Chapter One - The Repair and Signaling Responses to DNA Double-Strand Breaks

https://doi.org/10.1016/B978-0-12-407676-1.00001-9Get rights and content

Abstract

A DNA double-strand break (DSB) has long been recognized as a severe cellular lesion, potentially representing an initiating event for carcinogenesis or cell death. The evolution of DSB repair pathways as well as additional processes, such as cell cycle checkpoint arrest, to minimize the cellular impact of DSB formation was, therefore, not surprising. However, the depth and complexity of the DNA damage responses being revealed by current studies were unexpected. Perhaps the most surprising finding to emerge is the dramatic changes to chromatin architecture that arise in the DSB vicinity. In this review, we overview the cellular response to DSBs focusing on DNA repair pathways and the interface between them. We consider additional events which impact upon these DSB repair pathways, including regulated arrest of cell cycle progression and chromatin architecture alterations. Finally, we discuss the impact of defects in these processes to human disease.

Introduction

A first review entitled DNA Breakage and Repair for Advances in Genetics was written in 1998. At this time, the major focus was to describe and discuss the relatively newly identified genes encoding proteins that function in the major DNA double-strand break (DSB) repair pathway: DNA nonhomologous end-joining (NHEJ). This was an exciting time in the field with the emerging notion that the major DSB repair pathway in mammalian cells was distinct to homologous recombination (HR), the process predominantly exploited by lower organisms, gaining credence as the NHEJ genes were identified. Additionally, an unanticipated role for NHEJ during V(D)J recombination, a critical process in development of the immune response which rearranges and rejoins the subexon components of the immunoglobulin and T cell receptor genes, had been newly revealed. Thus, understanding the NHEJ process was of interest not just to those workers in the DNA damage response (DDR) field but additionally to immunologists. Now in 2013, together with Aaron Goodarzi, we venture to revisit this area. Although distinct to earlier years, the field remains dynamic, rapidly advancing, and exciting. We now have substantial insight into the basic processes of NHEJ and HR at a structural and biochemical level and a sound appreciation of their cellular roles. Moreover, a recently described process of Alternative-NHEJ (Alt-NHEJ) has been identified. The significance of DSB signal transduction responses has gained credence and insight into the process and its impact on the DDR is slowly emerging. Critical current questions are: how these responses interface, how they are influenced by chromatin structure, and how chromatin is changed to optimally promote DSB repair and avoid genomic instability? Most provocatively, how does the malfunction of these processes lead to chromosomal translocations and rearrangements? The field is substantially broader and more complex than in 1998, making the task of providing an overview more challenging. Here, we aim to provide a description of our current understanding of the DSB repair processes, the signaling response, the interplay between them and other metabolic processes involving DNA, and the impact of, and changes to, the chromatin environment.

Section snippets

Formation of DSBs

There is increasing recognition that the route by which a DSB arises strongly influences the pathway governing its repair. DSBs can arise in a developmentally programmed manner (such as V(D)J recombination, class switch recombination (CSR), or meiosis), following replication fork arrest or stalling, from endogenously arising DNA damage or from exogenous DNA-damaging agents such as ionizing radiation (IR). Each process produces DSBs of a distinctive nature (summarized in Figure 1.1). DSBs that

Mechanisms of DSB Rejoining

HR and NHEJ represent the two major DSB repair pathways; additionally, less well-understood processes have also been described.

DNA Damage Response Signaling

In addition to repair mechanisms, DSBs activate a signal transduction process that drives a range of cellular consequences. Ataxia telangiectasia mutated (ATM) protein lies at the core of the DSB signaling response although in certain circumstances (e.g., following DSB end resection or if DSBs become encountered at the replication fork), ataxia telangiectasia mutated and Rad3 related (ATR) can also trigger a signaling-related cascade. Several outstanding reviews on the choreography of DSB

Functions of the DDR Assembly

Ataxia telangiectasia (A-T), the human disorder caused by ATM mutation, is one of the most radiosensitive human conditions, demonstrating the importance of ATM signaling to the DSB response (Jeggo & Lavin, 2009). Studies of chromosomal breakage in A-T cells revealed increased persisting chromosome breaks (Jeggo & Lavin, 2009). However, DSB repair analysis assessed using procedures such as pulsed field gel electrophoresis (PFGE) or the rate of loss of the DSB marker, γH2AX, revealed nearly

Impact of cell cycle phase and resection

There is increasing evidence that the choice between DSB repair pathways is highly regulated and represents a significant function of IRIF assembly. Since HR is argued to be a more accurate DSB repair process and functions only in late S/G2, it was widely assumed that HR would represent the major DSB repair pathway in G2 phase (see below). However, studies focusing on the analysis of irradiated G2 cells (and inhibition of the progression of irradiated S phase cells into G2) have shown that, in

Contribution of Defects in DSB Rejoining Processes to Human Disease

Given the role of NHEJ in V(D)J recombination, a striking and expected phenotype of mice lacking NHEJ proteins is severe combined immunodeficiency (SCID). Mutations in NHEJ proteins (DNA ligase IV, XLF, Artemis, and DNA-PKcs) have now been identified in a subclass of SCID or CID patients, defined as radiosensitive-SCID (RS-SCID) (O'Driscoll et al., 2001, O'Driscoll and Jeggo, 2006). Such patients undergo bone marrow transplantation (BMT) frequently, and the identification of such patients is

Concluding Remarks

Here, we have overviewed the dramatic changes that arise as a consequence of DSB formation and consider how these changes impact upon the DSB repair process. Studies using lower organisms predicted that HR would represent the major DSB repair pathway in mammalian cells. However, it is increasingly evident that NHEJ carries out repair of most DSBs with HR functioning predominantly to handle lesions, including one-ended DSBs, at replication forks. One consideration underlying the greater

References (199)

  • M.A. Bogue et al.

    V(D)J recombination in Ku86-deficient mice: Distinct effects on coding, signal, and hybrid joint formation

    Immunity

    (1997)
  • A. Bothmer et al.

    Regulation of DNA End Joining, Resection, and Immunoglobulin Class Switch Recombination by 53BP1

    Molecular Cell

    (2011)
  • M.V. Botuyan et al.

    Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair

    Cell

    (2006)
  • D. Buck et al.

    Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly

    Cell

    (2006)
  • D.W. Chan et al.

    The DNA-dependent protein kinase is inactivated by autophosphorylation of the catalytic subunit

    The Journal of Biological Chemistry

    (1996)
  • R. Chayot et al.

    DNA polymerase mu is a global player in the repair of non-homologous end-joining substrates

    DNA Repair

    (2012)
  • I. Chiolo et al.

    Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair

    Cell

    (2011)
  • A. Ciccia et al.

    The DNA damage response: Making it safe to play with knives

    Molecular Cell

    (2010)
  • K.A. Coleman et al.

    The BRCA1-RAP80 complex regulates DNA repair mechanism utilization by restricting end resection

    The Journal of Biological Chemistry

    (2011)
  • M.A. Deardorff et al.

    RAD21 mutations cause a human cohesinopathy

    The American Journal of Human Genetics

    (2012)
  • J. Della-Maria et al.

    Human Mre11/human Rad50/Nbs1 and DNA ligase IIIalpha/XRCC1 protein complexes act together in an alternative nonhomologous end joining pathway

    The Journal of Biological Chemistry

    (2011)
  • L. Deriano et al.

    Roles for NBS1 in alternative nonhomologous end-joining of V(D)J recombination intermediates

    Molecular Cell

    (2009)
  • J. Drouet et al.

    DNA-dependent protein kinase and XRCC4-DNA ligase IV mobilization in the cell in response to DNA double strand breaks

    The Journal of Biological Chemistry

    (2005)
  • M. Falk et al.

    Chromatin structure influences the sensitivity of DNA to gamma-radiation

    Biochimica et Biophysica Acta

    (2008)
  • M. Falk et al.

    Higher-order chromatin structure in DSB induction, repair and misrepair

    Mutation Research

    (2010)
  • L. Feng et al.

    The Lys63-specific deubiquitinating enzyme BRCC36 is regulated by two scaffold proteins localizing in different subcellular compartments

    The Journal of Biological Chemistry

    (2010)
  • F. Garces et al.

    The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

    Molecular Cell

    (2011)
  • A.A. Goodarzi et al.

    ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin

    Molecular Cell

    (2008)
  • M. Hammel et al.

    XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair

    The Journal of Biological Chemistry

    (2011)
  • M. Hammel et al.

    Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex

    The Journal of Biological Chemistry

    (2010)
  • K.O. Hartley et al.

    DNA-dependent protein kinase catalytic subunit: A relative of phosphatidylinositol 3-kinase and the ataxia telangiectasia gene product

    Cell

    (1995)
  • J. Hilario et al.

    Visualizing protein-DNA interactions at the single-molecule level

    Current Opinion in Chemical Biology

    (2010)
  • K. Hiom et al.

    A stable RAG1-RAG2-DNA complex that is active in V(D)J cleavage

    Cell

    (1997)
  • G. Iliakis

    Backup pathways of NHEJ in cells of higher eukaryotes: Cell cycle dependence

    Radiotherapy and Oncology

    (2009)
  • A.V. Ivanov et al.

    PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing

    Molecular Cell

    (2007)
  • E.M. Kass et al.

    Collaboration and competition between DNA double-strand break repair pathways

    FEBS Letters

    (2010)
  • M.B. Kastan et al.

    A mammalian cell cycle checkpoint pathway utilizing p53 and GADD45 is defective in ataxia-telangiectasia

    Cell

    (1992)
  • K. Acs et al.

    The AAA-ATPase VCP/p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks

    Nature Structural & Molecular Biology

    (2011)
  • P. Andrade et al.

    Limited terminal transferase in human DNA polymerase mu defines the required balance between accuracy and efficiency in NHEJ

    Proceedings of the National Academy of Sciences of the United States of America

    (2009)
  • S.N. Andres et al.

    A human XRCC4-XLF complex bridges DNA

    Nucleic Acids Research

    (2012)
  • N. Ayoub et al.

    HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response

    Nature

    (2008)
  • N. Ayoub et al.

    Mobilization and recruitment of HP1: A bimodal response to DNA breakage

    Cell Cycle

    (2009)
  • C. Baldeyron et al.

    HP1alpha recruitment to DNA damage by p150CAF-1 promotes homologous recombination repair

    The Journal of Cell Biology

    (2011)
  • J.C. Bell et al.

    Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA

    Nature

    (2012)
  • N.K. Bernstein et al.

    Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase

    Nucleic Acids Research

    (2009)
  • A. Beucher et al.

    ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2

    The EMBO Journal

    (2009)
  • R.M. Blundred et al.

    DNA double-strand break repair, immunodeficiency and the RIDDLE syndrome

    Expert Review of Clinical Immunology

    (2011)
  • C. Boboila et al.

    Alternative end-joining catalyzes robust IgH locus deletions and translocations in the combined absence of ligase 4 and Ku70

    Proceedings of the National Academy of Sciences of the United States of America

    (2010)
  • V. Borde et al.

    Programmed induction of DNA double strand breaks during meiosis: Setting up communication between DNA and the chromosome structure

    Current Opinion in Genetics & Development

    (2013)
  • A. Bothmer et al.

    53BP1 regulates DNA resection and the choice between classical and alternative end joining during class switch recombination

    The Journal of Experimental Medicine

    (2010)
  • Cited by (181)

    • Kinome-wide screening uncovers a role for Bromodomain Protein 3 in DNA double-stranded break repair

      2023, DNA Repair
      Citation Excerpt :

      Thus, HDR accounts for an important portion of the DNA DSB activity in a wild-type human cell. Not surprisingly therefore, mutations of many HDR genes are associated with cancer predisposition in humans [4, 5]. One of the most critical HDR genes is Radiation Sensitive 51 (RAD51), which is responsible for the homology searches and strand exchanges required during HDR [6].

    View all citing articles on Scopus
    View full text