The replication checkpoint prevents fork stalling by reducing transcription
The replication checkpoint is essential for maintaining genome stability during replication stress. The prevailing view is that, without this pathway, stalled DNA replication forks lose structural integrity and collapse, preventing replication resumption and ultimately causing cell death. Here, we show that transcription is a major cause of replication stress in budding yeast checkpoint mutants. Checkpoint signaling limits replication defects by reducing RNA polymerase II and III occupancy at highly transcribed genes, particularly those encoding ribosomal proteins. Reducing transcription at these loci reduces fork stalling and the sensitivity of checkpoint mutants to hydroxyurea-induced replication stress. In human cells, transcription inhibition likewise improves replication recovery when ATR is inhibited, suggesting that this function is conserved. Together, our findings extend the canonical view of critical checkpoint functions: in addition to stabilizing stalled forks, it actively reduces RNA polymerase roadblocks that would otherwise impede their progression.