An exactly solvable model for RNA polymerase during the elongation stage

TL;DR

This paper introduces an exactly solvable Markovian model for RNA polymerase during elongation, explaining cooperative pushing and the effects of backtracking, with exact steady-state property calculations.

Contribution

It provides a rigorous mathematical framework for understanding RNAP kinetics, including backtracking effects, and derives conditions for cooperative pushing.

Findings

Backtracking can preserve cooperative pushing under certain conditions.

Exact steady-state distributions of RNAP headway are derived.

Average RNAP velocity and flux are computed explicitly.

Abstract

We consider a Markovian model for the kinetics of RNA Polymerase (RNAP) which provides a physical explanation for the phenomenon of cooperative pushing during transcription elongation observed in biochemical experiments on Escherichia coli and yeast RNAP. To study how backtracking of RNAP affects cooperative pushing we incorporate into this model backward (upstream) RNAP moves. With a rigorous mathematical treatment of the model we derive conditions on the mutual static and kinetic interactions between RNAP under which backtracking preserves cooperative pushing. This is achieved by exact computation of several key properties in the steady state of this model, including the distribution of headway between two RNAP along the DNA template and the average RNAP velocity and flux.