Elsevier

DNA Repair

Volume 56, August 2017, Pages 156-165
DNA Repair

Role of recombination and replication fork restart in repeat instability

https://doi.org/10.1016/j.dnarep.2017.06.018Get rights and content

Abstract

Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease. One important DNA repair mechanism to maintain genomic integrity is recombination. Though early studies dismissed recombination as a mechanism driving repeat expansion and instability, recent results indicate that mitotic recombination is a key pathway operating within repetitive DNA. The action is two-fold: first, it is an important mechanism to repair nicks, gaps, breaks, or stalled forks to prevent chromosome fragility and protect cell health; second, recombination can cause repeat expansions or contractions, which can be deleterious. In this review, we summarize recent developments that illuminate the role of recombination in maintaining genome stability at DNA repeats.

Introduction

Expanded tracts of repetitive DNA sequences are the cause of over 30 genetic diseases and can consist of trinucleotide or larger repetitive units [1], [2], [3], [4], [5]. The expandable repeats form stable non-B-form DNA structures which impede normal cellular processes like DNA replication and repair. Expanded trinucleotide repeats (TNRs) and other structure-forming repeats break at a greater frequency than non-repetitive DNA; types of DNA breaks that occur include nicks, gaps and double-stranded breaks (DSBs). These lesions must then be repaired in the context of the repetitive DNA. Much of the time the cell will succeed in repairing DNA damage at structure-forming repeats with fidelity, i.e. with no loss or gain of genetic material, thus preserving genome integrity. However, due to both the repetitive nature of the tract as well as the structure-forming potential, mistakes that lead to repeat expansions or contractions are relatively frequent.

There are multiple pathways that repair DNA damage that occurs within TNRs and other repetitive sequences. For example, nicks and gaps can be repaired by base excision repair (BER), or by transcription-coupled repair (TCR) within transcribed regions, both of which can generate TNR expansions (for recent reviews see [2], [5] and the review by Polyzos and McMurray in this issue). Damage that results in DSBs can be repaired by various types of end-joining, by annealing of processed ends, or by recombination-based mechanisms using either a sister chromatid or homolog as the template. In addition, recombination is a primary mechanism used in restarting stalled or collapsed replication forks and in repairing gaps left behind the replication fork. This review will summarize the current knowledge about the role of mitotic recombination in generating genomic changes within repetitive DNA. We will focus on structure-forming triplet repeats, but with comparisons to results found at other biologically relevant repeats and DNA structures.

Deletion of genes required for recombination results in increased breakage of expanded TNRs, suggesting that recombination is normally required for healing these DNA breaks [6], [7]. In replicating yeast cells, homologous recombination (HR) and ligase 4-dependent end joining (EJ) both contribute to the repair of breaks at CAG repeats [6]. Genome-wide studies to identify novel genes preventing DSBs at GAA and Alu repeats identified several recombinational repair proteins as important, among them the nuclease Mre11, whose absence increased fragility of both repeats [7], [8]. Additionally, dividing cells deficient in replication proteins exhibit cell cycle arrest and gross chromosomal rearrangements at Alu repeats because recombination intermediates cannot be resolved, which results in DSBs [8]. Failure to heal breaks at expanded TNR repeats can have dire consequences for cells. Yeast cells that lack Rad52 or Ligase 4 and have expanded CAG repeat tracts undergo frequent cell cycle arrest and cell death [9].

Traditionally, DNA repair using recombination has been considered to be an error-free form of repair. However, in actuality, recombination can be highly mutagenic and a source of genomic instability [10], [11], [12], [13]. Though they are required for repair and cell health, both HR and EJ can be mutagenic when they occur within repetitive DNA, resulting in a loss (contraction) or gain (expansion) of repeat units [14]. This is largely due to the challenges of replicating or aligning DNA across a repetitive region, especially one that has formed DNA secondary structures. These DNA structures are varied and include DNA hairpins (common in CAG/CTG and CGG/GCC repeats or inverted repeats), triplexes (formed by purine-rich repeats such as GAA/TTC) and G quadruplexes (for reviews see [5], [15], [16], [17]). Though the structures are different, the common theme is that they impede DNA transactions so that replication and repair cannot proceed with fidelity within the repetitive sequence. This inaccurate repair can lead to the incorporation of errors that can range from the aberrant insertion/deletion of DNA bases, as seen in TNR repeat genetic diseases, to genomic rearrangements and loss of heterozygosity, which are commonly seen in cancers. Historically, misalignment of alleles during meiotic crossover was shown to be a mechanism for (GCN)n repeat expansions that code for polyalanine tracts [18], but discounted as a mechanism for length changes of other TNRs, such as (CAG)n repeat tracts encoding polyglutamine. However, these early studies focused on meiotic recombination and did not explore mitotic recombination as a potential mechanism for repairing DNA damage at TNRs and causing repeat instability. The following sections will delve into the various roles of recombination during DNA repair, how each contributes to genomic maintenance of repeat sequences, and the current knowledge of how recombination pathways result in repeat instability.

Section snippets

Homology-dependent recombinational repair of forks stalled by DNA structures

Addition of repeat units by definition involves DNA synthesis. Incorporation of additional bases might arise as a result of strand slippage either during replication [19] or during fork restart [3]. DNA structures formed by repetitive DNA sequences are impediments for DNA synthesis and can cause fork stalling, or gaps behind the replication fork if bypassed. GAA/TCC triplexes and GGC/CCG repeats strongly interfere with replication progression, acting as site-specific barriers [20], [21], [22].

HR-dependent instability can cause large repeat expansions

Structure-forming DNA, including expanded CAG, CGG, GAA, and ATTCT repeats as well as palindrome-forming sequences, are natural fragile sites that cause chromosomal DSBs (reviewed in [5], [15], [90], [91], [92]). Consistently, expanded GAA/TTC repeats, Alu repeats, and internal telomeric repeats stimulate mitotic crossovers in yeast [93], [94], [95] and recombination in E. coli [96], [97], [98]. In yeast, the effect of DSB repair by HR on CAG repeat stability was assessed directly by induction

Conclusions

Many repetitive DNA sequences form secondary structures that serve as constant challenges to DNA replication and repair machineries, resulting in stalled forks, nicks, gaps, and DSBs. Recombination is an important pathway to repair these lesions, and serves as a powerful guardian of the genome. However, recombinational repair at repetitive DNA tracts can be tricky as it can also be a source of mutation, including repeat expansions and contractions. This dichotomy between recombination being a

Acknowledgements

Research in CHF’s laboratory is supported by the National Institutes of Health (award P01GM105473 and R01GM122880), National Science Foundation (MCB1330743), and Tufts University. The authors have no conflicts of interest to declare.

References (136)

  • J.B. Vannier et al.

    RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity

    Cell

    (2012)
  • K. Paeschke et al.

    DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase

    Cell

    (2011)
  • H. Sun et al.

    The bloom’s syndrome helicase unwinds G4 DNA

    J. Biol. Chem.

    (1998)
  • J. Shen et al.

    Unwinding the molecular basis of the Werner syndrome

    Mech. Ageing Dev.

    (2001)
  • N.L. Chan et al.

    The Werner syndrome protein promotes CAG/CTG repeat stability by resolving large (CAG)(n)/(CTG)(n) hairpins

    J. Biol. Chem.

    (2012)
  • M.J. Dixon et al.

    Examining the potential role of DNA polymerases η and ζ in triplet repeat instability in yeast

    DNA Repair

    (2002)
  • E.C. Minca et al.

    Multiple Rad5 activities mediate sister chromatid recombination to bypass DNA damage at stalled replication forks

    Mol. Cell

    (2010)
  • N.C. House et al.

    NuA4 initiates dynamic histone H4 acetylation to promote high-Fidelity sister chromatid recombination at postreplication gaps

    Mol. Cell

    (2014)
  • A.A. Shishkin et al.

    Large-scale expansions of Friedreich's ataxia GAA repeats in yeast

    Mol. Cell.

    (2009)
  • J.C. Kim et al.

    The balancing act of DNA repeat expansions

    Curr. Opin. Genet. Dev.

    (2013)
  • D.T. Kha et al.

    Pathways for double-strand break repair in genetically unstable Z-DNA-forming sequences

    J. Mol. Biol.

    (2010)
  • K.S. Lobachev et al.

    The Mre11 complex is required for repair of hairpin-capped double-strand breaks and prevention of chromosome rearrangements

    Cell

    (2002)
  • A. Pluciennik et al.

    Long CTG.CAG repeats from myotonic dystrophy are preferred sites for intermolecular recombination

    J. Biol. Chem.

    (2002)
  • M. Napierala et al.

    Long CTG.CAG repeat sequences markedly stimulate intramolecular recombination

    J. Biol. Chem.

    (2002)
  • M.L. Hebert et al.

    Roles of double-strand breaks, nicks, and gaps in stimulating deletions of CTG.CAG repeats by intramolecular DNA repair

    J. Mol. Biol.

    (2005)
  • E.P. Mimitou et al.

    DNA. end resection-unraveling the tail

    DNA Repair (Amst.)

    (2011)
  • J.R. Gatchel et al.

    Diseases of unstable repeat expansion: mechanisms and common principles

    Nat. Rev. Genet.

    (2005)
  • C.T. McMurray

    Mechanisms of trinucleotide repeat instability during human development

    Nat. Rev. Genet.

    (2010)
  • A. Lopez Castel et al.

    Expanded CTG repeat demarcates a boundary for abnormal CpG methylation in myotonic dystrophy patient tissues

    Hum. Mol. Genet.

    (2011)
  • K. Usdin et al.

    Repeat instability during DNA repair: insights from model systems

    Crit. Rev. Biochem. Mol. Biol.

    (2015)
  • R. Sundararajan et al.

    Double-strand break repair pathways protect against CAG/CTG repeat expansions, contractions and repeat-mediated chromosomal fragility in Saccharomyces cerevisiae

    Genetics

    (2010)
  • Y. Zhang et al.

    Genome-wide screen reveals replication pathway for quasi-palindrome fragility dependent on homologous recombination

    PLoS Genet.

    (2013)
  • R. Sundararajan et al.

    Expanded CAG/CTG repeat DNA induces a checkpoint response that impacts cell proliferation in Saccharomyces cerevisiae

    PLoS Genet.

    (2011)
  • A. Malkova et al.

    Mutations arising during repair of chromosome breaks

    Annu. Rev. Genet.

    (2012)
  • C.M. Carvalho et al.

    Mechanisms underlying structural variant formation in genomic disorders

    Nat. Rev. Genet.

    (2016)
  • W.D. Heyer

    Regulation of recombination and genomic maintenance

    Cold Spring Harb. Perspect. Biol.

    (2015)
  • K. Rodgers et al.

    Error-prone repair of DNA double-strand breaks

    J. Cell Physiol.

    (2016)
  • G.F. Richard et al.

    Mini- and microsatellite expansions: the recombination connection

    EMBO Rep.

    (2000)
  • M.L. Bochman et al.

    DNA secondary structures: stability and function of G-quadruplex structures

    Nat. Rev. Genet.

    (2012)
  • S.M. Mirkin

    Expandable DNA repeats and human disease

    Nature

    (2007)
  • S.T. Warren

    Polyalanine expansion in synpolydactyly might result from unequal crossing-over of HOXD13

    Science

    (1997)
  • R.I. Richards et al.

    Simple repeat DNA is not replicated simply

    Nat. Genet.

    (1994)
  • M.M. Krasilnikova et al.

    Replication stalling at Friedreich’s ataxia (GAA)n repeats in vivo

    Mol. Cell. Biol.

    (2004)
  • I. Voineagu et al.

    Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility

    Nat. Struct. Mol. Biol.

    (2009)
  • R. Pelletier et al.

    Replication and expansion of trinucleotide repeats in yeast

    Mol. Cell. Biol.

    (2003)
  • J.D. Cleary et al.

    Tissue- and age-specific DNA replication patterns at the CTG/CAG-expanded human myotonic dystrophy type 1 locus

    Nat. Struct. Mol. Biol.

    (2010)
  • G. Liu et al.

    Instability of (CTG)n*(CAG)n trinucleotide repeats and DNA synthesis

    Cell Biosci.

    (2012)
  • A. Kerrest et al.

    SRS2 and SGS1 prevent chromosomal breaks and stabilize triplet repeats by restraining recombination

    Nat. Struct. Mol. Biol.

    (2009)
  • J.H. Nguyen et al.

    Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats

    Nucleic Acids Res.

    (2017)
  • R.C. Heller et al.

    Replisome assembly and the direct restart of stalled replication forks

    Nat. Rev. Mol. Cell. Biol.

    (2006)

    • Cited by (38)

    • Homologous recombination within repetitive DNA

      2021, Current Opinion in Genetics and Development

    • Structure-forming repeats and their impact on genome stability

      2021, Current Opinion in Genetics and Development
      Citation Excerpt :

      Contractions are proposed to occur by bypass of the template structure by Pol δ, and are exacerbated by mutations that affect Pol δ processivity [23•]. Another response to lagging strand hairpins can be a template switch to copy from the sister chromatid, which has been shown by multiple groups to cause repeat expansions (see Ref. [17] for review). A new appreciation is that histone modifications are required to facilitate efficient D-loop extension during sister-chromatid recombination and prevent CAG repeat expansions in a yeast model.

    • Relocation of Collapsed Forks to the Nuclear Pore Complex Depends on Sumoylation of DNA Repair Proteins and Permits Rad51 Association

      2020, Cell Reports

    • Changing of the guard: How the Lyme disease spirochete subverts the host immune response

      2020, Journal of Biological Chemistry

    • The MCM8/9 complex: A recent recruit to the roster of helicases involved in genome maintenance

      2019, DNA Repair
      Citation Excerpt :

      Loss of function in any DNA repair helicase has the potential to lead to disease [54]. A variety of factors including genotoxic agents that cause DNA damage, DNA-protein crosslinks, protein complex collisions on chromosomes, and difficult to replicate sequences will all stall replication forks [55–58]. Analysis of cellular viability, protein localization/colocalization fluorescence microscopy, and coimmunoprecipitations using a variety of genotoxic agents in both animal and cell models indicate that MCM8/9 are likely involved in only a sub-set of DNA repair pathways dependent on the type of damage (Fig. 3).

    • Low microsatellite instability: A distinct instability type in gastric cancer?

      2023, Journal of Cancer Research and Clinical Oncology
    View all citing articles on Scopus
    1

    Current address: Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA 02215, USA.

    View full text
    © 2017 Elsevier B.V. All rights reserved.