The intra-S phase checkpoint directly regulates replication elongation to preserve the integrity of stalled replisomes

The intra-S phase checkpoint is essential to stabilize stalling/stalled replication forks. However, the mechanism underlying checkpoint regulation is poorly understood; two key questions remain to be answered: 1) why are stalling forks unstable when checkpoint is deficient, and 2) which protein(s) is the critical target of checkpoint regulation? Here, we demonstrate that CMG replicative helicase becomes uncoupled from stalled/blocked DNA polymerases in checkpoint-deficient cds1Chk2△ cells, likely reflecting physical separation of the helicase and polymerases. This uncoupling is prevented by the Cds1Chk2-mediated phosphorylation of Cdc45. We propose that replication elongation is directly regulated in response to replication fork stalling via phosphorylation of Cdc45, which significantly reduces CMG helicase processivity, in order to prevent helicase–polymerase uncoupling and promote replication fork stability.