Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression

Adam R. Stinchcombe, Charles S. Peskin, Daniel Tranchina

Research output: Contribution to journalArticle

Abstract

We present a generalization of a population density approach for modeling and analysis of stochastic gene expression. In the model, the gene of interest fluctuates stochastically between an inactive state, in which transcription cannot occur, and an active state, in which discrete transcription events occur; and the individual mRNA molecules are degraded stochastically in an independent manner. This sort of model in simplest form with exponential dwell times has been used to explain experimental estimates of the discrete distribution of random mRNA copy number. In our generalization, the random dwell times in the inactive and active states, T 0 and T 1, respectively, are independent random variables drawn from any specified distributions. Consequently, the probability per unit time of switching out of a state depends on the time since entering that state. Our method exploits a connection between the fully discrete random process and a related continuous process. We present numerical methods for computing steady-state mRNA distributions and an analytical derivation of the mRNA autocovariance function. We find that empirical estimates of the steady-state mRNA probability mass function from Monte Carlo simulations of laboratory data do not allow one to distinguish between underlying models with exponential and nonexponential dwell times in some relevant parameter regimes. However, in these parameter regimes and where the autocovariance function has negative lobes, the autocovariance function disambiguates the two types of models. Our results strongly suggest that temporal data beyond the autocovariance function is required in general to characterize gene switching.

Original languageEnglish (US)
Article number061919
JournalPhysical Review E
Volume85
Issue number6
DOIs
StatePublished - Jun 22 2012

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gene expression
Autocovariance Function
Messenger RNA
Gene Expression
Dwell Time
dwell
genes
Transcription
Gene
Unit of time
Model
random processes
random variables
Discrete Distributions
Independent Random Variables
estimates
Random process
lobes
Estimate
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ASJC Scopus subject areas

  • Condensed Matter Physics
  • Statistical and Nonlinear Physics
  • Statistics and Probability

Cite this

Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression. / Stinchcombe, Adam R.; Peskin, Charles S.; Tranchina, Daniel.

In: Physical Review E, Vol. 85, No. 6, 061919, 22.06.2012.

Research output: Contribution to journalArticle

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