Camptothecin-Induced Replication Stress Affects DNA Replication Profiling by E/L Repli-Seq

E/L Repli-seq is a powerful tool for detecting cell type-specific replication landscapes in mammalian cells, but its potential to monitor DNA replication under replication stress awaits better understanding. Here, we used E/L Repli-seq to examine the temporal order of DNA replication in human retinal pigment epithelium cells treated with the topoisomerase I inhibitor camptothecin. We found that the replication profiles by E/L Repli-seq exhibits characteristic patterns after replication-stress induction, including the loss of specific initiation zones within individual early replicating timing domains. We also observed global disappearance of the replication timing domain structures in the profiles, which can be explained by checkpoint-dependent suppression of replication initiation. Thus, our results demonstrate the effectiveness of E/L Repli-seq at identifying cells with replication-stress-induced altered DNA replication programs. Analysis of early and late replicating chromosomal regions in human RPE cells with and without CPT-induced replication stress.