Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes

Summary

Transcription hinders replication fork progression and stability. The ATR checkpoint and specialized DNA helicases assist DNA synthesis across transcription units to protect genome integrity. Combining genomic and genetic approaches together with the analysis of replication intermediates, we searched for factors coordinating replication with transcription. We show that the Sen1/Senataxin DNA/RNA helicase associates with forks, promoting their progression across RNA polymerase II (RNAPII)-transcribed genes. sen1 mutants accumulate aberrant DNA structures and DNA-RNA hybrids while forks clash head-on with RNAPII transcription units. These replication defects correlate with hyperrecombination and checkpoint activation in sen1 mutants. The Sen1 function at the forks is separable from its role in RNA processing. Our data, besides unmasking a key role for Senataxin in coordinating replication with transcription, provide a framework for understanding the pathological mechanisms caused by Senataxin deficiencies and leading to the severe neurodegenerative diseases ataxia with oculomotor apraxia type 2 and amyotrophic lateral sclerosis 4.

Abstract

Graphical Abstract

Highlights

► Sen1 associates with replication forks ► Sen1 assists fork progression across RNA-polymerase-II-transcribed genes ► Sen1 counteracts RNA-DNA hybrid accumulation in S phase ► Sen1 role in replication is separable from its transcription termination function

Abstract

Senataxin protects cells from the potentially deleterious consequences of head-on collisions between DNA replication and DNA transcription by preventing the accumulation of RNA-DNA hybrids that expose cells to genome instability.