Genome-wide replication dynamics quantification reveals stress-induced delayed/under-replication as a hallmark of CFSs

We report Repli-Seq analysis of the replication program in human lymphoblasts grown in the absence or in the presence of aphidicolin, an inhibitor of replicative DNA polymerases used in vitro to destabilize CFSs. We identified regions displaying specific replication delay upon aphidicolin treatment, resulting in under-replication. We then further study the mechanisms leading to such specific delayed/under-replication within CFSs and show that transcription-dependent segregation of initiation events out of the gene body generates long-traveling forks in large transcribed domains, which elicits the replication timing delay responsible for CFS instability upon replication stress. Overall design: Repli-Seq experiments of human lymphoblastoid cells grown in the absence (3 biological replicates) or in the presence of 600 nM aphidicolin of 16h (2 biological replicates).