Theoretical analysis of transcription process with polymerase stalling

TL;DR

This paper provides a theoretical analysis of how polymerase stalling, backtracking, bypass, and detachment influence the effective transcription rate and efficiency, revealing conditions under which these processes can enhance transcription.

Contribution

It introduces a mathematical framework to analyze the effects of polymerase stalling, backtracking, bypass, and detachment on transcription efficiency, offering new insights into transcription regulation mechanisms.

Findings

Detachment of stalled polymerase can increase transcription rate and efficiency.

Higher bypass rates generally decrease transcription effectiveness.

Under certain conditions, bypass can increase transcription rate when backtracking and detachment are absent.

Abstract

Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled, polymerase may backtrack along the template to the previous nucleotide to wait for the repair of the damaged site, or simply bypass the barrier or damaged site and consequently synthesize an incorrect messenger RNA, or degrade and detach from the template. Thus, the {\it effective} transcription rate (the rate to synthesize correct product mRNA) and the transcription {\it effectiveness} (the ratio of the {\it effective} transcription rate to the {\it effective} transcription initiation rate) are both influenced by polymerase stalling events. This study shows that, Without backtracking, detachment of stalled polymerase can also help to increase the {\it effective} transcription rate and transcription {\it effectiveness}. Generally, the increase of bypass rate of the stalled polymerase will lead to the decrease of the {\it effective} transcription rate and transcription {\it effectiveness}. But when both detachment rate and backtracking rate of the stalled polymerase vanish, the {\it effective} transcription rate may also be increased by the bypass mechanism.