Delayed stochastic modelling of prokaryotic transcription with abortive initiation
Date
2017
Authors
Sharma, Silky
University of Lethbridge. Faculty of Arts and Science
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Publisher
Lethbridge, Alta : University of Lethbridge, Dept. of Chemistry and Biochemistry
Abstract
A quantitative model for gene transcription should treat two main features: stochastic fluctuations due to low copy numbers, and time delays resulting from the lengthy sequence of reactions that form the transcription process. Bratsun et al. (PNAS, 102(41):14593-14598, 2005) proposed an algorithm by which we can include both of these features. I have studied a delay stochastic model for RNA transcription including abortive initiation. This study focused on the parametric dependence of the mean stationary RNA concentration and of the rise time, i.e. the characteristic time taken to achieve the stationary concentrations. The mean RNA concentration depends on initiation, elongation, polymerase arrest and RNA degradation rates including delays associated with clearance of promoter and polymerase arrest. Rise time depends on initiation, polymerase arrest, termination and RNA degradation rates. I have developed an analytic theory of rise time based on the delayed mass-action formalism to validate the simulation results.
Description
Keywords
abortive initiation , delay stochastic simulation model , prokaryotic transcription , rise time , RNA polymerase arrest , stochastic simulations