RNA polymerase interactions and elongation rate

Abstract

We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and cooperation, we introduce a stochastic model that allows for the exact analytical computation of the stationary properties of transcription elongation as a function of RNAP density, their interaction strength, nucleoside triphosphate concentration, and rate of pyrophosphate release. Cooperative pushing, i.e., an enhancement of the average RNAP velocity and elongation rate, arises due to stochastic pushing. This cooperative effect cannot be explained by steric hindrance alone but requires a sufficiently strong molecular repulsion. It disappears beyond a critical RNAP density, above which jamming due to collisions takes over. For strong stochastic blocking the cooperative pushing is suppressed at low RNAP densities, but a reappears at higher densities.Comment: 26 pages, 6 figure