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

Nature volume 555, pages 112116 (01 March 2018) | Download Citation


Oncogene-induced DNA replication stress contributes critically to the genomic instability that is present in cancer1,2,3,4. However, elucidating how oncogenes deregulate DNA replication has been impeded by difficulty in mapping replication initiation sites on the human genome. Here, 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 and 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, before all genic regions had 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-stranded 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.

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We thank U. Schibler, R. Pillai, M. Docquier and present and past laboratory members for helpful discussions; J. Bartek for the U2OS cells inducibly overexpressing cyclin E; M. Eilers for the U2OS MycER cells; R. Beroukhim and S. Schumacher for access to and help with TCGA cancer data sets; and N. Roggli for help with the graphics scripts and the Flow Cytometry and Genomics platforms of the University of Geneva. This work was supported by grants from the European Commission (ONIDDAC) and the Swiss Science National Foundation.

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  1. Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland

    • Morgane Macheret
    •  & Thanos D. Halazonetis


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T.D.H. and M.M. designed the experiments and wrote the paper; M.M. performed the experiments; T.D.H. wrote the computer scripts and performed the bioinformatic analyses with contributions from M.M.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Thanos D. Halazonetis.

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    Life Sciences Reporting Summary

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    Supplementary Figure 1

    This file contains the gating strategy used in the flow cytometry analyses.

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    This file contains Supplementary Tables 1-11.

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    Supplementary Data

    This file contains all the scripts and datasets required to process and plot the replication and transcription sequencing data.

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