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Abstract

DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing.

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2021-06-20
2024-04-19
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Literature Cited

  1. 1. 
    Bunting SF, Nussenzweig A. 2013. End-joining, translocations and cancer. Nat. Rev. Cancer 13:7443–54
    [Google Scholar]
  2. 2. 
    Lieber MR. 2010. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu. Rev. Biochem. 79:181–211
    [Google Scholar]
  3. 3. 
    Karanam K, Kafri R, Loewer A, Lahav G. 2012. Quantitative live cell imaging reveals a gradual shift between DNA repair mechanisms and a maximal use of HR in mid S phase. Mol. Cell 47:2320–29
    [Google Scholar]
  4. 4. 
    Haber JE. 2018. DNA repair: the search for homology. BioEssays 40:5e1700229
    [Google Scholar]
  5. 5. 
    Jasin M, Rothstein R. 2013. Repair of strand breaks by homologous recombination. Cold Spring Harb. Perspect. Biol. 5:11a012740
    [Google Scholar]
  6. 6. 
    Takata M, Sasaki MS, Sonoda E, Morrison C, Hashimoto M et al. 1998. Homologous recombination and non-homologous end-joining pathways of DNA double-strand break repair have overlapping roles in the maintenance of chromosomal integrity in vertebrate cells. EMBO J. 17:185497–508
    [Google Scholar]
  7. 7. 
    Sfeir A, Symington LS. 2015. Microhomology-mediated end joining: a back-up survival mechanism or dedicated pathway?. Trends Biochem. Sci. 40:11701–14
    [Google Scholar]
  8. 8. 
    Bhargava R, Onyango DO, Stark JM. 2016. Regulation of single-strand annealing and its role in genome maintenance. Trends Genet. 32:9566–75
    [Google Scholar]
  9. 9. 
    Ceccaldi R, Rondinelli B, D'Andrea AD 2016. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 26:152–64
    [Google Scholar]
  10. 10. 
    Scully R, Panday A, Elango R, Willis NA. 2019. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat. Rev. Mol. Cell Biol. 20:11698–714
    [Google Scholar]
  11. 11. 
    Walker JR, Corpina RA, Goldberg J. 2001. Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. Nature 412:6847607–14
    [Google Scholar]
  12. 12. 
    Falck J, Coates J, Jackson SP. 2005. Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage. Nature 434:7033605–11
    [Google Scholar]
  13. 13. 
    Jette N, Lees-Miller SP. 2015. The DNA-dependent protein kinase: a multifunctional protein kinase with roles in DNA double strand break repair and mitosis. Prog. Biophys. Mol. Biol. 117:2–3194–205
    [Google Scholar]
  14. 14. 
    Li Z, Otevrel T, Gao Y, Cheng H-L, Seed B et al. 1995. The XRCC4 gene encodes a novel protein involved in DNA double-strand break repair and V(D)J recombination. Cell 83:71079–89
    [Google Scholar]
  15. 15. 
    Ahnesorg P, Smith P, Jackson SP. 2006. XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Cell 124:2301–313
    [Google Scholar]
  16. 16. 
    Buck D, Malivert L, de Chasseval R, Barraud A, Fondanèche M-C et al. 2006. Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly. Cell 124:2287–99
    [Google Scholar]
  17. 17. 
    Ochi T, Blackford AN, Coates J, Jhujh S, Mehmood S et al. 2015. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair. Science 347:6218185–88
    [Google Scholar]
  18. 18. 
    Xing M, Yang M, Huo W, Feng F, Wei L et al. 2015. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway. Nat. Commun. 6:6233
    [Google Scholar]
  19. 19. 
    Grawunder U, Wilm M, Wu X, Kulesza P, Wilson TE et al. 1997. Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells. Nature 388:6641492–95
    [Google Scholar]
  20. 20. 
    Gu J, Lu H, Tsai AG, Schwarz K, Lieber MR. 2007. Single-stranded DNA ligation and XLF-stimulated incompatible DNA end ligation by the XRCC4-DNA ligase IV complex: influence of terminal DNA sequence. Nucleic Acids Res 35:175755–62
    [Google Scholar]
  21. 21. 
    Tsai CJ, Kim SA, Chu G 2007. Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends. PNAS 104:197851–56
    [Google Scholar]
  22. 22. 
    Vilenchik MM, Knudson AG 2003. Endogenous DNA double-strand breaks: production, fidelity of repair, and induction of cancer. PNAS 100:2212871–76
    [Google Scholar]
  23. 23. 
    Caldecott KW. 2008. Single-strand break repair and genetic disease. Nat. Rev. Genet. 9:8619–31
    [Google Scholar]
  24. 24. 
    Strumberg D, Pilon AA, Smith M, Hickey R, Malkas L, Pommier Y. 2000. Conversion of topoisomerase I cleavage complexes on the leading strand of ribosomal DNA into 5′-phosphorylated DNA double-strand breaks by replication runoff. Mol. Cell. Biol. 20:113977–87
    [Google Scholar]
  25. 25. 
    Balmus G, Pilger D, Coates J, Demir M, Sczaniecka-Clift M et al. 2019. ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks. Nat. Commun. 10:87
    [Google Scholar]
  26. 26. 
    de Lange T. 2018. Shelterin-mediated telomere protection. Annu. Rev. Genet. 52:223–47
    [Google Scholar]
  27. 27. 
    Alt FW, Zhang Y, Meng F-L, Guo C, Schwer B. 2013. Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell 152:3417–29
    [Google Scholar]
  28. 28. 
    Chaudhuri J, Alt FW. 2004. Class-switch recombination: interplay of transcription, DNA deamination and DNA repair. Nat. Rev. Immunol. 4:7541–52
    [Google Scholar]
  29. 29. 
    Gellert M. 1992. Molecular analysis of V(D)J recombination. Annu. Rev. Genet. 26:425–46
    [Google Scholar]
  30. 30. 
    Schatz DG, Swanson PC. 2011. V(D)J recombination: mechanisms of initiation. Annu. Rev. Genet. 45:167–202
    [Google Scholar]
  31. 31. 
    Stavnezer J, Schrader CE. 2014. IgH chain class switch recombination: mechanism and regulation. J. Immunol. 193:115370–78
    [Google Scholar]
  32. 32. 
    Ma Y, Pannicke U, Schwarz K, Lieber MR. 2002. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108:6781–94
    [Google Scholar]
  33. 33. 
    Bertocci B, De Smet A, Berek C, Weill J-C, Reynaud C-A. 2003. Immunoglobulin κ light chain gene rearrangement is impaired in mice deficient for DNA polymerase mu. Immunity 19:2203–11
    [Google Scholar]
  34. 34. 
    Bertocci B, De Smet A, Weill J-C, Reynaud C-A. 2006. Nonoverlapping functions of DNA polymerases mu, lambda, and terminal deoxynucleotidyltransferase during immunoglobulin V(D)J recombination in vivo. Immunity 25:131–41
    [Google Scholar]
  35. 35. 
    Komori T, Okada A, Stewart V, Alt FW. 1993. Lack of N regions in antigen receptor variable region genes of TdT-deficient lymphocytes. Science 261:51251171–75
    [Google Scholar]
  36. 36. 
    Okazaki I, Kinoshita K, Muramatsu M, Yoshikawa K, Honjo T. 2002. The AID enzyme induces class switch recombination in fibroblasts. Nature 416:340–45
    [Google Scholar]
  37. 37. 
    Yan CT, Boboila C, Souza EK, Franco S, Hickernell TR et al. 2007. IgH class switching and translocations use a robust non-classical end-joining pathway. Nature 449:7161478–82
    [Google Scholar]
  38. 38. 
    Woodbine L, Gennery AR, Jeggo PA. 2014. The clinical impact of deficiency in DNA non-homologous end-joining. DNA Repair 16:84–96
    [Google Scholar]
  39. 39. 
    Barnes DE, Stamp G, Rosewell I, Denzel A, Lindahl T. 1998. Targeted disruption of the gene encoding DNA ligase IV leads to lethality in embryonic mice. Curr. Biol. 8:251395–98
    [Google Scholar]
  40. 40. 
    Frank KM, Sekiguchi JM, Seidl KJ, Swat W, Rathbun GA et al. 1998. Late embryonic lethality and impaired V(D)J recombination in mice lacking DNA ligase IV. Nature 396:6707173–77
    [Google Scholar]
  41. 41. 
    Gao Y, Sun Y, Frank KM, Dikkes P, Fujiwara Y et al. 1998. A critical role for DNA end-joining proteins in both lymphogenesis and neurogenesis. Cell 95:7891–902
    [Google Scholar]
  42. 42. 
    Ghezraoui H, Piganeau M, Renouf B, Renaud J-B, Sallmyr A et al. 2014. Chromosomal translocations in human cells are generated by canonical nonhomologous end-joining. Mol. Cell 55:6829–42
    [Google Scholar]
  43. 43. 
    Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR et al. 2011. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144:127–40
    [Google Scholar]
  44. 44. 
    Sishc BJ, Davis AJ. 2017. The role of the core non-homologous end joining factors in carcinogenesis and cancer. Cancers 9:781
    [Google Scholar]
  45. 45. 
    Kefala Stavridi A, Appleby R, Liang S, Blundell TL, Chaplin AK 2020. Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining. Essays Biochem 64:5791–806
    [Google Scholar]
  46. 46. 
    Mohiuddin IS, Kang MH. 2019. DNA-PK as an emerging therapeutic target in cancer. Front. Oncol. 9:635
    [Google Scholar]
  47. 47. 
    Chu VT, Weber T, Wefers B, Wurst W, Sander S et al. 2015. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 33:5543–48
    [Google Scholar]
  48. 48. 
    Li G, Liu D, Zhang X, Quan R, Zhong C et al. 2018. Suppressing Ku70/Ku80 expression elevates homology-directed repair efficiency in primary fibroblasts. Int. J. Biochem. Cell Biol. 99:154–60
    [Google Scholar]
  49. 49. 
    Maruyama T, Dougan SK, Truttmann MC, Bilate AM, Ingram JR, Ploegh HL. 2015. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat. Biotechnol. 33:5538–42
    [Google Scholar]
  50. 50. 
    Robert F, Barbeau M, Éthier S, Dostie J, Pelletier J. 2015. Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing. Genome Med 7:193
    [Google Scholar]
  51. 51. 
    Kruhlak MJ, Celeste A, Dellaire G, Fernandez-Capetillo O, Müller WG et al. 2006. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J. Cell Biol. 172:6823–34
    [Google Scholar]
  52. 52. 
    Soutoglou E, Dorn JF, Sengupta K, Jasin M, Nussenzweig A et al. 2007. Positional stability of single double-strand breaks in mammalian cells. Nat. Cell Biol. 9:6675–82
    [Google Scholar]
  53. 53. 
    Graham TGW, Walter JC, Loparo JJ. 2016. Two-stage synapsis of DNA ends during non-homologous end joining. Mol. Cell 61:6850–58
    [Google Scholar]
  54. 54. 
    Reid DA, Keegan S, Leo-Macias A, Watanabe G, Strande NT et al. 2015. Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair. PNAS 112:20E2575–84
    [Google Scholar]
  55. 55. 
    Graham TGW, Carney SM, Walter JC, Loparo JJ. 2018. A single XLF dimer bridges DNA ends during nonhomologous end joining. Nat. Struct. Mol. Biol. 25:9877–84
    [Google Scholar]
  56. 56. 
    Wang JL, Duboc C, Wu Q, Ochi T, Liang S et al. 2018. Dissection of DNA double-strand-break repair using novel single-molecule forceps. Nat. Struct. Mol. Biol. 25:6482–87
    [Google Scholar]
  57. 57. 
    Brouwer I, Sitters G, Candelli A, Heerema SJ, Heller I et al. 2016. Sliding sleeves of XRCC4-XLF bridge DNA and connect fragments of broken DNA. Nature 535:566–69
    [Google Scholar]
  58. 58. 
    Zhao B, Watanabe G, Morten MJ, Reid DA, Rothenberg E, Lieber MR. 2019. The essential elements for the noncovalent association of two DNA ends during NHEJ synapsis. Nat. Commun. 10:3588
    [Google Scholar]
  59. 59. 
    Fok JHL, Ramos-Montoya A, Vazquez-Chantada M, Wijnhoven PWG, Follia V et al. 2019. AZD7648 is a potent and selective DNA-PK inhibitor that enhances radiation, chemotherapy and olaparib activity. Nat. Commun. 10:5065
    [Google Scholar]
  60. 60. 
    Zhao Y, Thomas HD, Batey MA, Cowell IG, Richardson CJ et al. 2006. Preclinical evaluation of a potent novel DNA-dependent protein kinase inhibitor NU7441. Cancer Res 66:105354–62
    [Google Scholar]
  61. 61. 
    Baumann P, West SC 1998. DNA end-joining catalyzed by human cell-free extracts. PNAS 95:2414066–70
    [Google Scholar]
  62. 62. 
    Jiang W, Crowe JL, Liu X, Nakajima S, Wang Y et al. 2015. Differential phosphorylation of DNA-PKcs regulates the interplay between end-processing and end-ligation during nonhomologous end-joining. Mol. Cell 58:1172–85
    [Google Scholar]
  63. 63. 
    Ruis BL, Fattah KR, Hendrickson EA. 2008. The catalytic subunit of DNA-dependent protein kinase regulates proliferation, telomere length, and genomic stability in human somatic cells. Mol. Cell. Biol. 28:206182–95
    [Google Scholar]
  64. 64. 
    Shao Z, Flynn RA, Crowe JL, Zhu Y, Liang J et al. 2020. DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis. Nature 579:291–96
    [Google Scholar]
  65. 65. 
    Uematsu N, Weterings E, Yano K, Morotomi-Yano K, Jakob B et al. 2007. Autophosphorylation of DNA-PKCS regulates its dynamics at DNA double-strand breaks. J. Cell Biol. 177:2219–29
    [Google Scholar]
  66. 66. 
    Gell D, Jackson SP. 1999. Mapping of protein-protein interactions within the DNA-dependent protein kinase complex. Nucleic Acids Res 27:173494–502
    [Google Scholar]
  67. 67. 
    Cui X, Yu Y, Gupta S, Cho Y-M, Lees-Miller SP, Meek K. 2005. Autophosphorylation of DNA-dependent protein kinase regulates DNA end processing and may also alter double-strand break repair pathway choice. Mol. Cell Biol. 25:2410842–52
    [Google Scholar]
  68. 68. 
    Ding Q, Reddy YVR, Wang W, Woods T, Douglas P et al. 2003. Autophosphorylation of the catalytic subunit of the DNA-dependent protein kinase is required for efficient end processing during DNA double-strand break repair. Mol. Cell Biol. 23:165836–48
    [Google Scholar]
  69. 69. 
    DeFazio LG, Stansel RM, Griffith JD, Chu G. 2002. Synapsis of DNA ends by DNA-dependent protein kinase. EMBO J 21:123192–200
    [Google Scholar]
  70. 70. 
    Sibanda BL, Chirgadze DY, Ascher DB, Blundell TL. 2017. DNA-PKcs structure suggests an allosteric mechanism modulating DNA double-strand break repair. Science 355:6324520–24
    [Google Scholar]
  71. 71. 
    Spagnolo L, Rivera-Calzada A, Pearl LH, Llorca O. 2006. Three-dimensional structure of the human DNA-PKcs/Ku70/Ku80 complex assembled on DNA and its implications for DNA DSB repair. Mol. Cell 22:4511–19
    [Google Scholar]
  72. 72. 
    Cottarel J, Frit P, Bombarde O, Salles B, Négrel A et al. 2013. A noncatalytic function of the ligation complex during nonhomologous end joining. J. Cell Biol. 200:2173–86
    [Google Scholar]
  73. 73. 
    Meek K, Douglas P, Cui X, Ding Q, Lees-Miller SP. 2007. trans autophosphorylation at DNA-dependent protein kinase's two major autophosphorylation site clusters facilitates end processing but not end joining. Mol. Cell Biol. 27:103881–90
    [Google Scholar]
  74. 74. 
    Andres SN, Modesti M, Tsai CJ, Chu G, Junop MS. 2007. Crystal structure of human XLF: a twist in nonhomologous DNA end-joining. Mol. Cell 28:61093–101
    [Google Scholar]
  75. 75. 
    Andres SN, Vergnes A, Ristic D, Wyman C, Modesti M, Junop M. 2012. A human XRCC4-XLF complex bridges DNA. Nucleic Acids Res 40:41868–78
    [Google Scholar]
  76. 76. 
    Li Y, Chirgadze DY, Bolanos-Garcia VM, Sibanda BL, Davies OR et al. 2008. Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ. EMBO J 27:1290–300
    [Google Scholar]
  77. 77. 
    Roy S, Andres SN, Vergnes A, Neal JA, Xu Y et al. 2012. XRCC4’s interaction with XLF is required for coding (but not signal) end joining. Nucleic Acids Res 40:41684–94
    [Google Scholar]
  78. 78. 
    Yano K, Morotomi-Yano K, Lee K-J, Chen DJ. 2011. Functional significance of the interaction with Ku in DNA double-strand break recognition of XLF. FEBS Lett 585:6841–46
    [Google Scholar]
  79. 79. 
    Bhargava R, Sandhu M, Muk S, Lee G, Vaidehi N, Stark JM. 2018. C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains. Nat. Commun. 9:2484
    [Google Scholar]
  80. 80. 
    Carney SM, Moreno AT, Piatt SC, Cisneros-Aguirre M, Lopezcolorado FW et al. 2020. XLF acts as a flexible connector during non-homologous end joining. eLife 9:e61920
    [Google Scholar]
  81. 81. 
    Normanno D, Négrel A, de Melo AJ, Betzi S, Meek K, Modesti M. 2017. Mutational phospho-mimicry reveals a regulatory role for the XRCC4 and XLF C-terminal tails in modulating DNA bridging during classical non-homologous end joining. eLife 6:e22900
    [Google Scholar]
  82. 82. 
    Yu Y, Mahaney BL, Yano K, Ye R, Fang S et al. 2008. DNA-PK and ATM phosphorylation sites in XLF/Cernunnos are not required for repair of DNA double strand breaks. DNA Repair 7:101680–92
    [Google Scholar]
  83. 83. 
    Hammel M, Rey M, Yu Y, Mani RS, Classen S et al. 2011. XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair. J. Biol. Chem. 286:3732638–50
    [Google Scholar]
  84. 84. 
    Ropars V, Drevet P, Legrand P, Baconnais S, Amram J et al. 2011. Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining. PNAS 108:3112663–68
    [Google Scholar]
  85. 85. 
    Ochi T, Wu Q, Chirgadze DY, Grossmann JG, Bolanos-Garcia VM, Blundell TL. 2012. Structural insights into the role of domain flexibility in human DNA ligase IV. Structure 20:71212–22
    [Google Scholar]
  86. 86. 
    Roy S, de Melo AJ, Xu Y, Tadi SK, Négrel A et al. 2015. XRCC4/XLF interaction is variably required for DNA repair and is not required for ligase IV stimulation. Mol. Cell. Biol. 35:173017–28
    [Google Scholar]
  87. 87. 
    Wu P-Y, Frit P, Meesala S, Dauvillier S, Modesti M et al. 2009. Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4. Mol. Cell. Biol. 29:113163–72
    [Google Scholar]
  88. 88. 
    Costantini S, Woodbine L, Andreoli L, Jeggo PA, Vindigni A. 2007. Interaction of the Ku heterodimer with the DNA ligase IV/Xrcc4 complex and its regulation by DNA-PK. DNA Repair 6:6712–22
    [Google Scholar]
  89. 89. 
    Nick McElhinny SA, Snowden CM, McCarville J, Ramsden DA 2000. Ku recruits the XRCC4-ligase IV complex to DNA ends. Mol. Cell. Biol. 20:92996–3003
    [Google Scholar]
  90. 90. 
    Fattah F, Lee EH, Weisensel N, Wang Y, Lichter N, Hendrickson EA. 2010. Ku regulates the non-homologous end joining pathway choice of DNA double-strand break repair in human somatic cells. PLOS Genet 6:2e1000855
    [Google Scholar]
  91. 91. 
    Xing M, Bjørås M, Daniel JA, Alt FW, Oksenych V. 2017. Synthetic lethality between murine DNA repair factors XLF and DNA-PKcs is rescued by inactivation of Ku70. DNA Repair 57:133–38
    [Google Scholar]
  92. 92. 
    Conlin MP, Reid DA, Small GW, Chang HH, Watanabe G et al. 2017. DNA ligase IV guides end-processing choice during nonhomologous end joining. Cell Rep 20:122810–19
    [Google Scholar]
  93. 93. 
    Berthelot V, Mouta-Cardoso G, Hégarat N, Guillonneau F, François J-C et al. 2016. The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. Nucleic Acids Res 44:104721–33
    [Google Scholar]
  94. 94. 
    Haahr P, Hoffmann S, Tollenaere MAX, Ho T, Toledo LI et al. 2016. Activation of the ATR kinase by the RPA-binding protein ETAA1. Nat. Cell Biol. 18:1196–207
    [Google Scholar]
  95. 95. 
    Balmus G, Barros AC, Wijnhoven PWG, Lescale C, Hasse HL et al. 2016. Synthetic lethality between PAXX and XLF in mammalian development. Genes Dev 30:192152–57
    [Google Scholar]
  96. 96. 
    Kumar V, Alt FW, Frock RL 2016. PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line. PNAS 113:3810619–24
    [Google Scholar]
  97. 97. 
    Kanno S, Kuzuoka H, Sasao S, Hong Z, Lan L et al. 2007. A novel human AP endonuclease with conserved zinc-finger-like motifs involved in DNA strand break responses. EMBO J 26:82094–103
    [Google Scholar]
  98. 98. 
    Grundy GJ, Rulten SL, Zeng Z, Arribas-Bosacoma R, Iles N et al. 2013. APLF promotes the assembly and activity of non-homologous end joining protein complexes. EMBO J 32:1112–25
    [Google Scholar]
  99. 99. 
    Cooper MP, Machwe A, Orren DK, Brosh RM, Ramsden D, Bohr VA. 2000. Ku complex interacts with and stimulates the Werner protein. Genes Dev 14:8907–12
    [Google Scholar]
  100. 100. 
    Grundy GJ, Rulten SL, Arribas-Bosacoma R, Davidson K, Kozik Z et al. 2016. The Ku-binding motif is a conserved module for recruitment and stimulation of non-homologous end-joining proteins. Nat. Commun. 7:11242
    [Google Scholar]
  101. 101. 
    Shamanna RA, Lu H, de Freitas JK, Tian J, Croteau DL, Bohr VA. 2016. WRN regulates pathway choice between classical and alternative non-homologous end joining. Nat. Commun. 7:13785
    [Google Scholar]
  102. 102. 
    Arnoult N, Correia A, Ma J, Merlo A, Garcia-Gomez S et al. 2017. Regulation of DNA repair pathway choice in S and G2 phases by the NHEJ inhibitor CYREN. Nature 549:7673548–52
    [Google Scholar]
  103. 103. 
    Hung PJ, Johnson B, Chen B-R, Byrum AK, Bredemeyer AL et al. 2018. MRI is a DNA damage response adaptor during classical non-homologous end joining. Mol. Cell 71:2332–42.e8
    [Google Scholar]
  104. 104. 
    Frit P, Ropars V, Modesti M, Charbonnier J-B, Calsou P. 2019. Plugged into the Ku-DNA hub: the NHEJ network. Prog. Biophys. Mol. Biol. 147:62–76
    [Google Scholar]
  105. 105. 
    Rulten SL, Grundy GJ. 2017. Non-homologous end joining: common interaction sites and exchange of multiple factors in the DNA repair process. BioEssays 39:31600209
    [Google Scholar]
  106. 106. 
    Tadi SK, Tellier-Lebègue C, Nemoz C, Drevet P, Audebert S et al. 2016. PAXX is an accessory c-NHEJ factor that associates with Ku70 and has overlapping functions with XLF. Cell Rep 17:2541–55
    [Google Scholar]
  107. 107. 
    Nemoz C, Ropars V, Frit P, Gontier A, Drevet P et al. 2018. XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nat. Struct. Mol. Biol. 25:10971–80
    [Google Scholar]
  108. 108. 
    Kim K, Min J, Kirby TW, Gabel SA, Pedersen LC, London RE. 2020. Ligand binding characteristics of the Ku80 von Willebrand domain. DNA Repair 85:102739
    [Google Scholar]
  109. 109. 
    Craxton A, Munnur D, Jukes-Jones R, Skalka G, Langlais C et al. 2018. PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair. Nat. Commun. 9:3877
    [Google Scholar]
  110. 110. 
    Zhang Y, He Q, Hu Z, Feng Y, Fan L et al. 2016. Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer. Nat. Struct. Mol. Biol. 23:6522–30
    [Google Scholar]
  111. 111. 
    Chowdhury D, Choi YE, Brault ME. 2013. Charity begins at home: non-coding RNA functions in DNA repair. Nat. Rev. Mol. Cell Biol. 14:3181–89
    [Google Scholar]
  112. 112. 
    De Ioannes P, Malu S, Cortes P, Aggarwal AK. 2012. Structural basis of DNA ligase IV-Artemis interaction in nonhomologous end-joining. Cell Rep. 2:61505–12
    [Google Scholar]
  113. 113. 
    Niewolik D, Pannicke U, Lu H, Ma Y, Wang L-CV et al. 2006. DNA-PKcs dependence of Artemis endonucleolytic activity, differences between hairpins and 5′ or 3′ overhangs. J. Biol. Chem. 281:4533900–9
    [Google Scholar]
  114. 114. 
    Riballo E, Kühne M, Rief N, Doherty A, Smith GCM et al. 2004. A pathway of double-strand break rejoining dependent upon ATM, Artemis, and proteins locating to γ-H2AX foci. Mol. Cell 16:5715–24
    [Google Scholar]
  115. 115. 
    Kawale AS, Akopiants K, Valerie K, Ruis B, Hendrickson EA et al. 2018. TDP1 suppresses mis-joining of radiomimetic DNA double-strand breaks and cooperates with Artemis to promote optimal nonhomologous end joining. Nucleic Acids Res. 46:178926–39
    [Google Scholar]
  116. 116. 
    Ma Y, Schwarz K, Lieber MR. 2005. The Artemis:DNA-PKcs endonuclease cleaves DNA loops, flaps, and gaps. DNA Repair 4:7845–51
    [Google Scholar]
  117. 117. 
    Beck BD, Lee S-S, Williamson E, Hromas RA, Lee S-H. 2011. Biochemical characterization of Metnase's endonuclease activity and its role in NHEJ repair. Biochemistry 50:204360–70
    [Google Scholar]
  118. 118. 
    Kusumoto R, Dawut L, Marchetti C, Wan Lee J, Vindigni A et al. 2008. Werner protein cooperates with the XRCC4-DNA ligase IV complex in end-processing. Biochemistry 47:287548–56
    [Google Scholar]
  119. 119. 
    Li S, Kanno S, Watanabe R, Ogiwara H, Kohno T et al. 2011. Polynucleotide kinase and aprataxin-like forkhead-associated protein (PALF) acts as both a single-stranded DNA endonuclease and a single-stranded DNA 3′ exonuclease and can participate in DNA end joining in a biochemical system. J. Biol. Chem. 286:4236368–77
    [Google Scholar]
  120. 120. 
    Grundy GJ, Rulten SL, Zeng Z, Arribas-Bosacoma R, Iles N et al. 2012. APLF promotes the assembly and activity of non-homologous end joining protein complexes. EMBO J 32:1112–25
    [Google Scholar]
  121. 121. 
    Lee JW, Harrigan J, Opresko PL, Bohr VA. 2005. Pathways and functions of the Werner syndrome protein. Mech. Ageing Dev. 126:179–86
    [Google Scholar]
  122. 122. 
    Tellier M, Chalmers R. 2019. The roles of the human SETMAR (Metnase) protein in illegitimate DNA recombination and non-homologous end joining repair. DNA Repair 80:26–35
    [Google Scholar]
  123. 123. 
    Fan W, Wu X. 2004. DNA polymerase λ can elongate on DNA substrates mimicking non-homologous end joining and interact with XRCC4-ligase IV complex. Biochem. Biophys. Res. Commun. 323:41328–33
    [Google Scholar]
  124. 124. 
    Ma Y, Lu H, Tippin B, Goodman MF, Shimazaki N et al. 2004. A biochemically defined system for mammalian nonhomologous DNA end joining. Mol. Cell 16:5701–13
    [Google Scholar]
  125. 125. 
    Uchiyama Y, Takeuchi R, Kodera H, Sakaguchi K. 2009. Distribution and roles of X-family DNA polymerases in eukaryotes. Biochimie 91:2165–70
    [Google Scholar]
  126. 126. 
    Xia W, Ci S, Li M, Wang M, Dianov GL et al. 2019. Two-way crosstalk between BER and c-NHEJ repair pathway is mediated by Pol-β and Ku70. FASEB J 33:1111668–81
    [Google Scholar]
  127. 127. 
    Nick McElhinny SA, Havener JM, Garcia-Diaz M, Juárez R, Bebenek K et al. 2005. A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining. Mol. Cell 19:3357–66
    [Google Scholar]
  128. 128. 
    Pryor JM, Waters CA, Aza A, Asagoshi K, Strom C et al. 2015. Essential role for polymerase specialization in cellular nonhomologous end joining. PNAS 112:33E4537–45
    [Google Scholar]
  129. 129. 
    Pryor JM, Conlin MP, Carvajal-Garcia J, Luedeman ME, Luthman AJ et al. 2018. Ribonucleotide incorporation enables repair of chromosome breaks by nonhomologous end joining. Science 361:64071126–29
    [Google Scholar]
  130. 130. 
    Koch CA, Agyei R, Galicia S, Metalnikov P, O'Donnell P et al. 2004. Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV. EMBO J 23:193874–85
    [Google Scholar]
  131. 131. 
    Clements PM, Breslin C, Deeks ED, Byrd PJ, Ju L et al. 2004. The ataxia-oculomotor apraxia 1 gene product has a role distinct from ATM and interacts with the DNA strand break repair proteins XRCC1 and XRCC4. DNA Repair 3:111493–502
    [Google Scholar]
  132. 132. 
    Ahel I, Rass U, El-Khamisy SF, Katyal S, Clements PM et al. 2006. The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates. Nature 443:7112713–16
    [Google Scholar]
  133. 133. 
    Ellenberger T, Tomkinson AE. 2008. Eukaryotic DNA ligases: structural and functional insights. Annu. Rev. Biochem. 77:313–38
    [Google Scholar]
  134. 134. 
    Champoux JJ. 2001. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70:369–413
    [Google Scholar]
  135. 135. 
    Cho J-E, Jinks-Robertson S. 2018. Topoisomerase I and genome stability: the good and the bad. Methods Mol. Biol. 1703:21–45
    [Google Scholar]
  136. 136. 
    Yang SW, Burgin AB, Huizenga BN, Robertson CA, Yao KC, Nash HA 1996. A eukaryotic enzyme that can disjoin dead-end covalent complexes between DNA and type I topoisomerases. PNAS 93:2111534–39
    [Google Scholar]
  137. 137. 
    Cortes Ledesma F, El Khamisy SF, Zuma MC, Osborn K, Caldecott KW 2009. A human 5′-tyrosyl DNA phosphodiesterase that repairs topoisomerase-mediated DNA damage. Nature 461:7264674–78
    [Google Scholar]
  138. 138. 
    Interthal H, Chen HJ, Champoux JJ. 2005. Human Tdp1 cleaves a broad spectrum of substrates, including phosphoamide linkages. J. Biol. Chem. 280:4336518–28
    [Google Scholar]
  139. 139. 
    Inamdar KV, Pouliot JJ, Zhou T, Lees-Miller SP, Rasouli-Nia A, Povirk LF. 2002. Conversion of phosphoglycolate to phosphate termini on 3′ overhangs of DNA double strand breaks by the human tyrosyl-DNA phosphodiesterase hTdp1. J. Biol. Chem. 277:3027162–68
    [Google Scholar]
  140. 140. 
    Roberts SA, Strande N, Burkhalter MD, Strom C, Havener JM et al. 2010. Ku is a 5′-dRP/AP lyase that excises nucleotide damage near broken ends. Nature 464:72921214–17
    [Google Scholar]
  141. 141. 
    Bétermier M, Bertrand P, Lopez BS. 2014. Is non-homologous end-joining really an inherently error-prone process?. PLOS Genet 10:1e1004086
    [Google Scholar]
  142. 142. 
    Lin WY, Wilson JH, Lin Y. 2013. Repair of chromosomal double-strand breaks by precise ligation in human cells. DNA Repair 12:7480–87
    [Google Scholar]
  143. 143. 
    Waters CA, Strande NT, Pryor JM, Strom CN, Mieczkowski P et al. 2014. The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining. Nat. Commun. 5:4286
    [Google Scholar]
  144. 144. 
    Feldmann E, Schmiemann V, Goedecke W, Reichenberger S, Pfeiffer P. 2000. DNA double-strand break repair in cell-free extracts from Ku80-deficient cells: implications for Ku serving as an alignment factor in non-homologous DNA end joining. Nucleic Acids Res 28:132585–96
    [Google Scholar]
  145. 145. 
    Labhart P. 1999. Ku-dependent nonhomologous DNA end joining in Xenopus egg extracts. Mol. Cell. Biol. 19:42585–93
    [Google Scholar]
  146. 146. 
    Stinson BM, Moreno AT, Walter JC, Loparo JJ. 2020. A mechanism to minimize errors during non-homologous end joining. Mol. Cell 77:51080–91.e8
    [Google Scholar]
  147. 147. 
    Budman J, Chu G. 2005. Processing of DNA for nonhomologous end-joining by cell-free extract. EMBO J 24:4849–60
    [Google Scholar]
  148. 148. 
    Ma Y, Lu H, Schwarz K, Lieber MR. 2005. Repair of double-strand DNA breaks by the human nonhomologous DNA end joining pathway: the iterative processing model. Cell Cycle 4:91193–200
    [Google Scholar]
  149. 149. 
    Akopiants K, Zhou R-Z, Mohapatra S, Valerie K, Lees-Miller SP et al. 2009. Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases λ and μ for nonhomologous end joining in human whole-cell extracts. Nucleic Acids Res 37:124055–62
    [Google Scholar]
  150. 150. 
    Celli GB, de Lange T. 2005. DNA processing is not required for ATM-mediated telomere damage response after TRF2 deletion. Nat. Cell Biol. 7:7712–18
    [Google Scholar]
  151. 151. 
    Lee JW, Yannone SM, Chen DJ, Povirk LF. 2003. Requirement for XRCC4 and DNA ligase IV in alignment-based gap filling for nonhomologous DNA end joining in vitro. Cancer Res 63:122–24
    [Google Scholar]
  152. 152. 
    Lee JW, Blanco L, Zhou T, Garcia-Diaz M, Bebenek K et al. 2004. Implication of DNA polymerase λ in alignment-based gap filling for nonhomologous DNA end joining in human nuclear extracts. J. Biol. Chem. 279:1805–11
    [Google Scholar]
  153. 153. 
    Perry JJP, Cotner-Gohara E, Ellenberger T, Tainer JA. 2010. Structural dynamics in DNA damage signaling and repair. Curr. Opin. Struct. Biol. 20:3283–94
    [Google Scholar]
  154. 154. 
    Reid DA, Conlin MP, Yin Y, Chang HH, Watanabe G et al. 2017. Bridging of double-stranded breaks by the nonhomologous end-joining ligation complex is modulated by DNA end chemistry. Nucleic Acids Res 45:41872–78
    [Google Scholar]
  155. 155. 
    Strande NT, Waters CA, Ramsden DA. 2012. Resolution of complex ends by nonhomologous end joining—better to be lucky than good?. Genome Integr 3:110
    [Google Scholar]
  156. 156. 
    Waters CA, Strande NT, Wyatt DW, Pryor JM, Ramsden DA. 2014. Nonhomologous end joining: a good solution for bad ends. DNA Repair 17:39–51
    [Google Scholar]
  157. 157. 
    Pfeiffer P, Thode S, Hancke J, Vielmetter W. 1994. Mechanisms of overlap formation in nonhomologous DNA end joining. Mol. Cell. Biol. 14:2888–95
    [Google Scholar]
  158. 158. 
    Roth DB, Wilson JH. 1986. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction. Mol. Cell. Biol. 6:124295–304
    [Google Scholar]
  159. 159. 
    Moon AF, Garcia-Diaz M, Batra VK, Beard WA, Bebenek K et al. 2007. The X family portrait: structural insights into biological functions of X family polymerases. DNA Repair 6:121709–25
    [Google Scholar]
  160. 160. 
    Symington LS, Gautier J. 2011. Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 45:247–71
    [Google Scholar]
  161. 161. 
    Yoo S, Dynan WS. 1999. Geometry of a complex formed by double strand break repair proteins at a single DNA end: recruitment of DNA-PKcs induces inward translocation of Ku protein. Nucleic Acids Res 27:244679–86
    [Google Scholar]
  162. 162. 
    Lee K-J, Saha J, Sun J, Fattah KR, Wang S-C et al. 2016. Phosphorylation of Ku dictates DNA double-strand break (DSB) repair pathway choice in S phase. Nucleic Acids Res 44:41732–45
    [Google Scholar]
  163. 163. 
    Brown JS, Lukashchuk N, Sczaniecka-Clift M, Britton S, le Sage C et al. 2015. Neddylation promotes ubiquitylation and release of Ku from DNA-damage sites. Cell Rep 11:5704–14
    [Google Scholar]
  164. 164. 
    Feng L, Chen J. 2012. The E3 ligase RNF8 regulates KU80 removal and NHEJ repair. Nat. Struct. Mol. Biol. 19:2201–6
    [Google Scholar]
  165. 165. 
    Ishida N, Nakagawa T, Iemura S-I, Yasui A, Shima H et al. 2017. Ubiquitylation of Ku80 by RNF126 promotes completion of nonhomologous end joining-mediated DNA repair. Mol. Cell. Biol. 37:4e00347–16
    [Google Scholar]
  166. 166. 
    Ismail IH, Gagné J-P, Genois M-M, Strickfaden H, McDonald D et al. 2015. The RNF138 E3 ligase displaces Ku to promote DNA end resection and regulate DNA repair pathway choice. Nat. Cell Biol. 17:111446–57
    [Google Scholar]
  167. 167. 
    Postow L, Funabiki H. 2013. An SCF complex containing Fbxl12 mediates DNA damage-induced Ku80 ubiquitylation. Cell Cycle 12:4587–95
    [Google Scholar]
  168. 168. 
    Postow L, Ghenoiu C, Woo EM, Krutchinsky AN, Chait BT, Funabiki H. 2008. Ku80 removal from DNA through double strand break-induced ubiquitylation. J. Cell Biol. 182:3467–79
    [Google Scholar]
  169. 169. 
    Meek K, Dang V, Lees-Miller SP. 2008. DNA-PK: the means to justify the ends?. Adv. Immunol. 99:33–58
    [Google Scholar]
  170. 170. 
    Weterings E, Verkaik NS, Brüggenwirth HT, Hoeijmakers JHJ, van Gent DC. 2003. The role of DNA dependent protein kinase in synapsis of DNA ends. Nucleic Acids Res 31:247238–46
    [Google Scholar]
  171. 171. 
    Reddy YVR, Ding Q, Lees-Miller SP, Meek K, Ramsden DA. 2004. Non-homologous end joining requires that the DNA-PK complex undergo an autophosphorylation-dependent rearrangement at DNA ends. J. Biol. Chem. 279:3839408–13
    [Google Scholar]
  172. 172. 
    Chan DW, Lees-Miller SP. 1996. The DNA-dependent protein kinase is inactivated by autophosphorylation of the catalytic subunit. J. Biol. Chem. 271:158936–41
    [Google Scholar]
  173. 173. 
    Douglas P, Cui X, Block WD, Yu Y, Gupta S et al. 2007. The DNA-dependent protein kinase catalytic subunit is phosphorylated in vivo on threonine 3950, a highly conserved amino acid in the protein kinase domain. Mol. Cell Biol. 27:51581–91
    [Google Scholar]
  174. 174. 
    Mahaney BL, Hammel M, Meek K, Tainer JA, Lees-Miller SP. 2013. XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem. Cell Biol. 91:131–41
    [Google Scholar]
  175. 175. 
    Roberts SA, Strande N, Burkhalter MD, Strom C, Havener JM et al. 2010. Ku is a 5′-dRP/AP lyase that excises nucleotide damage near broken ends. Nature 464:72921214–17
    [Google Scholar]
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