Work

Rule-Based Modeling of Transcriptional Attenuation at the Tryptophan Operon

Year: 2009

Type: conference-paper

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 π -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. These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Source: Winter Simulation Conference

DOI: 10.1109/wsc.2009.5429721

Authors: Céline Kuttler, Cédric Lhoussaine, Mirabelle Nebut

Institutions: Université de Lille, Université Lille 1, Centre National de la Recherche Scientifique

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Microsoft Research, Agence Nationale de la Recherche, Università degli Studi di Trento, Centre National de la Recherche Scientifique

Awards: G5683962838, G8368445640