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

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.
Original languageEnglish
Pages (from-to)P1084-1099.E6
Number of pages16
JournalMolecular Cell
Volume81
Issue number5
Early online date14 Jan 2021
DOIs
Publication statusPublished - 4 Mar 2021

Keywords

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

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