Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress

Oncogenes, by inducing DNA replication stress, are a critical factor underlying genomic instability in cancer. Towards better understanding the mechanisms by which oncogenes deregulate DNA replication, we characterized, genome-wide, the replication timing domains (REPLIseq), the replication initiation profile (EdUseq), the transcription profile (EUseq) and the DNA double-strand break profile (LAM-HTGTS) of cells before and after oncogene activation. We studied two U2OS model systems, in which either the cyclin E or the MYC oncogenes could be inducibly activated. Both oncogenes led to firing of ectopic replication origins that mapped to highly transcribed genes. We could show that, during G1 phase, these origins were normally erased by transcription, but that oncogenes, by accelerating S phase entry, allowed origins to fire prior to transcription having reached the 3' end of genes. Oncogene-induced origins gave rise to replication forks prone to collapse due to replication transcription conflicts and were associated with chromosomal rearrangements mapped in our model system, but also in a large cohort of human cancers.