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Mechanisms of trinucleotide repeat instability during human development

A Corrigendum to this article was published on 10 November 2010

Key Points

  • Trinucleotide expansion in human disease occurs at different stages and in different cell types during development. The status of cell division determines the mechanism of expansion.

  • Large expansions occur in non-dividing cells. Large repeat tracts are deleted in spermatogonia.

  • Pre-mutation alleles can expand or contract in dividing and non-dividing cells.

  • In non-dividing cells, expansion is likely to occur during excision repair. Candidate pathways are base excision repair or transcription-coupled repair.

  • Oxidative damage of DNA bases is corrected by base excision repair and expansion occurs during the process of removing oxidized bases. Loss of 7,8-dihydro-8-oxoguanine DNA glycosylase (OGG1, also known as N-glycosylase/DNA lyase) in mice suppresses expansion.

  • Cockayne syndrome protein CSB (also known as ERCC6) and xeroderma pigmentosum complementation group G (XPG) have been implicated in instability of CAG repeats in flies and in human cells.

  • In dividing cells, replication dependent repair mechanisms, such as polymerase 'back-up' and trans-lesion synthesis, are candidates for causing expansion.

  • Expansion is a two-step process in which DNA loops are formed and then incorporated into DNA. The two steps may occur by distinct mechanisms.

  • The mismatch repair system may be involved in forming the DNA loops that become expansions and may also be involved in loop incorporation into DNA.

  • Progress in this field will require the integration of various strategies, including genetic and biochemical methods and analysis of DNA repair crosstalk and chromatin dynamics.

Abstract

Trinucleotide expansion underlies several human diseases. Expansion occurs during multiple stages of human development in different cell types, and is sensitive to the gender of the parent who transmits the repeats. Repair and replication models for expansions have been described, but we do not know whether the pathway involved is the same under all conditions and for all repeat tract lengths, which differ among diseases. Currently, researchers rely on bacteria, yeast and mice to study expansion, but these models differ substantially from humans. We need now to connect the dots among human genetics, pathway biochemistry and the appropriate model systems to understand the mechanism of expansion as it occurs in human disease.

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Figure 1: Human germ cell development.
Figure 2: Loops formed during base excision repair by strand displacement: the toxic oxidation cycle.
Figure 3: Nucleotide excision repair and trinucleotide repeat loop formation.
Figure 4: Slippage model for small trinucleotide repeat length changes.
Figure 5: A model for loop formation based on polymerase stalling and restarting within a trinucleotide repeat.
Figure 6: Three models for loop incorporation into duplex DNA.

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References

  1. Mirkin, S. M. Expandable DNA repeats and human disease. Nature 447, 932–940 (2007).

    Article  CAS  PubMed  Google Scholar 

  2. Kovtun, I. V. & McMurray, C. T. Features of trinucleotide repeat instability in vivo. Cell Res. 18, 198–213 (2008).

    Article  CAS  PubMed  Google Scholar 

  3. La Spada, A. R. & Taylor, J. P. Repeat expansion disease: progress and puzzles in disease pathogenesis. Nature Rev. Genet. 11, 247–258 (2010). A comprehensive Review of recent progress in understanding the pathophysiology of expansion disease.

    Article  CAS  PubMed  Google Scholar 

  4. Dion, V. & Wilson, J. H. Instability and chromatin structure of expanded trinucleotide repeats. Trends Genet. 25, 288–297 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Kumari, D. & Usdin, K. Chromatin remodeling in the non-coding repeat expansion diseases. J. Biol. Chem. 284, 7413–7417 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Day, L. W. & Ranum, L. P. RNA pathogenesis of the myotonic dystrophies. Neuromuscul. Disord. 15, 5–16 (2005).

    Article  PubMed  Google Scholar 

  7. Slattery, J. P., Murphy, W. J. & O'Brien, S. J. Patterns of diversity among SINE elements isolated from three Y-chromosome genes in carnivores. Mol. Biol. Evol. 17, 825–829 (2000).

    Article  CAS  PubMed  Google Scholar 

  8. Petruska, J., Hartenstine, M. J. & Goodman, M. F. Analysis of strand slippage in DNA polymerase expansions of CAG/CTG triplet repeats associated with neurodegenerative disease. J. Biol. Chem. 273, 5204–5210 (1998).

    Article  CAS  PubMed  Google Scholar 

  9. Hartenstine, M. J., Goodman, M. F. & Petruska, J. Base stacking and even/odd behavior of hairpin loops in DNA triplet repeat slippage and expansion with DNA polymerase. J. Biol. Chem. 275, 18382–18390 (2000).

    Article  CAS  PubMed  Google Scholar 

  10. Fu, Y. H. et al. Variation of the CGG repeat at the Fragile X site results in genetic instability: resolution of the Sherman paradox. Cell 67, 1047–1058 (1991).

    Article  CAS  PubMed  Google Scholar 

  11. Sullivan, A. K., Crawford, D. C., Scott, E. H., Leslie, M. L. & Sherman, S. L. Paternally transmitted FMR1 alleles are less stable than maternally transmitted alleles in the common and intermediate size range. Am. J. Hum. Genet. 70, 1532–1544 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Helderman-van den Enden, A. T. et al. Monozygotic twin brothers with the fragile X syndrome: different CGG repeats and different mental capacities. J. Med. Genet. 36, 253–257 (1999).

    CAS  PubMed  Google Scholar 

  13. Tripathi, A., Kumar, K. V. & Chaube, S. K. Meiotic cell cycle arrest in mammalian oocytes. J. Cell. Physiol. 223, 592–600 (2010).

    CAS  PubMed  Google Scholar 

  14. Rifé, M. et al. Analysis of CGG variation through 642 meioses in fragile X families. Mol. Hum. Reprod. 10, 773–776 (2004). This study provided evidence that the earliest detected CGG expansions in female patients with FXS occurred in the primary oocytes, suggesting that expansion occurred in non-dividing cells in humans.

    Article  PubMed  CAS  Google Scholar 

  15. Sermon, K. et al. Preimplantation diagnosis for fragile X syndrome based on the detection of the non-expanded paternal and maternal CGG. Prenat. Diagn. 19, 1223–1230 (2000).

    Article  Google Scholar 

  16. Ashley-Koch, A. E. et al. Examination of factors associated with instability of the FMR1 CGG repeat. Am. J. Hum. Genet. 63, 776–785 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Bontekoe, C. J. et al. Instability of a (CGG)98 repeat in the Fmr1 promoter. Hum. Mol. Genet. 10, 1693–1699 (2001).

    Article  CAS  PubMed  Google Scholar 

  18. Entezam, A. et al. Regional FMRP deficits and large repeat expansions into the full mutation range in a new fragile X premutation mouse model. Gene 15, 125–134 (2007).

    Article  CAS  Google Scholar 

  19. Reyniers, E. et al. The full mutation in the FMR-1 gene of male fragile X patients is absent in their sperm. Nature Genet. 4, 143–146 (1993).

    Article  CAS  PubMed  Google Scholar 

  20. Malter, H. E. et al. Characterization of the full fragile X syndrome mutation in fetal gametes. Nature Genet. 15, 165–169 (1997). This work provided definitive evidence that the absence of the full mutation in male patients with FXS was due to deletion of CGG tracts in their germ cells at fetal stages of development.

    Article  CAS  PubMed  Google Scholar 

  21. Dean, N., Tan, S. & Ao, A. Instability in the transmission of the myotonic dystrophy CTG repeat in human oocytes and preimplantation embryos. Fertil. Steril. 86, 98–105 (2006).

    Article  CAS  PubMed  Google Scholar 

  22. De Temmerman, N. et al. Intergenerational instability of the expanded CTG repeat in the DMPK gene: studies in human gametes and preimplantation embryos. Am. J. Hum. Genet. 75, 325–329 (2004). This study indicated that the earliest detected CTG expansions in female patients with DM1 also occurred in the primary oocytes, suggesting that large expansion did not require replication.

    Article  CAS  PubMed  Google Scholar 

  23. Martorell, L. et al. Germline mutational dynamics in myotonic dystrophy: allele length and age effects. Neurology 62, 269–274 (2004). The results indicated that the largest length changes in CTG tracts in male patients with DM1 were observed for pre-mutation alleles and the highest frequency of contractions were observed in full mutation alleles.

    Article  CAS  PubMed  Google Scholar 

  24. Ashizawa, T. et al. Characteristics of intergenerational contractions of the CTG repeat in myotonic dystrophy. Am. J. Hum. Genet. 54, 414–423 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Lavedan, C. et al. Myotonic dystrophy: size- and sex-dependent dynamics of CTG meiotic instability, and somatic mosaicism. Am. J. Hum. Genet. 52, 875–883 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Jansen, G. et al. Gonosomal mosaicism in myotonic dystrophy patients: involvement of mitotic events in (CTG)n repeat variation and selection against extreme expansion in sperm. Am. J. Hum. Genet. 54, 575–585 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Savouret, C. et al. MSH2-dependent germinal CTG repeat expansions are produced continuously in spermatogonia from DM1 transgenic mice. Mol. Cell. Biol. 24, 629–637 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Savouret, C. et al. CTG repeat instability and size variation timing in DNA repair-deficient mice. EMBO J. 22, 2264–2273 (2003). This work provided evidence from knockout mice that dispelled the notion that the homologous recombination and non-homologous end joining pathways were major mechanisms for CTG expansions.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Fortune, M. T., Vassilopoulos, C., Coolbaugh, M. I., Sicilliano, M. J. & Mockton, D. G. Dramatic, expansion-biased, age-dependent, tissue-specific somatic mosaicism in a transgenic mouse model of triplet instability. Hum. Mol. Genet. 9, 439–445 (2000).

    Article  CAS  PubMed  Google Scholar 

  30. Kremer, B. et al. Sex-dependent mechanisms for expansions and contractions of the CAG repeat on affected Huntington disease chromosomes. Am. J. Hum. Genet. 57, 343–350 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Wheeler, V. C. et al. Factors associated with HD CAG repeat instability in Huntington disease. J. Med. Genet. 44, 695–701 (2007). This analysis of a large cohort of patients with HD is a comprehensive analysis of the factors governing expansion in HD. These factors include length, age-dependence and gender-dependence of expansion.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Norremolle, A., Sorensen, S. A., Fenger, K. & Hasholt, L. Correlation between magnitude of CAG repeat length alterations and length of the paternal repeat in paternally inherited Huntington's disease. Clin. Genet. 47, 113–119 (1995).

    Article  CAS  PubMed  Google Scholar 

  33. Telenius, H. et al. Molecular analysis of juvenile Huntington disease: the major influence on (CAG)n repeat length is the sex of the affected parent. Hum. Mol. Genet. 2, 1535–1540 (1993).

    Article  CAS  PubMed  Google Scholar 

  34. Kovtun, I. V., Therneau, T. M. & McMurray, C. T. Gender of the embryo contributes to CAG instability in transgenic mice containing a Huntington's disease gene. Hum. Mol. Genet. 9, 2767–2775 (2000).

    Article  CAS  PubMed  Google Scholar 

  35. Telenius, H. et al. Somatic and gonadal mosaicism of the Huntington disease gene CAG repeat in brain and sperm. Nature Genet. 6, 409–414 (1994).

    Article  CAS  PubMed  Google Scholar 

  36. Kovtun, I. V. & McMurray, C. T. Trinucleotide expansion in haploid germ cells by gap repair. Nature Genet. 27, 407–411 (2001).

    Article  CAS  PubMed  Google Scholar 

  37. Yoon, S. R., Dubeau, L., de Young, M., Wexler, N. S. & Arnheim, N. Huntington disease expansion mutations in humans can occur before meiosis is completed. Proc. Natl Acad. Sci. USA 100, 8834–8838 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Leeflang, E. P. et al. Analysis of germline mutation spectra at the Huntington's disease locus supports a mitotic mutation mechanism. Hum. Mol. Genet. 8, 173–183 (1999).

    Article  CAS  PubMed  Google Scholar 

  39. Kennedy, L. et al. Dramatic tissue-specific mutation length increases are an early molecular event in Huntington disease pathogenesis. Hum. Mol. Genet. 12, 3359–3367 (2003). This work provided the first strong evidence for the importance of age-dependent somatic instability in HD pathogenesis. The results demonstrated that increases of up to 1,000 CAG repeats occurred in human HD striatal cells early in the disease course. These increases might influence the age of disease onset.

    Article  CAS  PubMed  Google Scholar 

  40. Shelbourne, P. F. et al. Triplet repeat mutation length gains correlate with cell-type specific vulnerability in Huntington disease brain. Hum. Mol. Genet. 16, 1133–1142 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Mangiarini, L. et al. Instability of highly expanded CAG repeats in mice transgenic for the Huntington's disease mutation. Nature Genet. 15, 197–200 (1997).

    Article  CAS  PubMed  Google Scholar 

  42. Wheeler, V. C. et al. Length-dependent gametic CAG repeat instability in the Huntington's disease knock-in mouse. Hum. Mol. Genet. 8, 115–122 (1999).

    Article  CAS  PubMed  Google Scholar 

  43. Kovtun, I. V., Thornhill, A. R. & McMurray, C. T. Somatic deletion events occur during early embryonic development and modify the extent of CAG expansion in subsequent generations. Hum. Mol. Genet. 13, 3057–3068 (2004).

    Article  CAS  PubMed  Google Scholar 

  44. Gonitel, R. et al. DNA instability in postmitotic neurons. Proc. Natl Acad. Sci. USA 105, 3467–3472 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Kovtun, I. V. et al. OGG1 initiates age-dependent CAG trinucleotide expansion in somatic cells. Nature 447, 447–452 (2007). This work provided evidence for a direct causative link among oxidative DNA damage, BER and expansion during mouse development. Expansion occurred in the process of removing oxidized bases and depended on OGG1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Swami, M. et al. Somatic expansion of the Huntington's disease CAG repeat in the brain is associated with an earlier age of disease onset. Hum. Mol. Genet. 18, 3039–3047 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Koefoed, P. et al. Mitotic and meiotic instability of the CAG trinucleotide repeat in spinocerebellar ataxia type 1. Hum. Genet. 103, 564–569 (1998).

    Article  CAS  PubMed  Google Scholar 

  48. Kaytor, M. D., Burright, E. N., Duvick, L. A., Zoghbi, H. Y. & Orr, H. T. Increased trinucleotide repeat instability with advanced maternal age. Hum. Mol. Genet. 6, 2135–2139 (1997).

    Article  CAS  PubMed  Google Scholar 

  49. Morton, A. J. et al. Paradoxical delay in the onset of disease caused by super-long CAG repeat expansions in R6/2 mice. Neurobiol. Dis. 33, 331–341 (2009).

    Article  CAS  PubMed  Google Scholar 

  50. Richards, R. I. et al. Fragile X syndrome: genetic localisation by linkage mapping of two microsatellite repeats FRAXAC1 and FRAXAC2 which immediately flank the fragile site. J. Med. Genet. 28, 818–823 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Wolff, R. K., Plaetke, R., Jeffreys, A. J. & White, R. Unequal crossing over between homologous chromosomes is not the major mechanism involved in the generation of new alleles at VNTR loci. Genomics 5, 382–384 (1989).

    Article  CAS  PubMed  Google Scholar 

  52. Bjelland, S. & Seeberg, E. Mutagenicity, toxicity and repair of DNA base damage induced by oxidation. Mutat. Res. 531, 37–80 (2003).

    Article  CAS  PubMed  Google Scholar 

  53. Entezam, A., Lokanga, A. R., Le, W., Hoffman, G. & Usdin, K. Potassium bromate, a potent DNA oxidizing agent, exacerbates germline repeat expansion in a fragile X premutation mouse model. Hum. Mutat. 31, 611–616 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Goula, A. V. et al. Stoichiometry of base excision repair proteins correlates with increased somatic CAG instability in striatum over cerebellum in Huntington's disease transgenic mice. PLoS Genet. 5, e1000749 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Daube, S. S., Arad, G. & Livneh, A. Translesion replication by DNA polymerase β is modulated by sequence context and stimulated by fork-like flap structures in DNA. Biochemistry 39, 397–405 (2000).

    Article  CAS  PubMed  Google Scholar 

  56. Spiro, C. et al. Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats. Mol. Cell 4, 1079–1085 (1999).

    Article  CAS  PubMed  Google Scholar 

  57. Liu, Y. et al. Coordination between polymerase β and FEN1 can modulate CAG repeat expansion. J. Biol. Chem. 284, 28352–28366 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Henricksen, L. A., Veeraraghavan, J., Chafin, D. R. & Bambara, R. A. DNA ligase I competes with FEN1 to expand repetitive DNA sequences in vitro. J. Biol. Chem. 277, 22361–22369 (2002).

    Article  CAS  PubMed  Google Scholar 

  59. Asagoshi, K. et al. DNA polymerase β dependent long patch base excision repair in living cells. DNA Repair 9, 109–119 (2010).

    Article  CAS  PubMed  Google Scholar 

  60. Beard, W. A., Prasad, R. & Wilson, S. H. Activities and mechanism of DNA polymerase β. Meth. Enzymol. 408, 91–107 (2006).

    Article  CAS  Google Scholar 

  61. Kunkel, T. A. Evolving views of DNA replication (in) fidelity. Cold Spring Harb. Symp. Quant. Biol. 74, 91–101 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Kaplan, S., Itzkovitz, S. & Shapiro, E. A universal mechanism ties genotype to phenotype in trinucleotide diseases. PLoS Comput. Biol. 3, e235 (2007).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Rolseth, V. et al. Widespread distribution of DNA glycosylases removing oxidative DNA lesions in human and rodent brains. DNA Repair 7, 1578–1588 (2008).

    Article  CAS  PubMed  Google Scholar 

  64. Hazra, T. K. & Mitra, S. Purification and characterization of NEIL1 and NEIL2, members of a distinct family of mammalian DNA glycosylases for repair of oxidized bases. Meth. Enzymol. 408, 33–48 (2006).

    Article  CAS  Google Scholar 

  65. Takao, M. et al. A back-up glycosylase in Nth1 knock-out mice is a functional Nth (endonuclease III) homologue. J. Biol. Chem. 277, 42205–42213 (2002).

    Article  CAS  PubMed  Google Scholar 

  66. Cleaver, J. E., Lam, E. T. & Revet, I. Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity. Nature Rev. Genet. 10, 756–768 (2009).

    Article  CAS  PubMed  Google Scholar 

  67. Hanawalt, P. C. & Spivak, G. Transcription-coupled DNA repair: two decades of progress and surprises. Nature Rev. Mol. Cell Biol. 9, 958–970 (2008).

    Article  CAS  Google Scholar 

  68. Nouspikel, T. DNA repair in differentiated cells: some new answers to old questions. Neuroscience 145, 1183–1448 (2007).

    Article  CAS  Google Scholar 

  69. Staresincic, L. et al. Coordination of dual incision and repair synthesis in human nucleotide excision repair. EMBO J. 28, 1111–1120 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Dragileva, E. et al. Intergenerational and striatal CAG repeat instability in Huntington's disease knock-in mice involve different DNA repair genes. Neurobiol. Dis. 33, 37–47 (2009).

    Article  CAS  PubMed  Google Scholar 

  71. Lin, Y. & Wilson, J. H. Transcription-induced CAG repeat contraction in human cells is mediated in part by transcription-coupled nucleotide excision repair. Mol. Cell. Biol. 27, 6209–6217 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Jung, J. & Bonini, N. CREB-binding protein modulates repeat instability in a Drosophila model for polyQ disease. Science 315, 1857–1859 (2007). This work provided evidence that CAG instability could occur by a TCR process.

    Article  CAS  PubMed  Google Scholar 

  73. Lin, Y., Dion, V., & Wilson, J. H. Transcription promotes contraction of CAG repeat tracts in human cells. Nature Struct. Mol. Biol. 13, 179–180 (2006).

    Article  CAS  Google Scholar 

  74. Sarker, A. H. et al. Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne syndrome. Mol. Cell 20, 187–198 (2005).

    Article  CAS  PubMed  Google Scholar 

  75. Parsons, A. M., Sinden, R. R. & Izban, M. G. Transcriptional properties of RNA polymerase II within triplet repeat-containing DNA from the human myotonic dystrophy and fragile X loci. J. Biol. Chem. 273, 26998–27008 (1998).

    Article  CAS  PubMed  Google Scholar 

  76. Grabczyka, E. & Usdin, K. The GAA•TTC triplet repeat expanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner. Nucleic Acids Res. 28, 2815–2822 (2000).

    Article  Google Scholar 

  77. Fousteri, M. & Mullenders, L. H. F. Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects. Cell Res. 18, 73–84 (2008).

    Article  CAS  PubMed  Google Scholar 

  78. Kovtun, I. V. & McMurray, C. T. Crosstalk of DNA glycosylases with pathways other than base excision repair. DNA Repair 6, 517–529 (2007).

    Article  CAS  PubMed  Google Scholar 

  79. Wong, H.-K. et al. Cockayne syndrome B protein stimulates apurinic endonuclease 1 activity and protects against agents that introduce base excision repair intermediates. Nucleic Acids Res. 35, 4103–4113 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Thorslund, T. et al. Cooperation of the Cockayne syndrome group B protein and poly(ADP-ribose) polymerase 1 in the response to oxidative stress. Mol. Cell. Biol. 25, 7625–7636 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Khobta, A., Kitseraa, N., Speckmanna, B. & Epe, B. 8-Oxoguanine DNA glycosylase (Ogg1) causes a transcriptional inactivation of damaged DNA in the absence of functional Cockayne syndrome B (Csb) protein. DNA Repair 8, 309–317 (2009).

    Article  CAS  PubMed  Google Scholar 

  82. Dou, H., Mitra, S. & Hazra, T. K. Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2. J. Biol. Chem. 278, 49679–49684 (2003).

    Article  CAS  PubMed  Google Scholar 

  83. Kang, S., Jaworski, A., Ohshima, K. & Wells, R. D. Expansion and deletion of CTG repeats from human disease genes are determined by the direction of replication in E. coli. Nature Genet. 10, 213–218 (1995). This work demonstrated that slippage could generate small increases and decreases in TNR tracts depending on the direction of replication.

    Article  CAS  PubMed  Google Scholar 

  84. Kang, S., Ohshima, K., Shimizu, M., Amirhaeri, S. & Wells, R. D. Pausing of DNA synthesis in vitro at specific loci in CTG and CGG triplet repeats from human hereditary disease genes. J. Biol. Chem. 270, 27014–27021 (1995).

    Article  CAS  PubMed  Google Scholar 

  85. Viguera, E., Canceill, D. & Ehrlich, D. S. Replication slippage involves DNA polymerase pausing and dissociation. EMBO J. 20, 2587–2595 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Delagoutte, E., Goellner, G. M., Guo, J., Baldacci, G. & McMurray, C. T. Single-stranded DNA-binding protein in vitro eliminates the orientation-dependent impediment to polymerase passage on CAG/CTG repeats. J. Biol. Chem. 283, 13341–13356 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Goldberg, Y. P. et al. Molecular analysis of new mutations for Huntington's disease: intermediate alleles and sex of origin effects. Nature Genet. 5, 174–179 (1993). This work demonstrated how transmitted repeat tracts change at the threshold for HD and showed that pre-mutation alleles underwent roughly equal small losses and gains of repeats. However, after the repeat grew past the threshold, expansion became the dominant change.

    Article  CAS  PubMed  Google Scholar 

  88. Schweitzer, J. K. & Livingston, D. M. The effect of DNA replication mutations on CAG tract stability in yeast. Genetics 15, 953–963 (1999).

    Article  Google Scholar 

  89. Kroutil, L. C. & Kunkel, T. A. Deletion errors generated during replication of CAG repeats. Nucleic Acids Res. 27, 3481–3486 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Pinder, D. J., Blake, C. E., Lindsey, J. C. & Leach, D. R. Replication strand preference for deletions associated with DNA palindromes. Mol. Microbiol. 28, 719–727 (1998).

    Article  CAS  PubMed  Google Scholar 

  91. Gomes-Pereira, M., Fortune, M. T. & Monckton, D. G. Mouse tissue culture models of unstable triplet repeats: in vitro selection for larger alleles, mutational expansion bias and tissue specificity, but no association with cell division rates. Hum. Mol. Genet. 10, 845–854 (2001).

    Article  CAS  PubMed  Google Scholar 

  92. Mirkin, E. V. & Mirkin, S. M. Replication fork stalling at natural impediments. Microbiol. Mol. Biol. Rev. 71, 13–35 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Samadashwily, G. M., Raca, G. & Mirkin, S. M. Trinucleotide repeats affect DNA replication in vivo. Nature Genet. 17, 298–304 (1997).

    Article  CAS  PubMed  Google Scholar 

  94. Voineagu, I., Surka, C. F., Shishkin, A. A., Krasilnikova, M. M. & Mirkin, S. M. Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility. Nature Struct. Mol. Biol. 16, 226–228 (2009). This work provided definitive evidence that long repeat tracts blocked polymerase passage in vivo and suggested that expansion can depend on replication-dependent repair mechanisms.

    Article  CAS  Google Scholar 

  95. Krasilnikova, M. M. & Mirkin, S. M. Replication stalling at Friedreich's ataxia (GAA)n repeats in vivo. Mol. Cell. Biol. 24, 2286–2295 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Shishkin, A. A. et al. Large-scale expansions of Friedreich's ataxia GAA repeats in yeast. Mol. Cell 35, 82–92 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Pomerantz, R. T. & O'Donnell, M. Direct restart of a replication fork stalled by a head-on RNA polymerase. Science 327, 590–592 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Fouché, N., Özgür, S., Roy, D. & Griffith, J. D. Replication fork regression in repetitive DNAs. Nucleic Acids Res. 34, 6044–6050 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  99. Yang, Z., Lau, R., Marcadier, J. L., Chitayat, D. & Pearson, C. E. Replication inhibitors modulate instability of an expanded trinucleotide repeat at the myotonic dystrophy type 1 disease locus in human cells. Am. J. Hum. Genet. 73, 1092–1105 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Maul, R. W. & Sutton, M. D. Roles of the Escherichia coli RecA protein and the global SOS response in effecting DNA polymerase selection in vivo. J. Bacteriol. 187, 7607–7618 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Guo, C., Kosarek-Stancel, J. N., Tang, T. S. & Friedberg, E. C. Y-family DNA polymerases in mammalian cells. Cell. Mol. Life Sci. 66, 2363–2381 (2009).

    Article  CAS  PubMed  Google Scholar 

  102. Waters, L. S. et al. Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance. Microbiol. Mol. Biol. Rev. 73, 134–154 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Edmunds, C. E., Simpson, L. J. & Sale, J. E. PCNA ubiquitination and REV1 define temporally distinct mechanisms for controlling translesion synthesis in the avian cell line DT40. Mol. Cell 30, 4519–4529, (2008).

    Article  CAS  Google Scholar 

  104. Modrich, P. Mechanisms in eukaryotic mismatch repair. J. Biol. Chem. 281, 30305–30309 (2006).

    Article  CAS  PubMed  Google Scholar 

  105. Hou, C., Chan, N. L., Gu, L. & Li, G. M. Incision-dependent and error-free repair of (CAG)n/(CTG)n hairpins in human cell extracts. Nature Struct. Mol. Biol. 16, 869–675 (2009).

    Article  CAS  Google Scholar 

  106. Panigrahi, G. B., Lau, R., Montgomery, S. E., Leonard, M. R. & Pearson, C. E. Slipped (CTG)•(CAG) repeats can be correctly repaired, escape repair or undergo error-prone repair. Nature Struct. Mol. Biol. 12, 654–662 (2005).

    Article  CAS  Google Scholar 

  107. McMurray, C. T. Hijacking of the mismatch repair system to cause CAG expansion and cell death in neurodegenerative disease. DNA Repair 7, 1121–1134 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Manley, K., Shirley, T. L., Flaherty, L. & Messer, A. Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenic mice. Nature Genet. 23, 471–473 (1999). This work provided the first evidence that the MMR system causes rather than corrects repeat expansions.

    Article  CAS  PubMed  Google Scholar 

  109. Gomes-Pereira, M., Fortune, M. T., Ingram, L., McAbney, J. P. & Monckton, D. G. Pms2 is a genetic enhancer of trinucleotide CAG.CTG repeat somatic mosaicism: implications for the mechanism of triplet repeat expansion. Hum. Mol. Genet. 13, 1815–1825 (2004).

    Article  CAS  PubMed  Google Scholar 

  110. van den Broek, W. J. et al. Somatic expansion behaviour of the (CTG)n repeat in myotonic dystrophy knock-in mice is differentially affected by Msh3 and Msh6 mismatch-repair proteins. Hum. Mol. Genet. 11, 191–198 (2002).

    Article  CAS  PubMed  Google Scholar 

  111. Owen, B. A. et al. [CAG]n-hairpin DNA binds to Msh2-Msh3 and changes properties of mismatch recognition. Nature Struct. Mol. Biol. 12, 663–670 (2005).

    Article  CAS  Google Scholar 

  112. Tomé, S. et al. MSH2 ATPase domain mutation affects CTG•CAG repeat instability in transgenic mice. PLoS Genet. 5, e1000482 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  113. Kim, H. M. et al. Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair. EMBO J. 27, 2896–2906 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Tian, L., Gu, L. & Li, G. M. Distinct nucleotide binding/hydrolysis properties and molar ratio of MutSα and MutSβ determine their differential mismatch binding activities. J. Biol. Chem. 284, 11557–11562 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Owen, B. A. L., Lang, W. H. & McMurray, C. T. The nucleotide binding dynamics of human MSH2-MSH3 are lesion dependent. Nature Struct. Mol. Biol. 16, 550–557 (2009).

    Article  CAS  Google Scholar 

  116. Moore, H., Greenwell, P. W., Liu, C. P., Arnheim, N. & Petes, T. D. Triplet repeats form secondary structures that escape DNA repair in yeast. Proc. Natl Acad. Sci. USA 96, 1504–1509 (1999). This work demonstrated that repeats that could form structures were not repaired during meiosis, whereas unstructured repeats were removed. This indicated that the DNA secondary structure prevented the removal of looped expansion intermediates.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Gu, Y. et al. Human MutY homolog, a DNA glycosylase involved in base excision repair, physically and functionally interacts with mismatch repair proteins human MutS homolog 2/human MutS homolog 6. J.Biol. Chem. 277, 11135–11142 (2002).

    Article  CAS  PubMed  Google Scholar 

  118. Kulaksiz, G., Reardon, J. T. . & Sancar, A. Xeroderma pigmentosum complementation group E protein (XPE/DDB2): purification of various complexes of XPE and analyses of their damaged DNA binding and putative DNA repair properties. Mol. Cell. Biol. 25, 9784–9792 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Masutani, C. et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399, 700–704 (1999).

    Article  CAS  PubMed  Google Scholar 

  120. McCulloch, S. D., Kokoska, R. J., Garg, P., Burgers, P. M. & Kunkel, T. A. The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases δ and η. Nucleic Acids Res. 37, 2830–2840 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Yoshimura, M. et al. Vertebrate POLQ and POLβ cooperate in base excision repair of oxidative DNA damage. Mol. Cell 24, 115–125 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Braithwaite, E. K., Kedar, P. S. & Lan, L. DNA polymerase λ protects mouse fibroblasts against oxidative DNA damage and is recruited to sites of DNA damage/repair. J. Biol. Chem. 280, 31641–31647 (2005).

    Article  CAS  PubMed  Google Scholar 

  123. Libby, R. T. et al. CTCF cis-regulates trinucleotide repeat instability in an epigenetic manner: a novel basis for mutational hot spot determination. PLoS Genet. 4, e1000257 (2008). This work was the first to definitively demonstrate that chromosomal position could determine whether a repeat tract was unstable. The evidence suggested that chromatin context was a key factor in expansion.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  124. Brock, G. J., Anderson, N. H. & Monckton, D. G. Cis-acting modifiers of expanded CAG/CTG triplet repeat expandability: associations with flanking GC content and proximity to CpG islands. Hum. Mol. Genet. 8, 1061–1067 (1999).

    Article  CAS  PubMed  Google Scholar 

  125. Engel, N., Thorvaldsen, J. L. & Bartolomei, M. S. CTCF binding sites promote transcription initiation and prevent DNA methylation on the maternal allele at the imprinted H19/Igf2 locus. Hum. Mol. Genet. 17, 1306–1317 (2008).

    Article  CAS  Google Scholar 

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Acknowledgements

I would like to thank J. Majka, V. Platt, W. Lang, E. Xun, C. Canaria and S. Bernstein for critical discussions and comments. This work is supported by US National Institutes of Health grants NS062384, NS40738, GM066359, NS060115, NS069177 and CA092584.

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Glossary

Threshold length

In the context of trinucleotide repeat alleles, the number of trinucleotide repeats at which the tract becomes unstable.

Pre-mutation

The length of a pre-mutation trinucleotide repeat tract is within the normal range, but the pre-mutation allele has increased susceptibility to mutation in a subsequent transmission. Individuals with a pre-mutation allele will exhibit a normal phenotype but may have offspring who have a higher number of trinucleotide repeats and who might be affected by the disease.

Anticipation

The propensity of trinucleotide repeats above a certain threshold to increase (expand) during transmission to offspring, often causing increases in disease severity and decreases in the age of onset.

Fragile X syndrome

(Also known as Martin–Bell syndrome.) A genetic disorder caused by the expansion of a single trinucleotide gene sequence (CGG) on the X chromosome, which leads to loss of expression of the FMR1 gene.

Full mutation

A repeat tract that is unstable and of a length that is typically associated with disease. The term is often used to distinguish such cases from alleles of a shorter, pre-mutation length that are not associated with disease.

Normal length

In the context of trinucleotide repeat alleles, the range of repeat lengths in which the repeat tract is stable as the gene is passed to the next generation.

Myotonic dystrophy type 1

(Also known as Steinert's disease.) A chronic, slowly progressive, inherited, multi-systemic disease that has a severe congenital form and a milder childhood-onset form.

Huntington's disease

A neurodegenerative disease that is caused by an abnormal trinucleotide repeat (CAG) in the huntingtin (HTT) gene. Uncoordinated, involuntary movements and decline in mental cognition characterize the disease.

Homologous recombination

A type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA (known as double-strand breaks).

Crossover

The exchange of material between two chromosomes. It is one of the final phases of genetic recombination and occurs during prophase I of meiosis (diplotene) in a process called synapsis. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

Non-homologous end joining

A pathway that repairs double-strand breaks in DNA using a non-homologous chromosome. It typically uses short homologous DNA sequences, called microhomologies, to guide repair. Microhomologies are often present in single-strand overhangs on the ends of double-strand breaks.

Base excision repair

The cellular mechanism that is primarily responsible for removing small, non-helix-distorting base lesions from the genome. It is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication.

Long patch

In the context of base excision repair, long patch repair is when the gap-filling polymerase induces strand displacement at the single-strand break and restores normal Watson–Crick pairing by replacing a patch of two to 15 nucleotides.

Short patch

In the context of base excision repair, short patch repair is when the gap-filling polymerase replaces the damaged base with a single nucleotide to restore normal Watson–Crick pairing.

Polymerase β

The major DNA repair polymerase that is used in base excision repair.

Polymerase δ

The major polymerase that copies DNA on the discontinuous or lagging strand template during cell proliferation.

Polymerase ɛ

The major polymerase that copies the leading strand template during cell proliferation.

Apurinic

A site in duplex DNA that has lost guanine or adenine.

Polymerase slippage

The misalignment of the DNA polymerase during cell proliferation, typically at repetitive DNA sequences. Misalignment on the template strand causes a loss in DNA bases and misalignment on the daughter strand leads to a gain in DNA bases.

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McMurray, C. Mechanisms of trinucleotide repeat instability during human development. Nat Rev Genet 11, 786–799 (2010). https://doi.org/10.1038/nrg2828

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