Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination

Kyosuke Nakamura, Georg Kustatscher, Constance Alabert, Martina Hödl, Ignasi Forne, Moritz Völker-Albert, Shankha Satpathy, Tracey E. Beyer, Niels Mailand, Chunaram Choudhary, Axel Imhof, Juri Rappsilber, Anja Groth

    Research output: Contribution to journalArticlepeer-review

    49 Citations (Scopus)
    92 Downloads (Pure)

    Abstract

    Cells have evolved an elaborate DNA repair network to ensure complete and accurate DNA replication. Defects in these repair machineries can fuel genome instability and drive carcinogenesis while creating vulnerabilities that may be exploited in therapy. Here, we use nascent chromatin capture (NCC) proteomics to characterize the repair of replication-associated DNA double-strand breaks (DSBs) triggered by topoisomerase 1 (TOP1) inhibitors. We reveal profound changes in the fork proteome, including the chromatin environment and nuclear membrane interactions, and identify three classes of repair factors according to their enrichment at broken and/or stalled forks. ATM inhibition dramatically rewired the broken fork proteome, revealing that ataxia telangiectasia mutated (ATM) signalling stimulates DNA end resection, recruits PLK1, and concomitantly suppresses the canonical DSB ubiquitination response by preventing accumulation of RNF168 and BRCA1-A. This work and collection of replication fork proteomes provide a new framework to understand how cells orchestrate homologous recombination repair of replication-associated DSBs. By systematic proteomics profiling of replication forks challenged by the topoisomerase I inhibitor camptothecin, Nakamura et al. identify dedicated repair factors for broken replication forks, characterize their chromatin environment, and reveal that ATM and PLK1 promote homologous recombination by suppressing the canonical DNA double-strand break ubiquitination response at broken forks.

    Original languageEnglish
    Pages (from-to)1084-1099.e6
    Number of pages22
    JournalMolecular Cell
    Volume81
    Issue number5
    Early online date14 Jan 2021
    DOIs
    Publication statusPublished - 4 Mar 2021

    Keywords

    • ATM
    • BRCA1-A
    • Camptothecin
    • homologous recombination
    • nascent chromatin capture
    • NDRG3
    • NHEJ
    • PLK1
    • replication stress
    • UBAP2

    ASJC Scopus subject areas

    • Molecular Biology
    • Cell Biology

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