Trends in Cell Biology
Volume 26, Issue 1, January 2016, Pages 52-64
Journal home page for Trends in Cell Biology

Review
Special Issue: Quality Control
Repair Pathway Choices and Consequences at the Double-Strand Break

https://doi.org/10.1016/j.tcb.2015.07.009Get rights and content

Trends

Of the four known pathways for repairing DNA DSBs, some evolved towards high-fidelity processes (HR and C-NHEJ), while others are intrinsically mutagenic (alt-EJ and SSA).

Some repair pathways are end resection-independent (C-NHEJ), while others are end resection-dependent (HR, alt-EJ, and SSA). End resection likely plays a key role in dictating DNA repair pathway choice.

Homology-based repair pathways (HR, alt-EJ, and SSA) are competitive and mutually regulated around the RAD51 presynaptic and postsynaptic steps of HR.

Error-prone repair pathways can compensate for the loss of HR. Polθ (an alt-EJ polymerase) is upregulated in HR-deficient cancers: loss of the HR and Polθ-mediated alt-EJ pathways is synthetic lethal.

DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genomic integrity. Failure to repair a DSB has deleterious consequences, including genomic instability and cell death. Indeed, misrepair of DSBs can lead to inappropriate end-joining events, which commonly underlie oncogenic transformation due to chromosomal translocations. Typically, cells employ two main mechanisms to repair DSBs: homologous recombination (HR) and classical nonhomologous end joining (C-NHEJ). In addition, alternative error-prone DSB repair pathways, namely alternative end joining (alt-EJ) and single-strand annealing (SSA), have been recently shown to operate in many different conditions and to contribute to genome rearrangements and oncogenic transformation. Here, we review the mechanisms regulating DSB repair pathway choice, together with the potential interconnections between HR and the annealing-dependent error-prone DSB repair pathways.

Section snippets

Mechanisms of DNA DSB Repair

Detection and faithful repair of damaged DNA is essential for genome integrity. Many types of DNA lesions impede replication fork progression, resulting in replication fork collapse and DSB formation with loss of physical continuity of the genome [1]. The repair of DSBs involves four possible mechanisms (Figure 1). The first mechanism is C-NHEJ. In this mechanism, the DSB is repaired by blunt end ligation independently of sequence homology, but requiring many factors such as Ku70/80, DNA-PKcs,

Role of End Resection in DSB Repair Choice

Given that three of the pathways diverge at the early step of end resection and have different outcomes (Figure 1), it is likely that end resection dictates pathway choice and repair outcome [12]. The initial phase of end resection, called ‘end clipping’, is carried out by the structure-specific nuclease MRE11 and CtIP. In this phase, a relatively small number of base pairs (i.e., 20 bp in mammalian cells or 100–300 bp in yeast) are processed, making the DNA ends available for alt-EJ 13, 14. In

Homologous Recombination Control: The RAD51 Hub in Homology-Based Repair Pathway Choice

Once end resection has occurred, the C-NHEJ repair pathway is prevented and any of the three homology-based pathways, that is, SSA, alt-EJ, and HR, can be invoked. Usage of these pathways can be affected by regulation of and competition with the RAD51 presynaptic and postsynaptic steps. We focus on positive and negative regulators of RAD51 function. Upon DNA damage induction, the RPA complex initially competes with RAD51 for ssDNA binding in yeast and mammals 17, 40. However, RPA has also a

Connection between HR and alt-EJ

alt-EJ functions in S phase independently of C-NHEJ factors and, until recently, was considered a backup repair pathway for C-NHEJ for joining chromosomal DSBs, particularly during V(D)J recombination 2, 71, 72. However, recent advances have shown that the alt-EJ and HR pathways compete for the repair of DSBs 49, 73. While both alt-EJ and HR share a common initial resection mechanism [8], processing of resected ends in HR is catalyzed by the eukaryotic RecA homolog, RAD51, while PARP1 is

Annealing-Dependent DSB Repair Outcomes and Their Mutational Signatures

As the repair of DSBs, via annealing-dependent pathways, introduces insertions and/or deletions (Figure 5), one can predict that the use of such DNA repair mechanisms will leave behind a particular genomic signature, or ‘genomic scar’, distinct from that of HR-mediated repair, which usually preserves genomic integrity. As modern next-generation sequencing technologies can rapidly identify cancer risk alleles of many genes, genome-wide sequencing and loss of heterozygosity (LOH) profiling have

Concluding Remarks

Here, we have reviewed the current knowledge regarding pathways used for the repair of DSBs through the lens of clinical applications. We have discussed regulation of the four known DSB repair pathways and how error-prone DNA repair pathways can compensate for the loss of HR. Understanding the basic regulation of DNA repair mechanisms has led to advances in synthetic lethality-based drug development. For several decades, significant effort has focused on identifying unique oncoproteins or

Acknowledgments

We would like to thank Jessica C. Liu and Prabha Sarangi for editing the manuscript and helpful discussions. R.C. is a recipient of the Ovarian Cancer Research Fellowship (OCRF). B.R. is a recipient of the Italian Association for Cancer Research (AIRC) Fellowships for Abroad. This work was supported by National Institutes of Health (NIH) grants P50CA168504 and R01HL52725 and by grants from the OCRF and Breast Cancer Research Foundation (BCRF) to A.D.D.

References (105)

  • S.E. Peterson

    Activation of DSB processing requires phosphorylation of CtIP by ATR

    Mol. Cell

    (2013)
  • H. Chen

    RPA coordinates DNA end resection and prevents formation of DNA hairpins

    Mol. Cell

    (2013)
  • N. Ayoub

    The carboxyl terminus of Brca2 links the disassembly of Rad51 complexes to mitotic entry

    Curr. Biol.

    (2009)
  • G.L. Moldovan

    Inhibition of homologous recombination by the PCNA-interacting protein PARI

    Mol. Cell

    (2012)
  • F. Li

    Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates

    Mol. Cell

    (2008)
  • S. Schwendener

    Physical interaction of RECQ5 helicase with RAD51 facilitates its anti-recombinase activity

    J. Biol. Chem.

    (2010)
  • M.N. Islam

    A variant of the breast cancer type 2 susceptibility protein (BRC) repeat is essential for the RECQL5 helicase to interact with RAD51 recombinase for genome stabilization

    J. Biol. Chem.

    (2012)
  • J.A. Sommers

    FANCJ uses its motor ATPase to destabilize protein–DNA complexes, unwind triplexes, and inhibit RAD51 strand exchange

    J. Biol. Chem.

    (2009)
  • A. Grabarz

    A role for BLM in double-strand break repair pathway choice: prevention of CtIP/Mre11-mediated alternative nonhomologous end-joining

    Cell Rep.

    (2013)
  • J. Simandlova

    FBH1 helicase disrupts RAD51 filaments in vitro and modulates homologous recombination in mammalian cells

    J. Biol. Chem.

    (2013)
  • L.J. Barber

    RTEL1 maintains genomic stability by suppressing homologous recombination

    Cell

    (2008)
  • K. Gari

    The Fanconi anemia protein FANCM can promote branch migration of Holliday junctions and replication forks

    Mol. Cell

    (2008)
  • C.A. Adelman et al.

    Metabolism of postsynaptic recombination intermediates

    FEBS Lett.

    (2010)
  • J.D. Ward

    Overlapping mechanisms promote postsynaptic RAD-51 filament disassembly during meiotic double-strand break repair

    Mol. Cell

    (2010)
  • M. Audebert

    Effect of double-strand break DNA sequence on the PARP-1 NHEJ pathway

    Biochem. Biophys. Res. Commun.

    (2008)
  • M. McVey et al.

    MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings

    Trends Genet.

    (2008)
  • H.L. Klein

    The consequences of Rad51 overexpression for normal and tumor cells

    DNA Repair

    (2008)
  • J. Unno

    FANCD2 binds CtIP and regulates DNA-end resection during DNA interstrand crosslink repair

    Cell Rep.

    (2014)
  • O. Murina

    FANCD2 and CtIP cooperate to repair DNA interstrand crosslinks

    Cell Rep.

    (2014)
  • P. Sung

    Function of yeast Rad52 protein as a mediator between replication protein A and the Rad51 recombinase

    J. Biol. Chem.

    (1997)
  • C.C. Liang

    UHRF1 is a sensor for DNA interstrand crosslinks and recruits FANCD2 to initiate the Fanconi anemia pathway

    Cell Rep.

    (2015)
  • Y. Wu

    Rad51 protein controls Rad52-mediated DNA annealing

    J. Biol. Chem.

    (2008)
  • S. Nik-Zainal

    The life history of 21 breast cancers

    Cell

    (2012)
  • K.K. Chiruvella

    Repair of double-strand breaks by end joining

    Cold Spring Harb. Perspect. Biol.

    (2013)
  • M.J. Difilippantonio

    DNA repair protein Ku80 suppresses chromosomal aberrations and malignant transformation

    Nature

    (2000)
  • W.D. Heyer

    Regulation of homologous recombination in eukaryotes

    Annu. Rev. Genet.

    (2010)
  • L. Deriano et al.

    Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage

    Annu. Rev. Genet.

    (2013)
  • D. Simsek et al.

    Alternative end-joining is suppressed by the canonical NHEJ component Xrcc4-ligase IV during chromosomal translocation formation

    Nat. Struct. Mol. Biol.

    (2010)
  • Y. Zhang et al.

    An essential role for CtIP in chromosomal translocation formation through an alternative end-joining pathway

    Nat. Struct. Mol. Biol.

    (2011)
  • B. Corneo

    Rag mutations reveal robust alternative end joining

    Nature

    (2007)
  • M. Wang

    PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways

    Nucleic Acids Res.

    (2006)
  • H. Wang

    DNA ligase III as a candidate component of backup pathways of nonhomologous end joining

    Cancer Res.

    (2005)
  • L.S. Symington et al.

    Double-strand break end resection and repair pathway choice

    Annu. Rev. Genet.

    (2011)
  • L.N. Truong

    Microhomology-mediated end joining and homologous recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells

    Proc. Natl. Acad. Sci. U.S.A.

    (2013)
  • X. Chen

    Cell cycle regulation of DNA double-strand break end resection by Cdk1-dependent Dna2 phosphorylation

    Nat. Struct. Mol. Biol.

    (2011)
  • N. Bennardo

    Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair

    PLoS Genet.

    (2008)
  • M.H. Yun et al.

    CtIP-BRCA1 modulates the choice of DNA double-strand-break repair pathway throughout the cell cycle

    Nature

    (2009)
  • F. Polato

    CtIP-mediated resection is essential for viability and can operate independently of BRCA1

    J. Exp. Med.

    (2014)
  • N. Tomimatsu

    Phosphorylation of EXO1 by CDKs 1 and 2 regulates DNA end resection and repair pathway choice

    Nat. Commun.

    (2014)
  • T. Robert

    HDACs link the DNA damage response, processing of double-strand breaks and autophagy

    Nature

    (2011)
  • Cited by (0)

    View full text