37H10) Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Protein sequences, DNA sequences (92D20)

Review text

The authors express the mass function \(P_m(t)\) of the gene transcription in single cells, as a simple mathematical functions of the rate constants defined in the two-state model. The basic idea is to transform the master equations of \(P_m(t)\) into several special types of second-order ordinary differential equations using the method of characteristics (see for example the book of [\textit{L. C. Evans}, Partial differential equations. 2nd ed. Providence, RI: American Mathematical Society (2010; Zbl 1194.35001)]). In the second section, they derive the exact form of the probability generating function (Theorem 3 and Theorem 4) and express the probability mass function in elementary forms (Theorem 5 from the third section). The main results are given in Theorem 1 and Theorem 2 and their proofs are given in the last section. Also, some numerical examples are given. These results generalize some similar results due to \textit{J. Peccoud} and \textit{B. Ycart} [Theor. Popul. Biol. 48, No. 2, 222--234 (1995; Zbl 0865.92006)], D. T. Gillespie (2007), Tang M. (2008), S. Iyer-Biswas F. Hayot and C. Ayaprakash (2009) or B. Munsky, G. Neuert and A. van Oudenaarden (2012).

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Cited in

(30)

• Dynamics of gene expression based on epigenetic modifications
• The mean and noise of stochastic gene transcription with cell division
• The dynamics of gene transcription in random environments
• A generalized moment-based method for estimating parameters of stochastic gene transcription
• Modulation of nuclear and cytoplasmic mRNA fluctuations by time-dependent stimuli: analytical distributions
• Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation
• Theory of transcription bursting: stochasticity in the transcription rates
• Evolution of complex probability distributions in enzyme cascades
• Nonlinear dynamics and noise actuated by the cycle of gene inactivation in stochastic transcription
• Analytical formula and dynamic profile of mRNA distribution
• Distribution profiles in gene transcription activated by the cross-talking pathway
• The mean frequency of transcriptional bursting and its variation in single cells
• Modulation of first-passage time for bursty gene expression via random signals
• Fluctuations of mRNA distributions in multiple pathway activated transcription
• Reaction dynamics under confinement: an exact path integral treatment of a two-stage model of stochastic gene expression
• ON THE RELATION BETWEEN FLUCTUATION AND SCALING-LAW IN GENE EXPRESSION TIME SERIES FROM YEAST TO HUMAN
• Distribution modes and their corresponding parameter regions in stochastic gene transcription
• Exact and approximate distributions of protein and mRNA levels in the low-copy regime of gene expression
• Exact distributions in the full models of gene expression
• MONOTONIC DYNAMICS OF MRNA DEGRADATION BY TWO PATHWAYS
• On the distribution of transcription times
• Molecular distributions in gene regulatory dynamics
• Poisson distributions in stochastic dynamics of gene expression: what events do they count?
• Analytical Time-Dependent Distributions for Gene Expression Models With Complex Promoter Switching Mechanisms
• Noise and delay can shape distribution functions in stochastic reaction dynamics
• The dynamics of gene transcription Induced by variation in transcription kinetics
• Noise-induced bimodality in self-regulated gene networks with nonlinear promoter transitions and fast dimerization
• Geometric theory of distribution shapes for autoregulatory gene circuits
• Dynamical regulation of mRNA distribution by cross-talking signaling pathways
• Random dynamics of gene transcription activation in single cells

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