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

Abstract

Oncogene-induced DNA replication stress contributes critically to the genomic instability present in cancer1–4. However, elucidating how oncogenes deregulate DNA replication has been impeded by the difficulty in mapping replication initiation sites on the human genome. In this study, using a sensitive assay to monitor nascent DNA synthesis in early S phase, we identified thousands of replication initiation sites in cells before and after induction of the oncogenes CCNE1 or MYC. Remarkably, both oncogenes induced firing of a novel set of DNA replication origins that mapped within highly transcribed genes. These ectopic origins were normally suppressed by transcription during G1, but precocious entry into S phase, prior to all genic regions having been transcribed, allowed firing of origins within genes in cells with activated oncogenes. Forks from oncogene-induced origins were prone to collapse, as a result of conflicts between replication and transcription, and were associated with DNA double-strand break formation and chromosomal rearrangement breakpoints both in our experimental system and in a large cohort of human cancers. Thus, firing of intragenic origins caused by premature S phase entry represents a mechanism of oncogene-induced DNA replication stress that is relevant for genomic instability in human cancer.

A journey with common fragile sites: From S phase to telophase

“…Analysis of the consequences of drug‐mediated inhibition of transcription strongly suggested that a short G1 phase reduces the window of time during which ongoing transcription can clear the gene bodies of pre‐RC prior to replication initiation. The authors proposed that activation of intragenic origins induces conflicts between transcription and replication, which triggers the instability observed in these early regions . Together, these reports show that transcription shapes the initiation profile in both early and late replicating domains.…”

“…However, if the same mechanism operates at ERFSs and at CFSs, it remains to explain why, as discussed above, late replication is mandatory for CFS instability and why metaphase breaks map in the core of large transcribed fragile genes rather than in their 5′ and 3′ regions where initiation events also cluster. In addition, it would be interesting to determine how oncogene‐induced fragile regions mapped by Macheret and Halazonetis in early replicating domains relate to ERFSs. Further work will therefore be needed to reconcile the different sets of data, notably to clearly determine the role played by sequence‐dependent formation of secondary structures versus distribution of initiation events in fragile site setting.…”

Genomic instability in fragile sites—still adding the pieces

“…Cyclin E overexpression was shown to induce the occurrence of conflicts between the replication and transcription machineries due to increased numbers of simultaneously active replication forks . In a recent study, it was further shown that cyclin E overexpression and Myc activation induced a novel set of DNA replication origins that mapped within highly transcribed genes . These ectopic origins are normally suppressed by transcription during G1, but premature S‐phase entry, before all genes had been transcribed, allowed firing of origins within genes in cells with activated oncogenes.…”

Recent advances in understanding DNA replication: cell type–specific adaptation of the DNA replication program

“…Origin usage following oncogene activation was recently investigated genome-wide. The authors found that in these conditions new initiation zones, which were normally suppressed by transcription in G 1 , appear in intragenic regions 47 . These results also confirm an observation in drosophila showing that active transcription modulates MCM2-7 distribution 48 .…”