# Transcriptional bursts in a non-equilibrium model for gene regulation by supercoiling

## TL;DR

This paper presents a non-equilibrium stochastic model linking DNA supercoiling dynamics to transcriptional bursting, revealing how enzyme activity and gene arrangement influence gene expression patterns.

## Contribution

It introduces a novel model that captures the coupling between supercoiling and transcription, highlighting conditions that lead to bursty or wave-like gene expression behaviors.

## Key findings

- Bursty transcription occurs when transcription initiation and supercoiling dissipation timescales are separated.
- Supercoiling fluctuations at the promoter are non-Gaussian in the bursty phase.
- Gene orientation and activity control can switch between bursty and wave-like transcription modes.

## Abstract

We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a separation between the timescales of transcription initiation and supercoiling dissipation - the latter may either be diffusive or mediated by topological enzymes, such as type I or type II topoisomerases. In multigenic DNA domains we observe either bursty transcription, or transcription waves; the type of behaviour can be selected for by controlling gene activity and orientation. In the bursty phase, the statistics of supercoiling fluctuations at the promoter are markedly non-Gaussian.