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RNA Polymerase interactions and elongation rate.

V Belitsky1, G M Schütz2

  • 1Instituto de Matemática e Estátistica, Universidade de São Paulo, Rua do Matão, 1010, CEP 05508-090, São Paulo - SP, Brazil.

Journal of Theoretical Biology
|November 30, 2018
PubMed
Summary
This summary is machine-generated.

Non-steric molecular interactions between RNA polymerases (RNAP) on DNA tracks influence transcription elongation kinetics. Cooperative pushing enhances RNAP velocity, but jamming occurs at high densities.

Keywords:
CooperativityExclusion processMarkov modelRNA polymeraseTranscription elongation

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Biochemistry

Background:

  • Transcription elongation by RNA polymerase (RNAP) is a fundamental biological process.
  • RNAP motors move along DNA tracks, and their interactions can affect elongation rates.
  • Previous models often focused on steric hindrance, neglecting non-steric molecular interactions.

Purpose of the Study:

  • To investigate the impact of non-steric molecular interactions between RNAP motors on transcription elongation kinetics.
  • To develop a stochastic model for analyzing RNAP density, interaction strength, and other factors influencing elongation.
  • To understand the mechanisms of cooperative pushing and jamming in RNAP dynamics.

Main Methods:

  • Development of a stochastic model for transcription elongation.
  • Analytical computation of stationary properties of RNAP movement.
  • Analysis of RNAP density, interaction strength, NTP concentration, and pyrophosphate release rate.

Main Results:

  • Non-steric molecular interactions, not just steric hindrance, strongly determine transcription elongation kinetics.
  • Cooperative pushing, an enhanced RNAP velocity, arises from stochastic pushing and requires critical molecular repulsion.
  • Jamming due to collisions limits cooperative effects at high RNAP densities; reentrance regimes appear under specific conditions.

Conclusions:

  • Molecular repulsion and stochastic pushing play crucial roles in RNAP cooperative dynamics.
  • RNAP density is a critical factor determining the balance between cooperation and jamming.
  • The study provides a quantitative framework for understanding complex RNAP interactions during transcription.