ATR and TopBP1 oppose to control dormant origin building, providing a first defence against replication stress

Replication stress, a major hallmark of cancers, sources from replication fork slowing or blocking. In response, activation of extra-origins, otherwise dormant, supports the replication rate. Whether the DNA replication checkpoint drives this compensation process remained unclear. Here, DNA combing analyses show that a linear relationship ties inter-origin distances to fork speeds and that the slope of this line, called stressline, accurately quantifies compensation efficiency. Comparison of the slopes in human cells with different genotypes elicits a model whereby TopBP1 locks the step-wise building of dormant origins at the pre-initiation complex step. Under stress, ATR triggers TopBP1 eviction from this complex, independently of CHK1, allowing building to proceed. We also developed ATRAP-seq, a genome-wide procedure whose data support the model and strongly suggest that compensation efficiency and limiting factors jointly govern the pace of replication domain activation. Altogether our results provide a comprehensive mechanism accounting for genome protection through loose replication checkpoint activation.