Replication stress induces amplification of early replicating loci in the human genome

DNA replication stress, marked by slowed or stalled replication forks, is a major source of genomic instability in cancer and drives tumor evolution.The molecular pathways that stabilize, repair or restart individual replication forks are well characterized, yet little is known about how the DNA replication program responds to replication stress at a genome-wide scale.Here, we implemented high-throughput sequencing of nascent DNA synthesis to map loci where replication was able to re-start after release from global replication stress.Results showed replication restart occurred most efficiently in naturally early-replicating regions.Strikingly, we also observed nascent DNA synthesis near early-firing replication origins even in late S-phase cells recovering from replication stress, which presumably involved break-induced replication (BIR) of already duplicated regions.Such aberrant re-replication events correlated with significant copy number amplifications, suggesting a novel mechanism for pathogenic gene amplification.