# Transcription–replication collisions trigger high-fidelity replication reset

## TL;DR

The study reveals a new DNA repair mechanism in bacteria that prevents genome instability caused by transcription–replication collisions.

## Contribution

A novel replication reset mechanism is identified that resolves DNA ends without recombination or mutagenesis.

## Key findings

- TRCs cause replisome stalling and free DNA ends through rear-ending from trailing replisomes.
- DNA ends are resolved via replication reset, which degrades the stalled replicore without genome damage.
- This process avoids triggering recombination, DNA damage response, or mutagenesis.

## Abstract

Double-stranded DNA ends arise from external agents or cellular processes like transcription–replication collisions (TRCs), threatening genome stability. Here, we performed genomic CRISPRi screens to uncover DNA end formation factors in Escherichia coli. We discovered that translation–transcription decoupling causes DNA end formation through a TRC-dependent pathway, which is lethal when DNA end processing by RecBCD is disrupted, but not when recombination is disrupted. We find that TRCs cause replisome stalling followed by “rear-ending” from trailing replisomes which generates free DNA ends, rather than strand breaks. Surprisingly, these DNA ends are resolved through a process we call “replication reset”, where the stalled replicore is degraded, without triggering recombination, the DNA damage response, or mutagenesis. This hidden replicore-degradation resets the replication cycle without consequence for the genome. This discovery reveals a novel DNA safeguard mechanism for preserving genome stability when replication is disturbed and challenges the notion that TRCs necessarily cause genome instability in bacteria.

Graphical Abstract