Transcribing RNA polymerases: Dynamics of Twin Supercoiled Domains

TL;DR

This study uses simulations to explore the detailed torsional dynamics of DNA during transcription by RNA polymerase, revealing complex behaviors of supercoiled domains that differ from traditional models.

Contribution

The paper introduces a coarse-grained simulation approach to analyze the dynamics of twin supercoiled domains during transcription, highlighting behaviors not captured by simpler models.

Findings

Negatively supercoiled plectonemes form periodically upstream of RNAP.

Slow rotational relaxation prevents formation of positively supercoiled plectonemes ahead of RNAP.

Topological barriers influence the stability and dynamics of supercoiled domains.

Abstract

Gene transcription by a RNA Polymerase (RNAP) enzyme requires that double-stranded DNA be locally and transiently opened, which results in an increase of DNA supercoiling downstream of the RNAP and a decrease of supercoiling upstream of it. When the DNA is initially torsionally relaxed and the RNAP experiences sufficiently large rotational drag, these variations lead to positively supercoiled plectonemes ahead of the RNAPs and negatively supercoiled ones behind it, a feature known as ''Twin Supercoiled Domain'' (TSD). The present work aims at deciphering into some more detail the torsional dynamics of circular DNA molecules being transcribed by RNAP enzymes. To this end, we performed Brownian Dynamics simulations with a specially designed coarse-grained model. Depending on the superhelical density of the DNA molecule and the ratio of RNAP's twist injection rate and rotational relaxation speed, simulations reveal a rich panel of behaviors, which sometimes differ markedly from the crude TSD picture. In particular, for sufficiently slow rotational relaxation speed, positively supercoiled plectonemes never form ahead of a RNAP that transcribes a DNA molecule with physiological negative supercoiling. Rather, negatively supercoiled plectonemes form almost periodically at the upstream side of the RNAP and grow up to a certain length before detaching from the RNAP and destabilizing rapidly. The extent to which topological barriers hinder the dynamics of TSDs is also discussed. 2 SIGNIFICANCE : It has been known for four decades that a RNA Polymerase enzyme which transcribes torsionally relaxed DNA favors the formation of positively supercoiled plectonemes downstream of its position and negatively supercoiled ones upstream of it. How these plectonemes are born, how they evolve and eventually vanish, has however received little attention. We used coarse-grained modeling and Brownian Dynamics simulations to provide theoretical insight into this question, for both torsionally relaxed DNA and negatively supercoiled (bacterial) DNA. The contact maps obtained from these simulations reveal a rich dynamics, which depend essentially on the superhelical density of the DNA molecule and the torsional relaxation speed of the RNA Polymerase. Twin Supercoiled Domains are certainly NOT static features but instead very dynamic ones.