RNA Polymerase interactions and elongation rate

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. This models explains the origin of the experimentally observed effect of cooperative pushing. This enhancement of the average RNAP velocity and elongation rate, is shown to require a molecular repulsion beyond steric hindrance and in excess of a critical strength. It persists up to a critical RNAP density above which jamming due to mutual blocking takes over. Surprisingly, for strong repulsion and at the same time strong stochastic blocking, cooperative pushing is suppressed at low RNAP densities but a reentrance regime at intermediate densities appears. For a simpler model we report density anticorrelations along the track that arise from slow transcription sites.

V. Belitsky and G.M. Schütz, J. Theor. Biol., 462:370-380 (2019)