Stochastic simulations of genetic switch systems

Adiel Loinger*, Azi Lipshtat, Nathalie Q. Balaban, Ofer Biham

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

73 Scopus citations

Abstract

Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability, namely two stable states such that spontaneous transitions between them are rare. Induced transitions may take place as a result of an external stimulus. We study several variants of the genetic switch and examine the effects of cooperative binding, exclusive binding, protein-protein interactions, and degradation of bound repressors. We identify the range of parameters in which bistability takes place, enabling the system to function as a switch. Numerous studies have concluded that cooperative binding is a necessary condition for the emergence of bistability in these systems. We show that a suitable combination of network structure and stochastic effects gives rise to bistability even without cooperative binding. The average time between spontaneous transitions is evaluated as a function of the biological parameters.

Original languageAmerican English
Article number021904
JournalPhysical Review E
Volume75
Issue number2
DOIs
StatePublished - 9 Feb 2007

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