RNA Polymerase interactions and elongation rate

Author(s)

Belitsky, V. ^[1] ; Schuetz, G. M. ^[2]

Affiliation

^[1] Univ Sao Paulo, Inst Matemat & Estat, Rua Mardo 1010, BR-05508090 Sao Paulo, SP - Brazil

^[2] Forschungszentrum Julich, Inst Complex Syst Theoret Soft Matter & Biophys 2, D-52425 Julich - Germany

• Document type: Journal article
• Source: Journal of Theoretical Biology; v. 462, p. 370-380, FEB 7 2019.
• Web of Science Citations: 2

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 which cannot be explained by steric hindrance alone. The cooperative effect requires a molecular repulsion in excess of a critical strength and disappears beyond a critical RNAP density, above which jamming due to collisions takes over. For strong repulsion and at the same time strong stochastic blocking, cooperative pushing at low RNAP densities is suppressed, but a reentrance regime at higher densities appears. (C) 2018 Elsevier Ltd. All rights reserved. (AU)

• FAPESP's process: 17/20696-0 - From interacting particle systems to topological data analysis
• Grantee: Vladimir Belitsky
• Support Opportunities: Research Grants - Visiting Researcher Grant - International
• FAPESP's process: 17/10555-0 - Stochastic modeling of interacting systems
• Grantee: Fabio Prates Machado
• Support Opportunities: Research Projects - Thematic Grants