Rejoining of DNA Double-Strand Breaks as a Function of Overhang Length

REFERENCES

• Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. E. Seidman, J. A. Smith, and K. Struhl (ed.). 1997. Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
   Google Scholar
• Boulton, S. J., and S. P. Jackson. 1996. Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res. 24:4639–4648.
   PubMed Web of Science ®Google Scholar
• Boulton, S. J., and S. P. Jackson. 1996. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 15:5093–5103.
   PubMed Web of Science ®Google Scholar
• Brachmann, C. B., A. Davies, G. J. Cost, E. Caputo, J. Li, P. Hieter, and J. D. Boeke. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14:115–132.
   PubMed Web of Science ®Google Scholar
• Chappell, C., L. A. Hanakahi, F. Karimi-Busheri, M. Weinfeld, and S. C. West. 2002. Involvement of human polynucleotide kinase in double-strand break repair by non-homologous end joining. EMBO J. 21:2827–2832.
   PubMedGoogle Scholar
• Chen, L., K. Trujillo, W. Ramos, P. Sung, and A. E. Tomkinson. 2001. Promotion of Dnl4-catalyzed DNA end-joining by the Rad50/Mre11/Xrs2 and Hdf1/Hdf2 complexes. Mol. Cell 8:1105–1115.
   PubMedGoogle Scholar
• Chen, S., K. V. Inamdar, P. Pfeiffer, E. Feldmann, M. F. Hannah, Y. Yu, J. W. Lee, T. Zhou, S. P. Lees-Miller, and L. F. Povirk. 2001. Accurate in vitro end joining of a DNA double strand break with partially cohesive 3′-overhangs and 3′-phosphoglycolate termini: effect of Ku on repair fidelity. J. Biol. Chem. 276:24323–24330.
   PubMed Web of Science ®Google Scholar
• Connelly, J. C., and D. R. Leach. 2002. Tethering on the brink: the evolutionarily conserved Mre11-Rad50 complex. Trends Biochem. Sci. 27:410–418.
   PubMed Web of Science ®Google Scholar
• Coquerelle, T., A. Bopp, B. Kessler, and U. Hagen. 1973. Strand breaks and K′ end-groups in DNA of irradiated thymocytes. Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 24:397–404.
   PubMed Web of Science ®Google Scholar
• DeFazio, L. G., R. M. Stansel, J. D. Griffith, and G. Chu. 2002. Synapsis of DNA ends by DNA-dependent protein kinase. EMBO J. 21:3192–3200.
   PubMedGoogle Scholar
• Fishman-Lobell, J., and J. E. Haber. 1992. Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1. Science 258:480–484.
   PubMedGoogle Scholar
• Guirouilh-Barbat, J., S. Huck, P. Bertrand, L. Pirzio, C. Desmaze, L. Sabatier, and B. S. Lopez. 2004. Impact of the KU80 pathway on NHEJ-induced genome rearrangements in mammalian cells. Mol. Cell 14:611–623.
   PubMed Web of Science ®Google Scholar
• Ivanov, E. L., N. Sugawara, J. Fishman-Lobell, and J. E. Haber. 1996. Genetic requirements for the single-strand annealing pathway of double-strand break repair in Saccharomyces cerevisiae. Genetics 142:693–704.
   PubMed Web of Science ®Google Scholar
• Jackson, S. P. 2002. Sensing and repairing DNA double-strand breaks. Carcinogenesis 23:687–696.
   PubMed Web of Science ®Google Scholar
• Karathanasis, E., and T. E. Wilson. 2002. Enhancement of Saccharomyces cerevisiae end-joining efficiency by cell growth stage but not by impairment of recombination. Genetics 161:1015–1027.
   PubMedGoogle Scholar
• Karumbati, A. S., R. A. Deshpande, A. Jilani, J. R. Vance, D. Ramotar, and T. E. Wilson. 2003. The role of yeast DNA 3′-phosphatase Tpp1 and rad1/Rad10 endonuclease in processing spontaneous and induced base lesions. J. Biol. Chem. 278:31434–31443.
   PubMedGoogle Scholar
• Koch, C. A., R. Agyei, S. Galicia, P. Metalnikov, P. O'Donnell, A. Starostine, M. Weinfeld, and D. Durocher. 2004. Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV. EMBO J. 23:3874–3885.
   PubMed Web of Science ®Google Scholar
• Kramer, K. M., J. A. Brock, K. Bloom, J. K. Moore, and J. E. Haber. 1994. Two different types of double-strand breaks in Saccharomyces cerevisiae are repaired by similar RAD52-independent, nonhomologous recombination events. Mol. Cell. Biol. 14:1293–1301.
   PubMedGoogle Scholar
• Lee, J. W., L. Blanco, T. Zhou, M. Garcia-Diaz, K. Bebenek, T. A. Kunkel, Z. Wang, and L. F. Povirk. 2004. Implication of DNA polymerase lambda in alignment-based gap filling for nonhomologous DNA end joining in human nuclear extracts. J. Biol. Chem. 279:805–811.
   PubMed Web of Science ®Google Scholar
• Ma, J.-L., E. M. Kim, J. E. Haber, and S. E. Lee. 2003. Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double-strand breaks lacking overlapping end sequences. Mol. Cell. Biol. 23:8820–8828.
   PubMed Web of Science ®Google Scholar
• Ma, Y., U. Pannicke, K. Schwarz, and M. R. Lieber. 2002. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108:781–794.
   PubMed Web of Science ®Google Scholar
• Mahajan, K. N., S. A. N. McElhinny, B. S. Mitchell, and D. A. Ramsden. 2002. Association of DNA polymerase μ (pol μ) with Ku and ligase IV: role for pol μ in end-joining double-strand break repair. Mol. Cell. Biol. 22:5194–5202.
   PubMed Web of Science ®Google Scholar
• Moore, J. K., and J. E. Haber. 1996. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:2164–2173.
   PubMed Web of Science ®Google Scholar
• Mortensen, U. H., C. Bendixen, I. Sunjevaric, and R. Rothstein. 1996. DNA strand annealing is promoted by the yeast Rad52 protein. Proc. Natl. Acad. Sci. USA 93:10729–10734.
   PubMed Web of Science ®Google Scholar
• Prado, F., F. Cortes-Ledesma, P. Huertas, and A. Aguilera. 2003. Mitotic recombination in Saccharomyces cerevisiae. Curr. Genet. 42:185–198.
   PubMedGoogle Scholar
• Rudin, N., and J. E. Haber. 1988. Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences. Mol. Cell. Biol. 8:3918–3928.
   PubMedGoogle Scholar
• Sandoval, A., and P. Labhart. 2004. High G/C content of cohesive overhangs renders DNA end joining Ku-independent. DNA Repair 3:13–21.
   PubMedGoogle Scholar
• Schar, P., G. Herrmann, G. Daly, and T. Lindahl. 1997. A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double-strand breaks. Genes Dev. 11:1912–1924.
   PubMedGoogle Scholar
• Sharpless, N. E., D. O. Ferguson, R. C. O'Hagan, D. H. Castrillon, C. Lee, P. A. Farazi, S. Alson, J. Fleming, C. C. Morton, K. Frank, L. Chin, F. W. Alt, and R. A. DePinho. 2001. Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifications, and deletions. Mol. Cell 8:1187–1196.
   PubMedGoogle Scholar
• Sugawara, N., and J. E. Haber. 1992. Characterization of double-strand break-induced recombination: homology requirements and single-stranded DNA formation. Mol. Cell. Biol. 12:563–575.
   PubMed Web of Science ®Google Scholar
• Sugawara, N., G. Ira, and J. E. Haber. 2000. DNA length dependence of the single-strand annealing pathway and the role of Saccharomyces cerevisiae RAD59 in double-strand break repair. Mol. Cell. Biol. 20:5300–5309.
   PubMed Web of Science ®Google Scholar
• Tomer, G., and Z. Livneh. 1999. Analysis of unassisted translesion replication by the DNA polymerase III holoenzyme. Biochemistry 38:5948–5958.
   PubMedGoogle Scholar
• Vance, J. R., and T. E. Wilson. 2001. Repair of DNA strand breaks by the overlapping functions of lesion-specific and non-lesion-specific DNA 3′ phosphatases. Mol. Cell. Biol. 21:7191–7198.
   PubMedGoogle Scholar
• Vance, J. R., and T. E. Wilson. 2001. Uncoupling of 3′-phosphatase and 5′-kinase functions in budding yeast. Characterization of Saccharomyces cerevisiae DNA 3′-phosphatase (TPP1). J. Biol. Chem. 276:15073–15081.
   PubMed Web of Science ®Google Scholar
• Wang, H., A. R. Perrault, Y. Takeda, W. Qin, and G. Iliakis. 2003. Biochemical evidence for Ku-independent backup pathways of NHEJ. Nucleic Acids Res. 31:5377–5388.
   PubMedGoogle Scholar
• Wilson, T. E., U. Grawunder, and M. R. Lieber. 1997. Yeast DNA ligase IV mediates non-homologous DNA end joining. Nature 388:495–498.
   PubMed Web of Science ®Google Scholar
• Wilson, T. E., and M. R. Lieber. 1999. Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase beta (Pol4)-dependent pathway. J. Biol. Chem. 274:23599–23609.
   PubMedGoogle Scholar
• Wu, X., T. E. Wilson, and M. R. Lieber. 1999. A role for FEN-1 in nonhomologous DNA end joining: the order of strand annealing and nucleolytic processing events. Proc. Natl. Acad. Sci. USA 96:1303–1308.
   PubMedGoogle Scholar
• Yu, X., and A. Gabriel. 2003. Ku-dependent and Ku-independent end-joining pathways lead to chromosomal rearrangements during double-strand break repair in Saccharomyces cerevisiae. Genetics 163:843–856.
   PubMed Web of Science ®Google Scholar