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Rule-based modeling of transcriptional attenuation at the tryptophan operon

Abstract : Transcriptional attenuation at E.coli's tryptophan operon is a prime example of RNA-mediated gene regulation. In this paper, we present a discrete stochastic model of the fine-grained control of attenuation, based on chemical reactions. Stochastic simulation of our model confirms results that were previously obtained by master or differential equations. Our approach is easier to understand than master equations, although mathematically well founded. It is compact due to rule schemas that define finite sets of chemical reactions. Object-centered languages based on the pi-calculus would yield less intelligible models. Such languages are confined to binary interactions, whereas our model heavily relies on reaction rules with more than two reactants, in order to concisely capture the control of attenuation.
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Submitted on : Saturday, January 9, 2010 - 8:19:32 PM
Last modification on : Thursday, April 15, 2021 - 11:22:02 AM
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  • HAL Id : hal-00445566, version 1


Celine Kuttler, Cédric Lhoussaine, Mirabelle Nebut. Rule-based modeling of transcriptional attenuation at the tryptophan operon. Transactions on Computational Systems Biology, Springer, 2010, XII, pp.199-228. ⟨hal-00445566⟩



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