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Push back to respond better: regulatory inhibition of the DNA double-strand break response

Nature Reviews Molecular Cell Biology volume 14, pages 661–672 (2013)Cite this article

Subjects

Key Points

  • The response to DNA double-strand breaks (DSBs) is a highly dynamic signalling pathway that needs constant modulation by positive and negative control points. The negative regulation of DSB signalling is crucial to ensure the correct sequence and magnitude of signalling and repair reactions, to set the boundaries of the DNA damage-induced chromatin compartment and to reverse DNA damage-induced signalling events once DNA repair is completed.

  • Negative regulation of the DSB response occurs through various mechanisms, including the enzymatic removal of post-translational modifications and the modulation of protein stability.

  • Chromatin-based DSB signalling is orchestrated by ATM (ataxia-telangiectasia mutated)-dependent phosphorylation events and RING finger 8 (RNF8)–RNF168-mediated chromatin ubiquitylation. As a consequence, cells use numerous phosphatases and deubiquitylating enzymes to balance the activities of ATM and RNF8–RNF168. In addition, RNF168 is a limiting component of DSB signalling and determines the boundaries of the DNA damage domain on chromatin.

  • Negative regulatory mechanisms are also crucial for homologous recombination-mediated DSB repair. Key nodes of negative regulation are the commitment to DNA end resection via CtBP-interacting protein (CtIP) and the ordered assembly of first replication protein A (RPA) and then RAD51 on end-resected DNA.

  • Cells use negative regulatory mechanisms to suppress DNA damage responses in physiological settings in which DNA repair reactions are not desirable, for example at telomeres and during mitosis. In addition, to evade detection and promote the transmission of their genome, DNA viruses have developed strategies to subvert and manipulate the cellular DSB response machinery.

Abstract

Single DNA lesions such as DNA double-strand breaks (DSBs) can cause cell death or trigger genome rearrangements that have oncogenic potential, and so the pathways that mend and signal DNA damage must be highly sensitive but, at the same time, selective and reversible. When initiated, boundaries must be set to restrict the DSB response to the site of the lesion. The integration of positive and, crucially, negative control points involving post-translational modifications such as phosphorylation, ubiquitylation and acetylation is key for building fast, effective responses to DNA damage and for mitigating the impact of DNA lesions on genome integrity.

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Figure 1: Negative regulation is a central component of the DSB response.
Figure 2: The chromatin-associated ATM signal transduction pathway.
Figure 3: Regulation of H2A.X phosphorylation.
Figure 4: Regulation of chromatin ubiquitylation.
Figure 5: Physiological inhibition of the ATM pathway.
Figure 6: Regulation of CtIP-mediated end resection.

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Acknowledgements

The authors apologize to those whose important findings could not be mentioned as primary literature and/or cited owing to space constraints. The authors thank R. Szilard for critically reading the manuscript and S. Boulton for comments and for supporting S.P.'s participation in this Review. S.P. is supported by an European Molecular Biology Organization (EMBO) long-term fellowship. D.D. is the Thomas Kierans Chair in Mechanisms of Cancer Development and a Canada Research Chair (Tier 1) in Molecular Mechanisms of Genome Integrity. Work in the laboratory of D.D. is supported by a grant-in-aid from the Krembil Foundation.

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  1. Stephanie Panier

    Present address: Present address: DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms, London EN6 3LD, UK.,

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  1. The Lunenfeld–Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, M5G 1X5, Ontario, Canada

    Stephanie Panier & Daniel Durocher

  2. Department of Molecular Genetics, University of Toronto, M5S 3E1, Ontario, Canada

    Daniel Durocher

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PowerPoint slides

Glossary

DNA damage checkpoint

Signalling pathways that delay or arrest cell cycle progression in response to DNA damage.

Linker histone

Histone that is structurally and functionally distinct from nucleosomal core histones. It provides an interaction platform for numerous chromatin components and participates in the formation of the 30 nm chromatin fibre by linking nucleosome core particles.

Bromodomain

Protein–protein interaction domain that binds to acetylated Lys residues.

RING

Protein domain that is present in many E3 ubiquitin ligases. Contains conserved His and Cys residues and coordinates two Zn2+ ions.

E3 ubiquitin ligases

Key enzymes in the ubiquitylation reaction that are required for the attachment of ubiquitin moieties to a substrate protein. The E3 provides substrate specificity to a multistep reaction that first involves an E1 activating enzyme followed by an E2 ubiquitin-conjugating enzyme and then an E3 ubiquitin ligase.

26S proteasome

A large multisubunit protease complex that degrades polyubiquitylated proteins with certain ubiquitin chain topology. In mammals, it consists of a 20S proteolytic core particle and one or two 19S regulatory particles.

Degradative ubiquitin conjugates

Polyubiquitin chains that target proteins for degradation by the 26S proteasome. The best-studied examples are Lys48-linked ubiquitin chains.

Regulatory ubiquitylation

The addition of ubiquitin conjugates that regulate protein function instead of acting as a signal for proteasomal degradation. An example for regulatory ubiquitin conjugates are Lys63-linked ubiquitin chains.

E2 ubiquitin-conjugating enzymes

Enzymes that are required for the second step during ubiquitin conjugation. They receive activated ubiquitin from the E1 activating enzyme and then interact with an E3 ubiquitin ligase to attach the ubiquitin moiety to the substrate protein.

LRM

Small, linear motif that can be found adjacent to some ubiquitin-binding domains. Provides ligand specificity to ubiquitin-dependent protein–protein interactions.

JAMM–MPN+

A Zn2+-coordinating protein domain that confers isopeptidase activity and is present in a small subset of deubiquitylating enzymes. It is also known as the JAB1–MPN–MOV34 metalloenzyme domain.

Polycomb group

A group of proteins that have important roles in the maintenance of homeotic gene repression during development and stem cell renewal.

Tudor domains

Protein–protein interaction domains that were first found in the Drosophila melanogaster protein Tudor. These domains bind to methylated Arg or Lys residues.

Prolyl isomerase

Catalyses the cis–trans isomerization of peptide bonds that are amino-terminal to Pro residues in polypeptide chains.

Fanconi anaemia pathway

A DNA damage signalling pathway that coordinates the repair of DNA interstrand crosslinks. Germline mutations in genes encoding key components of this pathway are the underlying cause of Fanconi anaemia, which is characterized by congenital defects, cancer susceptibility and cellular hypersensitivity to DNA crosslinking agents.

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Panier, S., Durocher, D. Push back to respond better: regulatory inhibition of the DNA double-strand break response. Nat Rev Mol Cell Biol 14, 661–672 (2013). https://doi.org/10.1038/nrm3659

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