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

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

  • Mol Cell. 2021 Mar 4;81(5):1084-1099.e6. doi: 10.1016/j.molcel.2020.12.025.
Kyosuke Nakamura 1,  Georg Kustatscher 2,  Constance Alabert 3,  Martina Hödl 3,  Ignasi Forne 4,  Moritz Völker-Albert 4,  Shankha Satpathy 5,  Tracey E Beyer 1,  Niels Mailand 5,  Chunaram Choudhary 5,  Axel Imhof 4,  Juri Rappsilber 6,  Anja Groth 7
Affiliations

Affiliations

  • 1 The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
  • 2 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
  • 3 Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
  • 4 Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg- Martinsried, Germany.
  • 5 The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
  • 6 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany. Electronic address: juri.rappsilber@tu-berlin.de.
  • 7 The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark. Electronic address: anja.groth@cpr.ku.dk.
PMID: 33450211 DOI: 10.1016/j.molcel.2020.12.025
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.

Keywords

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

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