Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Perspective
  • Published:

DNA resection in eukaryotes: deciding how to fix the break

Nature Structural & Molecular Biology volume 17, pages 11–16 (2010)Cite this article

Subjects

Abstract

DNA double-strand breaks are repaired by different mechanisms, including homologous recombination and nonhomologous end-joining. DNA-end resection, the first step in recombination, is a key step that contributes to the choice of DSB repair. Resection, an evolutionarily conserved process that generates single-stranded DNA, is linked to checkpoint activation and is critical for survival. Failure to regulate and execute this process results in defective recombination and can contribute to human disease. Here I review recent findings on the mechanisms of resection in eukaryotes, from yeast to vertebrates, provide insights into the regulatory strategies that control it, and highlight the consequences of both its impairment and its deregulation.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The repair of DNA double-strand breaks (DSBs).
Figure 2: Mechanism of resection in budding yeast.
Figure 3: Regulation of resection in budding yeast.

Similar content being viewed by others

References

  1. Aguilera, A. & Gómez-González, B. Genome instability: a mechanistic view of its causes and consequences. Nat. Rev. Genet. 9, 204–217 (2008).

    Article  CAS  PubMed  Google Scholar 

  2. Lieber, M.R. The mechanism of human nonhomologous DNA end joining. J. Biol. Chem. 283, 1–5 (2008).

    Article  CAS  PubMed  Google Scholar 

  3. Krogh, B.O. & Symington, L.S. Recombination proteins in yeast. Annu. Rev. Genet. 38, 233–271 (2004).

    Article  CAS  PubMed  Google Scholar 

  4. McVey, M. & Lee, S.E. MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. Trends Genet. 24, 529–538 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Dynan, W.S. & Yoo, S. Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids. Nucleic Acids Res. 26, 1551–1559 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Huertas, P., Cortes-Ledesma, F., Sartori, A.A., Aguilera, A. & Jackson, S.P. CDK targets Sae2 to control DNA-end resection and homologous recombination. Nature 455, 689–692 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Lee, K., Zhang, Y. & Lee, S. Saccharomyces cerevisiae ATM orthologue suppresses break-induced chromosome translocations. Nature 454, 543–546 (2008).

    Article  CAS  PubMed  Google Scholar 

  8. Huertas, P. & Jackson, S.P. Human CtIP mediates cell cycle control of DNA end resection and double strand break repair. J. Biol. Chem. 284, 9558–9565 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Yun, M.H. & Hiom, K. CtIP-BRCA1 modulates the choice of DNA double-strand-break repair pathway throughout the cell cycle. Nature 459, 460–463 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Harrison, J.C. & Haber, J.E. Surviving the breakup: the DNA damage checkpoint. Annu. Rev. Genet. 40, 209–235 (2006).

    Article  CAS  PubMed  Google Scholar 

  11. Jazayeri, A. et al. ATM- and cell cycle-dependent regulation of ATR in response to DNA double-strand breaks. Nat. Cell Biol. 8, 37–45 (2006).

    Article  CAS  PubMed  Google Scholar 

  12. Amundsen, S.K. & Smith, G.R. Interchangeable parts of the Escherichia coli recombination machinery. Cell 112, 741–744 (2003).

    Article  CAS  PubMed  Google Scholar 

  13. Gravel, S., Chapman, J.R., Magill, C. & Jackson, S.P. DNA helicases Sgs1 and BLM promote DNA double-strand break resection. Genes Dev. 22, 2767–2772 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Khakhar, R.R., Cobb, J., Bjergbaek, L., Hickson, I. & Gasser, S.M. RecQ helicases: multiple roles in genome maintenance. Trends Cell Biol. 13, 493–501 (2003).

    Article  CAS  PubMed  Google Scholar 

  15. Limbo, O. et al. Ctp1 is a cell-cycle-regulated protein that functions with Mre11 complex to control double-strand break repair by homologous recombination. Mol. Cell 28, 134–146 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Mimitou, E.P. & Symington, L.S. Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 455, 770–774 (2008).

    Article  CAS  PubMed  Google Scholar 

  17. Penkner, A. et al. A conserved function for a Caenorhabditis elegans Com1/Sae2/CtIP protein homolog in meiotic recombination. EMBO J. 26, 5071–5082 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Sartori, A.A. et al. Human CtIP promotes DNA end resection. Nature 450, 509–514 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Tran, P.T., Erdeniz, N., Symington, L.S. & Liskay, R.M. EXO1-A multi-tasking eukaryotic nuclease. DNA Repair (Amst.) 3, 1549–1559 (2004).

    Article  CAS  Google Scholar 

  20. Uanschou, C. et al. A novel plant gene essential for meiosis is related to the human CtIP and the yeast COM1/SAE2 gene. EMBO J. 26, 5061–5070 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zhu, Z., Chung, W.H., Shim, E., Lee, S. & Ira, G. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134, 981–994 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Williams, R.S., Williams, J.S. & Tainer, J.A. Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template. Biochem. Cell Biol. 85, 509–520 (2007).

    Article  CAS  PubMed  Google Scholar 

  23. Paull, T.T. & Gellert, M. The 3′ to 5′ exonuclease activity of Mre 11 facilitates repair of DNA double-strand breaks. Mol. Cell 1, 969–979 (1998).

    Article  CAS  PubMed  Google Scholar 

  24. Bressan, D.A., Olivares, H.A., Nelms, B.E. & Petrini, J.H. Alteration of N-terminal phosphoesterase signature motifs inactivates Saccharomyces cerevisiae Mre11. Genetics 150, 591–600 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Lavin, M.F. ATM and the Mre11 complex combine to recognize and signal DNA double-strand breaks. Oncogene 26, 7749–7758 (2007).

    Article  CAS  PubMed  Google Scholar 

  26. Buis, J. et al. Mre11 nuclease activity has essential roles in DNA repair and genomic stability distinct from ATM activation. Cell 135, 85–96 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Trujillo, K.M., Yuan, S.S., Lee, E.Y. & Sung, P. Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95. J. Biol. Chem. 273, 21447–21450 (1998).

    Article  CAS  PubMed  Google Scholar 

  28. Falck, J., Coates, J.A. & Jackson, S.P. Conserved modes of recruitment of ATM, ATR and DNA-PKcs to sites of DNA damage. Nature 434, 605–611 (2005).

    Article  CAS  PubMed  Google Scholar 

  29. Nakada, D., Matsumoto, K. & Sugimoto, K. ATM-related Tel1 associates with double-strand breaks through an Xrs2-dependent mechanism. Genes Dev. 17, 1957–1962 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Usui, T., Petrini, J.H. & Morales, M. rad50S alleles of the Mre11 complex: questions answered and questions raised. Exp. Cell Res. 312, 2694–2699 (2006).

    Article  CAS  PubMed  Google Scholar 

  31. McKee, A.H. & Kleckner, N. A general method for identifying recessive diploid-specific mutations in Saccharomyces cerevisiae, its application to the isolation of mutants blocked at intermediate stages of meiotic prophase and characterization of a new gene SAE2. Genetics 146, 797–816 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Neale, M.J., Pan, J. & Keeney, S. Endonucleolytic processing of covalent protein–linked DNA double-strand breaks. Nature 436, 1053–1057 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Prinz, S., Amon, A. & Klein, F. Isolation of COM1, a new gene required to complete meiotic double-strand break-induced recombination in Saccharomyces cerevisiae. Genetics 146, 781–795 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Clerici, M., Mantiero, D., Lucchini, G. & Longhese, M.P. The Saccharomyces cerevisiae Sae2 protein promotes resection and bridging of double strand break ends. J. Biol. Chem. 280, 38631–38638 (2005).

    Article  CAS  PubMed  Google Scholar 

  35. Lengsfeld, B.M., Rattray, A.J., Bhaskara, V., Ghirlando, R. & Paull, T.T. Sae2 is an endonuclease that processes hairpin DNA cooperatively with the Mre11/Rad50/Xrs2 complex. Mol. Cell 28, 638–651 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Jazayeri, A., Balestrini, A., Garner, E., Haber, J.E. & Costanzo, V. Mre11-Rad50-Nbs1-dependent processing of DNA breaks generates oligonucleotides that stimulate ATM activity. EMBO J. 27, 1953–1962 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Maringele, L. & Lydall, D. Telomerase- and recombination-independent immortalization of budding yeast. Genes Dev. 18, 2663–2675 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Mantiero, D., Clerici, M., Lucchini, G. & Longhese, M.P. Dual role for Saccharomyces cerevisiae Tel1 in the checkpoint response to double-strand breaks. EMBO Rep. 8, 380–387 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Moreau, S., Morgan, E.A. & Symington, L.S. Overlapping functions of the Saccharomyces cerevisiae Mre11, Exo1 and Rad27 nucleases in DNA metabolism. Genetics 159, 1423–1433 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Bae, S.H. et al. Dna2 of Saccharomyces cerevisiae possesses a single-stranded DNA-specific endonuclease activity that is able to act on double-stranded DNA in the presence of ATP. J. Biol. Chem. 273, 26880–26890 (1998).

    Article  CAS  PubMed  Google Scholar 

  41. Horejsí, Z. et al. Distinct functional domains of Nbs1 modulate the timing and magnitude of ATM activation after low doses of ionizing radiation. Oncogene 23, 3122–3127 (2004).

    Article  PubMed  Google Scholar 

  42. Chen, L., Nievera, C.J., Lee, A.Y. & Wu, X. Cell cycle-dependent complex formation of BRCA1.CtIP.MRN is important for DNA double-strand break repair. J. Biol. Chem. 283, 7713–7720 (2008).

    Article  CAS  PubMed  Google Scholar 

  43. Yu, X., Fu, S., Lai, M., Baer, R. & Chen, J. BRCA1 ubiquitinates its phosphorylation-dependent binding partner CtIP. Genes Dev. 20, 1721–1726 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Nimonkar, A.V., Ozsoy, A.Z., Genschel, J., Modrich, P. & Kowalczykowski, S.C. Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair. Proc. Natl. Acad. Sci. USA 105, 16906–16911 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Kim, J.H. et al. Isolation of human Dna2 endonuclease and characterization of its enzymatic properties. Nucleic Acids Res. 34, 1854–1864 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Duxin, J.P. et al. Human Dna2 is a nuclear and mitochondrial DNA maintenance protein. Mol. Cell. Biol. 29, 4274–4282 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Liao, S., Toczylowski, T. & Yan, H. Identification of the Xenopus DNA2 protein as a major nuclease for the 5′→3′ strand-specific processing of DNA ends. Nucleic Acids Res. 36, 6091–6100 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Hopkins, B.B. & Paull, T.T. The P. furiosus mre11/rad50 complex promotes 5′ strand resection at a DNA double-strand break. Cell 135, 250–260 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Zheng, L. et al. MRE11 complex links RECQ5 helicase to sites of DNA damage. Nucleic Acids Res. 37, 2645–2657 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Aylon, Y., Liefshitz, B. & Kupiec, M. The CDK regulates repair of double-strand breaks by homologous recombination during the cell cycle. EMBO J. 23, 4868–4875 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Ira, G. et al. DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431, 1011–1017 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Zierhut, C. & Diffley, J.F. Break dosage, cell cycle stage and DNA replication influence DNA double strand break response. EMBO J. 27, 1875–1885 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Gu, B. & Chen, P.L. Expression of PCNA-binding domain of CtIP, a motif required for CtIP localization at DNA replication foci, causes DNA damage and activation of DNA damage checkpoint. Cell Cycle 8, 1409–1420 (2009).

    Article  CAS  PubMed  Google Scholar 

  54. Lazzaro, F. et al. Histone methyltransferase Dot1 and Rad9 inhibit single-stranded DNA accumulation at DSBs and uncapped telomeres. EMBO J. 27, 1502–1512 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Grenon, M. et al. Docking onto chromatin via the Saccharomyces cerevisiae Rad9 Tudor domain. Yeast 24, 105–119 (2007).

    Article  CAS  PubMed  Google Scholar 

  56. Linding, R. et al. Systematic discovery of in vivo phosphorylation networks. Cell 129, 1415–1426 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Akamatsu, Y. et al. Molecular characterization of the role of the Schizosaccharomyces pombe nip1+/ctp1+ gene in DNA double-strand break repair in association with the Mre11-Rad50-Nbs1 complex. Mol. Cell. Biol. 28, 3639–3651 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Yu, X. & Chen, J. DNA damage-induced cell cycle checkpoint control requires CtIP, a phosphorylation-dependent binding partner of BRCA1 C-terminal domains. Mol. Cell. Biol. 24, 9478–9486 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Lisby, M., Barlow, J.H., Burgess, R.C. & Rothstein, R. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118, 699–713 (2004).

    Article  CAS  PubMed  Google Scholar 

  60. Clerici, M., Mantiero, D., Guerini, I., Lucchini, G. & Longhese, M.P. The Yku70-Yku80 complex contributes to regulate double-strand break processing and checkpoint activation during the cell cycle. EMBO Rep. 9, 810–818 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Barlow, J.H., Lisby, M. & Rothstein, R. Differential regulation of the cellular response to DNA double-strand breaks in G1. Mol. Cell 30, 73–85 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Baroni, E., Viscardi, V., Cartagena-Lirola, H., Lucchini, G. & Longhese, M.P. The functions of budding yeast Sae2 in the DNA damage response require Mec1- and Tel1-dependent phosphorylation. Mol. Cell. Biol. 24, 4151–4165 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Warmerdam, D.O., Freire, R., Kanaar, R. & Smits, V.A. Cell cycle-dependent processing of DNA lesions controls localization of Rad9 to sites of genotoxic stress. Cell Cycle 8, 1765–1774 (2009).

    Article  CAS  PubMed  Google Scholar 

  64. Shimada, K., Pasero, P. & Gasser, S.M. ORC and the intra-S-phase checkpoint: a threshold regulates Rad53p activation in S phase. Genes Dev. 16, 3236–3252 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Morin, I. et al. Checkpoint-dependent phosphorylation of Exo1 modulates the DNA damage response. EMBO J. 27, 2400–2410 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Zhang, Y. et al. Role of Dnl4-Lif1 in nonhomologous end-joining repair complex assembly and suppression of homologous recombination. Nat. Struct. Mol. Biol. 14, 639–646 (2007).

    Article  CAS  PubMed  Google Scholar 

  67. Chen, L. et al. Effect of amino acid substitutions in the Rad50 ATP binding domain on DNA double strand break repair in yeast. J. Biol. Chem. 280, 2620–2627 (2005).

    Article  CAS  PubMed  Google Scholar 

  68. Stracker, T.H., Theunissen, J.W., Morales, M. & Petrini, J.H. The Mre11 complex and the metabolism of chromosome breaks: the importance of communicating and holding things together. DNA Repair (Amst.) 3, 845–854 (2004).

    Article  CAS  Google Scholar 

  69. Chen, P.L. et al. Inactivation of CtIP leads to early embryonic lethality mediated by G1 restraint and to tumorigenesis by haploid insufficiency. Mol. Cell. Biol. 25, 3535–3542 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Waltes, R. et al. Human RAD50 deficiency in an Nijmegen Breakage Syndrome-like disorder. Am. J. Hum. Genet. 84, 605–616 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Chinnadurai, G. CtIP, a candidate tumor susceptibility gene is a team player with luminaries. Biochim. Biophys. Acta 1765, 67–73 (2006).

    CAS  PubMed  Google Scholar 

  72. Wu, G. & Lee, W.H. CtIP, a multivalent adaptor connecting transcriptional regulation, checkpoint control and tumor suppression. Cell Cycle 5, 1592–1596 (2006).

    Article  CAS  PubMed  Google Scholar 

  73. Cheok, C.F. et al. Roles of the Bloom's syndrome helicase in the maintenance of genome stability. Biochem. Soc. Trans. 33, 1456–1459 (2005).

    Article  CAS  PubMed  Google Scholar 

  74. Lord, C.J. & Ashworth, A. Targeted therapy for cancer using PARP inhibitors. Curr. Opin. Pharmacol. 8, 363–969 (2008).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

I would like to apologize to all authors whose work could not be cited due to space limitations. I am grateful to all the members of S. Jackson's laboratory in Cambridge, UK, for helpful discussions and especially to S. Jackson, A. Kaidi, J. Harrigan, K. Miller and R. Belotserkovskaya for their helpful suggestions and comments on the manuscript. I would also like to thank BBSRC and Cancer Research UK for funding my work.

Author information

Authors and Affiliations

  1. The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK

    Pablo Huertas

Authors
  1. Pablo Huertas
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pablo Huertas.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Huertas, P. DNA resection in eukaryotes: deciding how to fix the break. Nat Struct Mol Biol 17, 11–16 (2010). https://doi.org/10.1038/nsmb.1710

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1710

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing