Stochastic modeling of the torpedo mechanism of eukaryotic transcription termination

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Murphy, Reba-Jean
University of Lethbridge. Faculty of Arts and Science
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Lethbridge, Alta : University of Lethbridge, Dept. of Chemistry and Biochemistry
The torpedo mechanism is a type of eukaryotic transcription termination completed by RNAPII and consists of a chase-down of RNAPII by the exonuclease Xrn2 on the 3' flanking region of the RNA transcript. A biochemical model of the mechanism is detailed. By applying Gillespie simulations and using a one-dimensional biased random walk, the effects of the relative speeds of RNAPII to Xrn2 and the size of the intergenic region on termination via the torpedo mechanism are explored. The success rates of termination in terms of the likelihood of downstream gene interference, the distribution of successful termination times, and the distribution of nucleotides synthesized by RNAPII in the termination region are discussed.
biochemical models , Gillespie algorithms , random walks , torpedo termination mechanism , transcription termination