Source: http://www.asmscience.org/content/book/10.1128/9781555816704.ch18
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Detection of DSB-specific protein binding by using the chromatin immunoprecipitation assay. Following targeted DSB introduction, e.g., by using HO endonuclease expression (shown on the right), a suspected DSB-binding protein is immunoprecipitated using a specific antibody (Ab). DNA-protein cross-linking ensures the coimmunoprecipitation of the protein with bound chromosomal DNA from the vicinity of the HO site. Following cross-link reversal, a selected portion of this DNA can be amplified using PCR with appropriate primers. Gel electrophoresis may reveal a DNA product of the expected size. In the control without DSB, no specific DNA sequence is coimmunoprecipitated (left side), and the same PCR does not yield a significant amount of the DNA product. An experimental example is shown in Fig. 19–8 (see Chapter 19).
Rad51 assembles into ring-shaped heptamers. (A) The crystal structure of full-length Pyrococcus furiosus Rad51 ( 388 ) reveals a C-terminal ATPase domain consisting of a Rossman nucleotide-binding fold, the elbow linker, and the N-terminal helix-hairpin-helix (HhH). The ATPase domain is structurally similar to the bacterial RecA protein and contains the signature Walker A and B motifs found in many nucleotide hydrolases. The elbow linker and HhH participate in subunit interactions. (B) In the absence of DNA, Rad51 can assemble into heptameric rings in which the N-terminal HhH domain packs against the ATPase active site of a neighboring subunit. This interaction may regulate ATP hydrolysis in response to assembly of the circular rings or extended filaments when bound to DNA.
Rad52 self-associates into a ring-shaped ssDNA-binding protein. (A) A three-dimensional reconstruction of electron micrographs of human RAD52 reveals a ring-shaped heptamer ( 415 ). (B) In other studies, the crystal structure of an N-terminal fragment of human RAD52 (residues 1 to 209 ) that has single-strand annealing activity shows assembly of an undecameric ring with a deep groove containing positively charged residues (grey). This groove is the proposed ssDNA-binding surface of RAD52. The other half of RAD52 (not present in the crystal structure) presumably mediates interactions with RAD51.
Phenotypes and activities conferred by Rad51 paralogs. In this scheme, the contacts made among the depicted proteins and the symbolized Rad51 helical filament reflect known protein interactions. The protein groups labeled A to D refer to protein complexes that have been isolated by various investigators.
The BRC peptide motif caps the subunit interface of RAD51. The BRC repeat peptide (grey) from BRCA2 binds tightly to RAD51 (gold), blocking the subunit interface of RAD51 that mediates self-assembly into a filament. The crystal structure of the BRC-RAD51 complex reveals the details of the interaction ( 323 ).
SSB domains of BRCA2. A crystal structure of a C-terminal region from the BRCA2 protein ( 493 ) resulted in the discovery of OB-fold domains that are associated with ssDNA-binding functions (see chapter 8), suggesting a direct role of BRCA2 in recombination.
SDSA and BIR as examples of DSB-induced, one-ended reactions. In both cases, the invading 3’ end is extended by DNA synthesis. For SDSA, DNA synthesis is limited and the extended strand is eventually displaced and anneals with the complementary single strand from the other DSB end. For BIR, a likely model involves the establishment of a replication fork and DNA synthesis using the displaced strand as a lagging-strand template, possibly to the end of the chromosome. In the end, one Holliday junction needs to be resolved. This is a likely mechanism to repair a broken telomere, resulting in a large region where heterozygosity is lost.
Model for repair of DNA ICL in E. coli. (A) Cross-linked DNA is shown. (B) The UvrABC endonuclease generates two incisions flanking the psoralen adduct on the furan-adducted DNA strand (incision 1 ). (C) A gap is generated 3’ to the cross-link, for example by the 5’-3’ exonuclease of Pol I or by another UvrABC cleavage. (D) The gap is a substrate for RecA-mediated recombination utilizing an invading homologous DNA strand. (E) The other arm of the cross-link can then be incised by the UvrABC endonuclease (incision 2 ), leading to the excision of a complex 11-or 12-mer oligonucleotide structure. (F) DNA repair is completed by repair synthesis and ligation.
1. Abdu, U.,, A. González-Reyes,, A. Ghabrial, and, T. Schüpbach. 2003. The Drosophila spn-D gene encodes a RAD51C-like protein that is required exclusively during meiosis. Genetics 165: 197– 204.
2. Aboussekhra, A.,, R. Chanet,, A. Adjiri, and, F. Fabre. 1992. Semi-dominant suppressors of Srs2 helicase mutation of Saccharomyces cerevisiae map in the RAD51 gene, whose sequence predicts a protein with similarities to procaryotic RecA proteins. Mol. Cell. Biol. 12 :3224– 3234.
3. Aboussekhra, A.,, R. Chanet,, Z. Zgaga,, C. Cassier-Chauvat,, M. Heude, and, F. Fabre. 1989. RADH, a gene of Saccharomyces cerevisiae encoding a putative DNA helicase involved in DNA repair. Characteristics of radH mutants and sequence of the gene. Nucleic Acids Res. 17: 7211– 7220.
4. Abraham, J.,, B. Lemmers,, M. P. Hande,, M. E. Moynahan,, C. Chahwan,, A. Ciccia,, J. Essers,, K. Hanada,, R. Chahwan,, A. K. Khaw,, P. McPherson,, A. Shehabeldin,, R. Laister,, C. Arrowsmith,, R. Kanaar,, S. C. West,, M. Jasin, and, R. Hakem. 2003. Eme1 is involved in DNA damage processing and maintenance of genomic stability in mammalian cells. EMBO J. 22 :6137– 6147.
5. Abrahams, P. J.,, B. A. Huitema, and, A. J. van der Eb. 1984. Enhanced reactivation and enhanced mutagenesis of herpes simplex virus in normal human and xeroderma pigmentosum cells. Mol. Cell. Biol. 4 :2341– 2346.
6. Adair, G. M.,, R. L. Rolig,, D. Moore-Faver,, M. Zabelshansky,, J. H. Wilson, and, R. S. Nairn. 2000. Role of ERCC1 in removal of long non-homologous tails during targeted homologous recombination. EMBO J. 19 :5552– 5561.
7. Aguilera, A., 2001. The connection between transcription and genomic instability. EMBO J. 21 :195– 201.
8. Aguilera, A., and, H. L. Klein. 1988. Genetic control of intrachromosomal recombination in Saccharomyces cerevisiae. I. Isolation and genetic characterization of hyper-recombination mutations. Genetics 119 :779– 790.
9. Ahmad, S. I.,, F. Hanakoa, and, S. H. Kirk. 2002. Molecular biology of Fanconi anaemia—an old problem, a new insight. Bioessays 24 :4439– 4448.
10. Ahmad, S. I., and, I. B. Holland. 1985. Isolation and analysis of a mutant of E. coli hyper-resistant to near-ultraviolet light plus 8-methoxy-psoralen. Mutat. Res. 151 :43– 48.
11. Aihara, H.,, Y. Ito,, H. Kurumizaka,, S. Yokoyama, and, T. Shibata. 1999. The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR. J. Mol. Biol. 290 :495– 504.
12. Albala, J. S.,, M. P. Thelen,, C. Prange,, W. Fan,, M. Christensen,, L. H. Thompson, and, G. G. Lennon. 1997. Identification of a novel human RAD51 homolog, RAD51B. Genomics 46 :476– 479.
13. Alexeev, A.,, A. Mazin, and, S. C. Kowalczykowski. 2003. Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat. Struct. Biol. 10 :182– 186.
14. Alexiadis, V., and, J. T. Kadonaga. 2002. Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 16 :2767– 2771.
15. Allers, T., and, M. Lichten. 2001. Differential timing and control of noncrossover and crossover recombination during meiosis. Cell 106: 47– 57.
16. Anderson, S. F.,, B. P. Schlegel,, T. Nakajima,, E. S. Wolpin, and, J. D. Parvin. 1998. BRCA1 protein is linked to the RNA polymerase II holoenzyme complex via RNA helicase A. Nat. Genet. 19 :254– 256.
17. Aono, N.,, T. Sutani,, T. Tomonaga,, S. Mochida, and, M. Yanagida. 2002. Cnd2 has dual roles in mitotic condensation and interphase. Nature 417 :197– 202.
18. Arbel, A.,, D. Zenvirth, and, G. Simchen. 1999. Sister chromatid-based DNA repair is mediated by RAD54, not by DMC1 or TID1. EMBO J. 18: 2648– 2658.
19. Bai, Y., and, L. S. Symington. 1996. A Rad52 homolog is required for RAD51 -independent mitotic recombination in Saccharomyces cerevisiae. Genes Dev. 10 :2025– 2037.
20. Bailis, A. M.,, L. Arthur, and, R. Rothstein. 1992. Genome rearrangement in top3 mutants in Saccharomyces cerevisiae requires a functional RAD1 excision repair gene. Mol. Cell. Biol. 12 :4988– 4993.
21. Bailis, A. M., and, R. Rothstein. 1990. A defect in mismatch repair in Saccharomyces cerevisiae stimulates ectopic recombination between homeologous genes by an excision repair dependent process. Genetics 126: 535– 547.
22. Barber, L. J.,, T. A. Ward,, J. A. Hartley, and, P. J. McHugh. 2005. DNA interstrand cross-link repair in the Saccharomyces cerevisiae cell cycle: overlapping roles for PSO2 (SNM1) with MutS factors and EXO1 during S phase. Mol. Cell. Biol. 25: 2297– 2309.
23. Bardwell, L.,, A. J. Cooper, and, E. C. Friedberg. 1992. Stable and specific association between the yeast recombination and DNA repair proteins RAD1 and RAD10 in vitro. Mol. Cell. Biol. 12 :3041– 3049.
24. Barker, D. G.,, A. L. Johnson, and, L. H. Johnston. 1985. An improved assay for DNA ligase reveals temperature-sensitive activity in cdc9 mutants of Saccharomyces cerevisiae. Mol. Gen. Genet. 200: 458– 462.
25. Bärtsch, S.,, L. E. Kang, and, L. S. Symington. 2000. RAD51 is required for the repair of plasmid double-stranded DNA gaps from either plasmid or chromosomal templates. Mol. Cell. Biol. 20: 1194– 1205.
26. Basile, G.,, M. Aker, and, R. K. Mortimer. 1992. Nucleotide sequence and transcriptional regulation of the yeast recombinational repair gene RAD51. Mol. Cell. Biol. 12: 3235– 3246.
27. Baumann, P.,, F. E. Benson, and, S. C. West. 1996. Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro. Cell 87 :757– 766.
28. Baumann, P., and, S. C. West. 1997. The human Rad51 protein: polarity of strand transfer and stimulation by hRP-A. EMBO J. 16 :5198– 5206.
29. Becker, P. B., and, W. Hörz. 2002. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71 :247– 273.
30. Benathen, I. A., and, C. A. Beam. 1977. The genetic control of X-ray resistance in budding yeast cells. Radiat. Res. 69 :99– 116.
31. Benson, F. E.,, P. Baumann, and, S. C. West. 1998. Synergistic actions of Rad51 and Rad52 in recombination and DNA repair. Nature 39 :401– 404.
32. Benson, F. E.,, A. Stasiak, and, S. C. West. 1994. Purification and characterization of human Rad51 protein, an analogue of E. coli RecA. EMBO J. 13: 5764– 5771.
33. Bessho, T.,, D. Mu, and, A. Sancar. 1997. Initiation of DNA inter-strand cross-link repair in humans: the nucleotide excision repair system makes dual incisions 5’ to the cross-linked base and removes a 22- to 28-nucleotide-long damage-free strand. Mol. Cell. Biol. 17 :6822– 6830.
34. Bezzubova, O.,, A. Shinohara,, R. G. Mueller,, H. Ogawa, and, J. M. Buerstedde. 1993. A chicken RAD51 homologue is expressed at high levels in lymphoid and reproductive organs. Nucleic Acids Res. 21 :1577– 1580.
35. Bezzubova, O.,, A. Silbergleit,, Y. Yamaguchi-Iwai,, S. Takeda, and, J.-M. Buerstedde. 1997. Reduced X-ray resistance and homologous recombination frequencies in a RAD54“’” mutant of the chicken DT40 cell line. Cell 89: 185– 193.
36. Bezzubova, O. Y.,, H. Schmidt,, K. Ostermann,, W.-D. Heyer, and, J.-M. Buerstedde. 1993. Identification of a chicken RAD52 homologue suggests conservation of the RAD52 recombination pathway throughout the evolution of higher eukaryotes. Nucleic Acids Res. 21: 5945– 5949.
37. Bianco, P. R.,, R. B. Tracy, and, S. C. Kowalczykowski. 1998. DNA strand exchange proteins: a biochemical and physical comparison. Front. Biosci. 3 :D570– D603.
38. Birkenbihl, R. P., and, S. Subramani. 1992. Cloning and characterization of rad21, an essential gene of Schizosaccharomyces pombe involved in DNA double-strand-break repair. Nucleic Acids Res. 20: 6605– 6611.
39. Bishop, D.,, D. Park,, L. Xu, and, N. Kleckner. 1992. DCM1: a meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression. Cell 69: 439– 456.
40. Bishop, D. K., 1994. RecA homologs Dmc1 and Rad51 interact to form multiple nuclear complexes prior to meiotic chromosome synapsis. Cell 79 :1081– 1092.
41. Boddy, M. N.,, P.-H. L. Gaillard,, W. H. McDonald,, P. Shanahan,, J. R. Yates III, and, P. Russell. 2001. Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell 107 :537– 548.
42. Boddy, M. N.,, A. Lopez-Girona,, P. Shanahan,, H. Interthal,, W.-D. Heyer, and, P. Russell. 2000. Damage tolerance protein Mus81 associates with the FHA1 domain of checkpoint kinase Cds1. Mol. Cell. Biol. 20 :8758– 8766.
43. Boddy, M. N.,, P. Shanahan,, W. H. McDonald,, A. Lopez-Girona,, E. Noguchi,, I. J. Yates, and, P. Russell. 2003. Replication checkpoint kinase Cds1 regulates recombinational repair protein Rad60. Mol. Cell. Biol. 23: 5939– 5946.
44. Bork, P.,, N. Blomberg, and, M. Nilges. 1996. Internal repeats in the BRCA2 protein sequence. Nat. Genet. 13 :22– 23.
45. Bork, P.,, K. Hofmann,, P. Bucher,, A. F. Neuwald,, S. F. Altschul, and, E. V. Koonin. 1997. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J. 11 :68– 76.
46. Bosco, G., and, J. E. Haber. 1998. Chromosome break-induced DNA replication leads to nonreciprocal translocations and telomere capture. Genetics 150 :1037– 1047.
47. Braybrooke, J. P.,, K. G. Spink,, J. Thacker, and, I. D. Hickson. 2000. The RAD51 family member, RAD51L3, is a DNA-stimulated ATPase that forms a complex with XRCC2. J. Biol. Chem. 275 :29100– 29106.
48. Brendel, M., and, J. A. Henriques. 2001. The pso mutants of Saccharomyces cerevisiae comprise two groups: one deficient in DNA repair and another with altered mutagen metabolism. Mutat. Res. 489: 79– 96.
49. Brendel, M., and, A. Ruhland. 1984. Relationships between functionality and genetic toxicology of selected DNA damaging agents. Mutat. Res. 133 :51– 85.
50. Brendel, V.,, L. Brocchieri,, S. J. Sandler,, A. J. Clark, and, S. Karlin. 1997. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 44 :528– 541.
51. Brenneman, M. A.,, B. M. Wagener,, C. A. Miller,, C. Allen, and, J. A. Nickoloff. 2002. XRCC3 controls the fidelity of homologous recombination: roles for XRCC3 in late stages of recombination. Mol. Cell 10 :387– 395.
52. Brenneman, M. A.,, A. E. Weiss,, J. A. Nickoloff, and, D. J. Chen. 2000. XRCC3 is required for efficient repair of chromosome breaks by homologous recombination. Mutat. Res. 459: 89– 97.
53. Bridges, B. A., 1984. Further characterization of repair of 8-meth-oxypsoralen crosslinks in UV-excision-defective Escherichia coli. Mutat. Res. 132 :153– 160.
54. Bridges, B. A., and, M. Stannard. 1982. A new pathway for repair of cross-linkable 8-methoxypsoralen mono-adducts in Uvr strains of Escherichia coli. Mutat. Res. 92: 9– 14.
55. Bridges, B. A., and, A. von Wright. 1981. Influence of mutations at the rep gene on survival of Escherichia coli following ultraviolet light irradiation or 8-methoxypsoralen photosensitization: evidence for a recA + rep +-dependent pathway for repair of DNA crosslinks. Mutat. Res. 82: 229– 238.
56. Brock, J.-A. K., and, K. Bloom. 1994. A chromosome breakage assay to monitor mitotic forces in budding yeast. J. Cell Sci. 107 :891– 902.
57. Brzovic, P. S.,, J. R. Keeffe,, H. Nishikawa,, K. Miyamoto,, D. Fox , III, M. Fukuda,, T. Ohta, and, R. Klevit. 2003. Binding and recogni- tion in the assembly of an active BRCA1/BARD1 ubiquitin-ligase complex. Proc. Natl. Acad. Sci. USA 100 :5646– 5651.
58. Buerstedde, J. M., and, S. Takeda. 1991. Increased ratio of targeted to random integration after transfection of chicken B cell lines. Cell 67 :179– 188.
59. Burke, J. F., and, A. E. Mogg. 1993. UV-stimulated recombination in mammalian cells is not dependent upon DNA replication. Mutat. Res. 294 :309– 315.
60. Calderon, I. L.,, C. R. Contopoulou, and, R. K. Mortimer. 1983. Isolation and characterization of yeast DNA repair genes. II. Isolation of plasmids that complement the mutations rad50–1, rad51–1, rad54–3, rad55–3. Curr. Genet. 7: 93– 100.
61. Callebaut, I.,, D. Moshous,, J. P. Mornon, and, J. P. de Villartay. 2002. Metallo-β-lactamase fold within nucleic acids processing enzymes: the β-CASP family. Nucleic Acids Res. 30 :3592– 3601.
62. Campbell, C., and, D. P. Romero. 1998. Identification and characterization of the RAD51 gene from the ciliate Tetrahymena thermophila. Nucleic Acids Res. 26: 3165– 3172.
63. Cantor, S. B.,, D. W. Bell,, S. Ganesan,, E. M. Kass,, R. Drapkin,, S. Grossman,, D. C. Wahrer,, D. C. Sgroi,, W. S. Lane,, D. A. Haber, and, D. M. Livingston. 2001. BACH1, a novel helicase-like protein, interacts directly with BRCA1 and contributes to its DNA repair function. Cell 105 :149– 160.
64. Cartwright, R.,, A. M. Dunn,, P. J. Simpson,, C. E. Tambini, and, J. Thacker. 1998. Isolation of novel human and mouse genes of the recA/RAD51 recombination-repair gene family. Nucleic Acids Res. 26: 1653– 1659.
65. Cassier, C., and, E. Moustacchi. 1981. Mutagenesis induced by mono- and bifunctional alkylating agents in yeast mutants sensitive to photo-addition of furocoumarins (pso). Mutat. Res. 84: 37– 47.
66. Cerutti, H.,, M. Osman,, P. Grandoni, and, A. T. Jagendorf. 1992. A homolog of Escherichia coli RecA protein in plastids of higher plants. Proc. Natl. Acad. Sci. USA 89: 8068– 8072.
67. Chanet, R.,, C. Cassier, and, E. Moustacchi. 1985. Genetic control of the bypass of mono-adducts and of the repair of cross-links photoinduced by 8-methoxypsoralen in yeast. Mutat. Res. 145 :145– 155.
68. Chapman, M. S., and, I. M. Verma. 1996. Transcriptional activation by BRCA1. Nature 382 :678– 679.
69. Chen, C.-F.,, P.-L. Chen,, Q. Zhong,, Z. D. Sharp, and, W.-H. Lee. 1999. Expression of BRC repeats in breast cancer cells disrupts the BRCA2-Rad51 complex and leads to radiation hypersensitivity and loss of G2/M checkpoint control. J. Biol. Chem. 274 :32931– 32935.
70. Chen, J.,, D. P. Silver,, D. Walpita,, S. B. Cantor,, A. F. Gazdar,, G. Tomlinson,, F. J. Couch,, B. L. Weber,, T. Ashley,, D. M. Livingston, and, R. Scully. 1998. Stable interaction between the products of the BRCA1 and BRCA2 tumor suppressor genes in mitotic and meiotic cells. Mol. Cell 2: 317– 328.
71. Chen, P.-L.,, C.-F. Chen,, Y. Chen,, J. Xiao,, Z. D. Sharp, and, W.-H. Lee. 1998. The BRC repeats in BRCA2 are critical for RAD51 binding and resistance to methyl methanesulfonate treatment. Proc. Natl. Acad. Sci. USA 95 :5287– 5292.
72. Chen, X.-B.,, R. Melchionna,, C.-M. Denis,, P.-H. L. Gaillard,, A. Blasina,, I. Van de Weyer,, M. N. Boddy,, P. Russell,, J. Vialard, and, C. H. McGowan. 2001. Human Mus81-associated endonuclease cleaves Holliday junctions in vitro. Mol. Cell 8 :1117– 1127.
73. Cheng, S.,, A. Sancar, and, J. E. Hearst. 1991. RecA-dependent incision of psoralen-crosslinked DNA by (A)BC excinuclease. Nucleic Acids Res. 19 :657– 663.
74. Cheng, S.,, B. van Houten,, H. B. Gamper,, A. Sancar, and, J. E. Hearst. 1988. Use of psoralen-modified oligonucleotides to trap three-stranded RecA-DNA complexes and repair of these cross-linked complexes by ABC excinuclease. J. Biol. Chem. 263: 15110.
75. Ciccia, A.,, A. Constantinou, and, S. C. West. 2003. Identification and characterization of the human Mus81-Eme1 endonuclease. J. Biol. Chem. 278 :25172– 25178.
76. Clever, B.,, H. Interthal,, J. Schmuckli-Maurer,, J. King,, M. Sigrist, and, W.-D. Heyer. 1997. Recombinational repair in yeast: functional interactions between Rad51 and Rad54 proteins. EMBO J. 16 :2535– 2544.
77. Cole, G. M.,, D. Schild,, S. T. Lovett, and, R. K. Mortimer. 1987. Regulation of RAD54- and RAD52-lacZ gene fusions in Saccharomyces cerevisiae in response to DNA damage. Mol. Cell. Biol. 7: 1078– 1084.
78. Cole, G. M.,, D. Schild, and, R. K. Mortimer. 1989. Two DNA repair and recombination genes in Saccharomyces cerevisiae, RAD52 and RAD54, are induced during meiosis. Mol. Cell. Biol. 9: 3101– 3104.
79. Cole, R. S., 1973. Repair of DNA containing interstrand crosslinks in Escherichia coli: sequential excision and recombination. Proc. Natl. Acad. Sci. USA 70: 1064– 1068.
80. Connolly, B.,, C. I. White, and, J. E. Haber. 1988. Physical monitoring of mating type switching in Saccharomyces cerevisiae. Mol. Cell. Biol. 8: 2342– 2349.
81. Connor, F.,, D. Bertwistle,, P. J. Mee,, G. M. Ross,, S. Swift,, E. Grigorieva,, V. L. J. Tybulewicz, and, A. Ashworth. 1997. Tumorigenesis and a DNA repair defect in mice with a truncating Brca2 mutation. Nat. Genet. 17: 423– 430.
82. Constantinou, A.,, X.-B. Chen,, C. H. McGowan, and, S. C. West. 2002. Holliday junction resolution in human cells: two junction endonucleases with distinct substrate specificities. EMBO J. 21 :5577– 5585.
83. Contopoulou, C. R.,, V. E. Cook, and, R. K. Mortimer. 1987. Analysis of DNA double strand breakage and repair using orthogonal field alternation gel electrophoresis. Yeast 3 :71– 76.
84. Cromie, G. A.,, J. C. Connelly, and, D. R. F. Leach. 2001. Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans. Mol. Cell 8 :1163– 1174.
85. Cummings, W. J., and, M. E. Zolan. 1998. Functions of DNA repair genes during meiosis. Curr. Top. Dev. Biol. 37 :117– 140.
86. D’Amours, D., and, S. P. Jackson. 2002. The Mre11 complex: at the crossroads of DNA repair and checkpoint signalling. Nat. Rev. Mol. Cell Biol. 3 :317– 327.
87. D’Andrea, A. D., 2003. The Fanconi road to cancer. Genes Dev. 17 :1933– 1936.
88. D’Andrea, A. D., and, M. Grompe. 2003. The Fanconi anaemia/BRCA pathway. Nat. Rev. Cancer 3 :23– 34.
89. Dardalhon, M., and, D. Averbeck. 1995. Pulsed-field gel electrophoresis analysis of the repair of psoralen plus UVA induced DNA photoadducts in Saccharomyces cerevisiae. Mutat. Res. 336: 49– 60.
90. Dardalhon, M.,, B. Demassy,, A. Nicolas, and, D. Averbeck. 1998. Mitotic recombination and localized DNA double-strand breaks are induced after 8-methoxypsoralen and UVA irradiation in Saccharomyces cerevisiae. Curr. Genet. 34: 30– 42.
91. Datta, A., and, S. Jinks-Robertson. 1995. Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 268 :1616– 1619.
92. Davies, A. A.,, J.-Y. Masson,, M. J. McIlwrath,, A. Z. Stasiak,, A. Stasiak,, A. R. Venkitaraman, and, S. C. West. 2001. Role of BRCA2 in control of the RAD51 recombination and DNA repair protein. Mol. Cell 7 :273– 282.
93. Davis, A. P., and, L. S. Symington. 2004. RAD51-dependent break-induced replication in yeast. Mol. Cell. Biol. 24 :2344– 2351.
94. Deans, B.,, C. S. Griffin,, M. Maconochie, and, J. Thacker. 2000. Xrcc2 is required for genetic stability, embryonic neurogenesis and viability in mice. EMBO J. 19 :6675– 6685.
95. Deng, W. P., and, J. A. Nickoloff. 1994. Preferential repair of UV damage in highly transcribed DNA diminishes UV-induced intrachromosomal recombination in mammalian cells. Mol. Cell. Biol. 14 :391– 399.
96. De Silva, I. U.,, P. J. McHugh,, P. H. Clingen, and, J. A. Hartley. 2000. Defining the roles of nucleotide excision repair and recombination in the repair of DNA interstrand cross-links in mammalian cells. Mol. Cell. Biol. 20: 7980– 7990.
97. Digweed, M.,, S. Rothe,, I. Demuth,, R. Scholz,, D. Schindler,, M. Stumm,, M. Grompe,, A. Jordan, and, K. Sperling. 2002. Attenuation of the formation of DNA-repair foci containing RAD51 in Fanconi anaemia. Carcinogenesis 23 :1121– 1126.
98. Doe, C. L.,, J. S. Ahn,, J. Dixon, and, M. C. Whitby. 2002. Mus81-Eme1 and Rqh1 involvement in processing stalled and collapsed replication forks. J. Biol. Chem. 277 :32753– 32759.
99. Donovan, J. W.,, G. T. Milne, and, D. T. Weaver. 1994. Homotypic and heterotypic protein associations control Rad51 function in double-strand break repair. Genes Dev. 8 :2552– 2562.
100. Dosanjh, M. K.,, D. W. Collins,, W. Fan,, G. G. Lennon,, J. S. Albala,, Z. Shen, and, D. Schild. 1998. Isolation and characterization of RAD51C, a new human member of the RAD51 family of related genes. Nucleic Acids Res. 26 :1179– 1184.
101. Dresser, M. E.,, D. J. Ewing,, M. N. Conrad,, A. M. Dominguez,, R. Barstead,, H. Jiang, and, T. Kodadek. 1997. DMC1 functions in a Saccharomyces cerevisiae meiotic pathway that is largely independent of the RAD51 pathway. Genetics 147: 533– 544.
102. Dronkert, M. L., and, R. Kanaar. 2001. Repair of DNA inter-strand cross-links. Mutat. Res. 486 :217– 247.
103. Dronkert, M. L. G.,, H. B. Beverloo,, R. D. Johnson,, J. H. J. Hoeijmakers,, M. Jasin, and, R. Kanaar. 2000. Mouse RAD54 affects DNA double-strand break repair and sister chromatid exchange. Mol. Cell. Biol. 20: 3147– 3156.
104. Dronkert, M. L. G.,, J. de Wit,, M. Boeve,, M. L. Vasconcelos,, H. van Steeg,, T. L. R. Tan,, J. H. J. Hoeijmakers, and, R. Kanaar. 2000. Disruption of mouse SNM1 causes increased sensitivity to the DNA inter-strand cross-linking agent mitomycin C. Mol. Cell. Biol. 20: 4553– 4561.
105. Dunn, B.,, P. Szauter,, M. L. Pardue, and, J. W. Szostak. 1984. Transfer of yeast telomeres to linear plasmids by recombination. Cell 39 :191– 201.
106. Eggler, A. L.,, R. B. Inman, and, M. M. Cox. 2002. The Rad51- dependent pairing of long DNA substrates is stabilized by replication protein A. J. Biol. Chem. 277 :39280– 39288.
107. Eisen, J. A.,, K. Sweder, and, P. C. Hanawalt. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and function. Nucleic Acids Res. 23 :2715– 2723.
108. Elias-Arnanz, M.,, A. A. Firmenich, and, P. Berg. 1996. Saccharomyces cerevisiae mutants defective in plasmid-chromosome recombination. Mol. Gen. Genet. 252: 530– 538.
109. Elmroth, K.,, J. Nygren,, L. J. Erkell, and, R. Hultborn. 2000. Radiation-induced double-strand breaks in mammalian DNA: influence of temperature and DMSO. Int. J. Radiat. Biol. 76 :1501– 1508.
110. Emery, H. S.,, D. Schild,, D. E. Kellogg, and, R. K. Mortimer. 1991. Sequence of RAD54, a Saccharomyces cerevisiae gene involved in recombination and repair. Gene 104: 103– 106.
111. Esposito, M. S.,, D. T. Maleas,, K. A. Bjornstad, and, C. V. Bruschi. 1982. Simultaneous detection of changes in chromosome number, gene conversion and intergenic recombination during mitosis of Saccharomyces cerevisiae: spontaneous and ultraviolet light induced events. Curr. Genet. 6: 5– 11.
112. Esposito, M. S.,, R. M. Ramirez, and, C. V. Bruschi. 1994. Re- combinators, recombinases and recombination genes of yeasts. Curr. Genet. 25 :1– 11.
113. Esposito, R. E., and, S. Klapholz. 1981. Meiosis and ascospore development, p., 211– 287. In J. N. Strathern,, E. W. Jones, and, J. R. Broach (ed.), The Molecular Biology of the Yeast Saccharomyces. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
114. Essers, J.,, R. W. Hendriks,, S. M. A. Swagemakers,, C. Troelstra,, J. de Wit,, D. Bootsma,, J. H. J. Hoeijmakers, and, R. Kanaar. 1997. Disruption of mouse RAD54 reduces ionizing radiation resistance and homologous recombination. Cell 89: 195– 204.
115. Essers, J.,, A. B. Houtsmuller,, L. van Veelen,, C. Paulusma,, A. L. Nigg,, A. Pastink,, W. Vermeulen,, J. H. J. Hoeijmakers, and, R. Kanaar. 2002. Nuclear dynamics of RAD52 group homologous recombination proteins in response to DNA damage. EMBO J. 21: 2030– 2037.
116. Essers, J.,, H. van Steeg,, J. de Wit,, S. M. A. Swagemakers,, M. Vermeij,, J. H. J. Hoeijmakers, and, R. Kanaar. 2000. Homologous and non-homologous recombination differentially affect DNA damage repair in mice. EMBO J. 19 :1703– 1710.
117. Fairbairn, D. W.,, P. L. Olive, and, K. L. O’Neill. 1995. The comet assay: a comprehensive review. Mutat. Res. 339 :37– 59.
118. Fan, S.,, J. Wang,, R. Yuan,, Y. Ma,, Q. Meng,, M. R. Erdos,, R. G. Pestell,, F. Yuan,, K. J. Auborn,, I. D. Goldberg, and, E. M. Rosen. 1999. BRCA1 inhibition of estrogen receptor signaling in transfected cells. Science 284 :1354– 1356.
119. Fasullo, M.,, P. Dave, and, R. Rothstein. 1994. DNA-damaging agents stimulate the formation of directed reciprocal translocations in Saccharomyces cerevisiae. Mutat. Res. 314: 121– 133.
120. Fishman-Lobell, J., and, J. 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.
121. Fishman-Lobell, J.,, N. Rudin, and, J. E. Haber. 1992. Two alternative pathways of double-strand break repair that are kinetically separable and independently modulated. Mol. Cell. Biol. 12 :1292– 1303.
122. Foray, N.,, C. F. Arlett, and, E. P. Malaise. 1997. Radiation-induced DNA double-strand breaks and the radiosensitivity of human cells: a closer look. Biochimie 79 :567– 575.
123. Fornace, A. J., Jr., 1983. Recombination of parent and daughter strand DNA after UV-irradiation in mammalian cells. Nature 304 :552– 554.
124. Fortin, G. S., and, L. S. Symington. 2002. Mutations in yeast Rad51 that partially bypass the requirement for Rad55 and Rad57 in DNA repair by increasing the stability of Rad51-DNA complexes. EMBO J. 21 :3160– 3170.
125. Fousteri, M. I., and, A. R. Lehmann. 2000. A novel SMC protein complex in Schizosaccharomyces pombe contains the Rad18 DNA repair protein. EMBO J. 19: 1691– 1702.
126. Frankenberg-Schwager, M., 1990. Induction, repair and biological relevance of radiation-induced DNA lesions in eukaryotic cells. Radiat. Environ. Biophys. 29 :273– 292.
127. Frankenberg-Schwager, M., and, D. Frankenberg. 1990. DNA double-strand breaks: their repair and relationship to cell killing in yeast. Int. J. Radiat. Biol. 58 :569– 575.
128. Freedman, J., and, S. Jinks-Robertson. 2002. G enetic requirements for spontaneous and transcription-stimulated mitotic recombination in Saccharomyces cerevisiae. Genetics 162: 15– 27.
129. Freemont, P. S., 2000. RING for destruction? Curr. Biol. 10 :R84– R87.
130. French, C. A.,, J.-Y. Masson,, C. S. Griffin,, P. O’R egan,, S. C. West, and, J. Thacker. 2002. Role of mammalian RAD51L2 (RAD51C) in recombination and genetic stability. J. Biol. Chem. 277 :19322– 19330.
131. Friedberg, E. C., and, L. B. Meira. 2000. Database of mouse strains carrying targeted mutations in genes affecting cellular responses to DNA damage. Version 4. Mutat. Res. 459: 243– 274.
132. Friedl, A. A.,, M. Kiechle,, B. Fellerhoff, and, F. Eckardt-Schupp. 1998. Radiation-induced chromosome aberrations in Saccharomyces cerevisiae. Influence of DNA repair pathways. Genetics 148: 975– 988.
133. Friedl, A. A.,, A. Kraxenberger, and, F. Eckardt-Schupp. 1995. Use of pulsed-field gel electrophoresis for studies of DNA double-strand break repair in the yeast Saccharomyces cerevisiae. GenoMethods 1: 75– 88.
134. Fujimori, A.,, S. Tachiiri,, E. Sonoda,, L. H. Thompson,, P. K. Dhar,, M. Hiraoka,, S. Takeda,, Y. Zhang,, M. Reth, and, M. Takata. 2001. Rad52 partially substitutes for the Rad51 paralog XRCC3 in maintaining chromsomal integrity in vertebrate cells. EMBO J. 20 :5513– 5520.
135. Game, J. C., 1993. DNA double-strand breaks and the RAD50-RAD57 genes in Saccharomyces. Semin. Cancer Biol. 4: 73– 83.
136. Game, J. C., 1983. Radiation-sensitive mutants and repair in yeast, p., 109– 137. In J. F. T. Spencer,, D. M. Spencer, and, A. R. W. Smith (ed.), Yeast Genetics: Fundamental and Applied Aspects. Springer Verlag, New York, N.Y.
137. Game, J. C.,, L. H. Johnston, and, R. C. von Borstel. 1979. Enhanced mitotic recombination in a ligase deficient mutant of the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 76: 4589– 4592.
138. Game, J. C., and, R. K. Mortimer. 1974. A genetic study of X-ray sensitive mutants in yeast. Mutat. Res. 24 :281– 292.
139. Game, J. C.,, T. J. Zamb,, R. J. Braun,, M. A. Resnick, and, R. M. Roth. 1980. The role of radiation (rad) genes in meiotic recombination in yeast. Genetics 94 :51– 68.
140. Garcia-Higuera, I.,, T. Taniguchi,, S. Ganesan,, M. S. Meyn,, C. Timmers,, J. Hejna,, M. Grompe, and, A. D. D’Andrea. 2001. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol. Cell 7 :249– 262.
141. Gasior, S. L.,, H. Olivares,, U. Ear,, D. M. Hari,, R. Weichselbaum, and, D. K. Bishop. 2001. Assembly of RecA-like recombinases: distinct roles for mediator proteins in mitosis and meiosis. Proc. Natl. Acad. Sci. USA 98: 8411– 8418.
142. Gasior, S. L.,, A. K. Wong,, Y. Kora,, A. Shinohara, and, D. K. Bishop. 1998. Rad52 associates with RPA and functions with Rad55 and Rad57 to assemble meiotic recombination complexes. Genes Dev. 12 :2208– 2221.
143. Gentil, A.,, A. Margot, and, A. Sarasin. 1983. Effect of UV- irradiation on genetic recombination of simian virus 40 mutants, p., 385– 396. In E. C. Friedberg and P. C. Hanawalt (ed.), Cellular Responses to DNA Damage. Alan R. Liss, Inc., New York, N.Y.
144. Godthelp, B. C.,, W. W. Wiegant,, A. van Duijn-Goedhart,, O. D. Schärer,, P. P. W. van Buul,, R. Kanaar, and, M. Z. Zdzienicka. 2002. Mammalian Rad51C contributes to DNA cross-link resistance, sister chromatid cohesion and genomic stability. Nucleic Acids Res. 30 :2172– 2182.
145. Golin, J. E., and, H. Tampe. 1988. Coincident recombination during mitosis in Saccharomyces: distance-dependent and -independent components. Genetics 119 :541– 547.
146. Golub, E. I.,, O. V. Kovalenko,, R. C. Gupta,, D. C. Ward, and, C. M. Radding. 1997. Interaction of human recombination proteins Rad51 and Rad54. Nucleic Acids Res. 25 :4106– 4110.
147. Gorbalenya, A. E., and, E. V. Koonin. 1993. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Cell Biol. 3 :419– 429.
148. Gordienko, I., and, W. D. Rupp. 1998. A specific 3’ exonuclease activity of UvrABC. EMBO J. 17 :626– 633.
149. Gowen, L. C.,, B. L. Johnson,, A. M. Latour,, K. K. Sulik, and, B. H. Koller. 1996. Brca1 deficiency results in early embryonic lethality characterized by neuroepithelial abnormalities. Nat. Genet. 12 :191– 194.
150. Grey, M.,, A. Düsterhöft,, J. A. P. Henriques, and, M. Brendel. 1996. Allelism of PSO4 and PRP19 links pre-mRNA processing with recombination and error-prone DNA repair in Saccharomyces cerevisiae. Nucleic Acids Res. 24 :4009– 4014.
151. Grishchuk, A. L., and, J. Kohli. 2003. Five RecA-like proteins of Schizosaccharomyces pombe are involved in meiotic recombination. Genetics 165 :1031– 1043.
152. Grossmann, K. F.,, A. M. Ward,, M. E. Matkovic,, A. E. Folias, and, R. E. Moses. 2001. S. cerevisiae has three pathways for DNA interstrand crosslink repair. Mutat. Res. 487 :73– 83.
153. Gupta, R. C.,, L. R. Bazemore,, E. I. Golub, and, C. M. Radding. 1997. Activities of human recombination protein Rad51. Proc. Natl. Acad. Sci. USA 94 :463– 468.
154. Gupta, R. C.,, E. Folta-Stogniew,, S. O’M alley,, M. Takahashi, and, C. M. Radding. 1999. Rapid exchange of A:T base pairs is essential for recognition of DNA homology by human Rad51 recombination protein. Mol. Cell 4 :705– 714.
155. Haaf, T.,, E. I. Golub,, G. Reddy, and, C. M. Radding. 1995. Nuclear foci of mammalian Rad51 recombination protein in somatic cells after DNA damage and its localization in synaptonemal complexes. Proc. Natl. Acad. Sci. USA 92 :2298– 2302.
156. Haaf, T.,, E. Raderschall,, G. Reddy,, D. C. Ward,, C. M. Radding, and, E. I. Golub. 1999. Sequestration of mammalian Rad51-recombination protein into micronuclei. J. Cell Biol. 144 :11– 20.
157. Haber, J. E., 1992. Exploring the pathways of homologous recombination. Curr. Opin. Cell Biol. 4 :401– 412.
158. Haber, J. E., 1998. Mating-type gene switching in Saccharomyces cerevisiae. Annu. Rev. Genet. 32 :561– 599.
159. Haber, J. E., and, W. D. Heyer. 2001. The fuss about Mus81. Cell 107 :551– 554.
160. Haber, J. E., and, W.-Y. Leung. 1996. Lack of chromosome territoriality in yeast: promiscuous rejoining of broken chromosome ends. Proc. Natl. Acad. Sci. USA 93 :13949– 13954.
161. Habu, T.,, T. Taki,, A. West,, Y. Nishimune, and, T. Morita. 1996. The mouse and human homologs of DMC1, the yeast meiosis-specific recombination gene, have a common unique form of exon skipped transcript in meiosis. Nucleic Acids Res. 24 :470– 477.
162. Hakem, R.,, J. L. de la Pompa,, C. Sirard,, R. Mo,, M. Woo,, A. Hakem,, A. Wakeham,, J. Potter,, A. Reitmair,, F. Billia,, E. Firpo,, C. C. Hui,, J. Roberts,, J. Rossant, and, T. W. Mak. 1996. The tumor suppressor gene Brca1 is required for embryonic cellular proliferation in the mouse. Cell 85: 1009– 1023.
163. Harris, P. V.,, O. M. Mazina,, E. A. Leonhardt,, R. B. Case,, J. B. Boyd, and, K. C. Burtis., 1996. Molecular cloning of Drosophila mus308, a gene involved in DNA cross-link repair with homology to prokaryotic DNA polymerase I genes. Mol. Cell. Biol. 16 :5764– 5771.
164. Harris, R. S.,, Q. Kong, and, N. Maizels. 1999. Somatic hypermutation and the three R’s: repair, replication and recombination. Mutat. Res. 436 :157– 178.
165. Harrison, A. R., and, J. M. Ford. 2002. BRCA1 induces DNA damage recognition factors and enhances nucleotide excision repair. Nat. Genet. 32 :180– 184.
166. Havas, K.,, A. Flaus,, M. Phelan,, R. Kingston,, P. A. Wade,, D. M. J. Lilley, and, T. Owen-Hughes. 2000. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 103 :1133– 1142.
167. Haynes, R. H., and, B. A. Kunz. 1981. DNA repair and mutagenesis in yeast, p. 371– 414. In J. N. Strathern,, E. W. Jones, and, J. R. Broach (ed.), The Molecular Biology of the Yeast Saccharomyces, vol. I. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
168. Hays, S. L.,, A. A. Firmenich, and, P. Berg. 1995. Complex formation in yeast double-strand break repair—participation of RAD51, RAD52, RAD55, and RAD57 proteins. Proc. Natl. Acad. Sci. USA 92 :6925– 6929.
169. Hearst, J. E.,, S. T. Isaacs,, D. Kanne,, H. Rapoport, and, K. Straub. 1984. The reaction of the psoralens with deoxyribonucleic acid. Q. Rev. Biophys. 17 :1– 44.
170. Henry-Mowatt, J.,, D. Jackson,, J. Y. Masson,, P. A. Johnson,, P. M. Clements,, F. E. Benson,, L. H. Thompson,, S. Takeda,, S. C. West, and, K. W. Caldecott. 2003. XRCC3 and Rad51 modulate replication fork progression on damaged vertebrate chromosomes. Mol. Cell 11 :1109– 1117.
171. Heyer, W.-D., 1994. The search for the right partner: homologous pairing and DNA strand exchange proteins in eukaryotes. Experientia 50 :223– 233.
172. Hiramoto, T.,, T. Nakanishi,, T. Sumiyoshi,, T. Fukuda,, S. Matsuura,, H. Tauchi,, K. Komatsu,, Y. Shibasaki,, H. Inui,, M. Watatani,, M. Yasutomi,, K. Sumii,, G. Kajiyama,, N. Kamada,, K. Miyagawa, and, K. Kamiya. 1999. Mutations of a novel human RAD54 homologue, RAD54B, in primary cancer. Oncogene 18 :3422– 3426.
173. Ho, K. S. Y., 1975. Induction of DNA double-strand breaks by X-rays in a radiosensitive strain of the yeast Saccharomyces cerevisiae. Mutat. Res. 30 :327– 334.
174. Ho, K. S. Y., and, R. K. Mortimer. 1975. Induction of dominant lethality by X-rays in a radiosensitive strain of yeast. Mutat. Res. 20 :45– 51.
175. Ho, K. S. Y., and, R. K. Mortimer. 1975. Two mutations which confer temperature-sensitive radiation sensitivity in the yeast Saccharomyces cerevisiae. Mutat. Res. 33 :157– 164.
176. Holmes, A. M., and, J. E. Haber. 1999. Double-strand break repair in yeast requires both leading and lagging strand DNA polymerases. Cell 96 :415– 424.
177. Houghtaling, S.,, C. Timmers,, M. Noll,, M. J. Finegold,, S. N. Jones,, M. S. Meyn, and, M. Grompe. 2003. Epithelial cancer in Fanconi anemia complementation group D2 (Fancd2) knockout mice. Genes Dev. 17 :2021– 2035.
178. Howlett, N. G.,, T. Taniguchi,, S. Olson,, B. Cox,, Q. Waisfisz,, C. de Die-Smulders,, N. Persky,, M. Grompe,, H. Joenje,, G. Pals,, H. Ikeda,, E. A. Fox, and, A. D. D’A ndrea. 2002. Biallelic inactivation of BRCA2 in Fanconi anemia. Science 297 :606– 609.
179. Hu, Y. F.,, Z. L. Hao, and, R. Li. 1999. Chromatin remodeling and activation of chromosomal DNA replication by an acidic transcriptional activation domain from BRCA1. Genes Dev. 13 :637– 642.
180. Huertas, P., and, A. Aguilera. 2003. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol. Cell 12 :711– 721.
181. Interthal, H., and, W. D. Heyer. 2000. MUS81 encodes a novel helix-hairpin-helix protein involved in the response to UV- and methylation-induced DNA damage in Saccharomyces cerevisiae. Mol. Gen. Genet. 263 :812– 827.
182. Ira, G., and, J. E. Haber. 2002. Characterization of RAD51- independent break-induced replication that acts preferentially with short homologous sequences. Mol. Cell. Biol. 22 :6384– 6392.
183. Ira, G.,, A. Malkova,, G. Liberi,, M. Foiani, and, J. E. Haber. 2003. Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast. Cell 115 :401– 411.
184. 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.
185. Jachymczyk, W. J.,, R. C. von Borstel,, M. R. A. Mowat, and, P. J. Hastings. 1981. Repair of interstrand cross-links in DNA of Saccharomyces cerevisiae requires two systems for DNA repair: the RAD3 system and the RAD51 system. Mol. Gen. Genet. 182 :196– 205.
186. Jackson, J. A., and, G. R. Fink. 1981. Gene conversion between duplicated genetic elements in yeast. Nature 292 :306– 311.
187. Jaco, I.,, P. Munoz,, F. Goytisolo,, J. Wesoly,, S. Bailey,, G. Taccioli, and, M. A. Blasco. 2003. Role of mammalian Rad54 in telomere length maintenance. Mol. Cell. Biol. 23 :5572– 5580.
188. Jha, B.,, F. Ahne, and, F. Eckardt-Schupp. 1993. The use of a double-marker shuttle vector to study DNA double-strand break repair in wild-type and radiation-sensitive mutants of the yeast Saccharomyces cerevisiae. Curr. Genet. 23 :402– 407.
189. Jiang, H.,, Y. Q. Xie,, P. Houston,, K. Stemke-Hale,, U. H. Mortensen,, R. Rothstein, and, T. Kodadek. 1996. Direct association between the yeast Rad51 and Rad54 recombination proteins. J. Biol. Chem. 271 :3181– 3186.
190. Joenje, H., and, K. J. Patel. 2001. The emerging genetic and molecular basis of Fanconi anaemia. Nat. Rev. Genet. 2 :446– 457.
191. Johnson, R. D., and, M. Jasin. 2001. Double-strand-break-induced homologous recombination in mammalian cells. Biochem. Soc. Trans. 29 :196– 201.
192. Johnson, R. D., and, M. Jasin. 2000. Sister chromatid gene conversion is a prominent double-strand break repair pathway in mammalian cells. EMBO J. 19 :3398– 3407.
193. Johnson, R. D.,, N. Liu, and, M. Jasin. 1999. Mammalian XRCC2 promotes the repair of DNA double-strand breaks by homologous recombination. Nature 401 :397– 399.
194. Johnson, R. D., and, L. S. Symington. 1995. Functional differences and interactions among the putative RecA homologs Rad51, Rad55, and Rad57. Mol. Cell. Biol. 15 :4843– 4850.
195. Johnston, L. H., 1990. Periodic events in the cell cycle. Curr. Opin. Cell Biol. 2 :274– 279.
196. Jones, B. K., and, A. T. Yeung. 1990. DNA base composition determines the specificity of UvrABC endonuclease incision of a psoralen cross-link. J. Biol. Chem. 265 :3489– 3496.
197. Jones, B. K., and, A. T. Yeung. 1988. Repair of 4,5’,8-trimethylpsoralen monoadducts and cross-links by the Escherichia coli UVRABC endonuclease. Proc. Natl. Acad. Sci. USA 85 :8410– 8414.
198. Kadyk, L. C., and, L. H. Hartwell. 1993. Replication-dependent sister chromatid recombination in rad1 mutants of Saccharomyces cerevisiae. Genetics 133 :469– 487.
199. Kadyk, L. C., and, L. H. Hartwell. 1992. Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae. Genetics 132 :387– 402.
200. Kaliraman, V.,, J. R. Mullen,, W. M. Fricke,, S. A. Bastin-Shanower, and, S. J. Brill. 2001. Functional overlap between Sgs1-Top3 and the Mms4-Mus81 enodnuclease. Genes Dev. 15 :2730– 2740.
201. Kanaar, R.,, C. Troelstra,, S. M. A. Swagemakers,, J. Essers,, B. Smit,, J.-H. Franssen,, A. Pastink,, O. Y. Bezzubova,, J.-M. Buerstedde,, B. Clever,, W.-D. Heyer, and, J. H. J. Hoeijmakers. 1996. Human and mouse homologs of the Saccharomyces cerevisiae RAD54 repair gene: evidence for functional conservation. Curr. Biol. 6 :828– 838.
202. Kans, J. A., and, R. K. Mortimer. 1991. Nucleotide sequence of the RAD57 gene of Saccharomyces cerevisiae. Gene 105 :139– 140.
203. Keil, R. L., and, G. S. Roeder. 1984. cis-acting, recombination stimulating activity in a fragment of the ribosomal DNA of S. cerevisiae. Cell 39 :377– 386.
204. Kerr, P., and, A. Ashworth. 2001. New complexities for BRCA1 and BRCA2. Curr. Biol. 11 :R668– R676.
205. King, M. C.,, J. B. Mandell, and the New York Breast Cancer Study Group. 2003. Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science 302 :643– 646.
206. Kitao, H., and, Z. M. Yuan. 2002. Regulation of ionizing radiation-induced Rad52 nuclear foci formation by c-Abl-mediated phosphorylation. J. Biol. Chem. 277 :48944– 48948.
207. Kleff, S.,, B. Kemper, and, R. Sternglanz. 1992. Identification and characterization of yeast mutants and the gene for a cruciform cutting endonuclease. EMBO J. 11 :699– 704.
208. Kleiman, F. E., and, J. L. Manley. 1999. Functional interaction of BRCA1-associated BARD1 with polyadenylation factor CstF-50. Science 285 :1576– 1579.
209. Klein, H. L., 1997. RDH54, a RAD54 homologue in Saccharomyces cerevisiae, is required for mitotic diploid-specific recombination and repair and for meiosis. Genetics 147 :1533– 1543.
210. Kohn, K. W.,, R. A. G. Ewig,, L. C. Erickson, and, L. A. Zwelling. 1981. Measurement of strand breaks and cross-links by alkaline elution, p. 379– 401. In E. C. Friedberg and, P. C. Hanawalt (ed.), DNA Repair—a Laboratory Manual of Research Procedures, vol. 1, part B, Marcel Dekker, Inc., New York, N.Y.
211. Kojic, M.,, C. F. Kostrub,, A. R. Buchman, and, W. K. Holloman. 2002. BRCA2 homolog required for proficiency in DNA repair, recombination, and genome stability in Ustilago maydis. Mol. Cell 10 :683– 691.
212. Kolodkin, A. L.,, A. J. S. Klar, and, F. Stahl. 1986. Double-strand breaks can initiate meiotic recombination in Saccharomyces cerevisiae. Cell 46 :733– 740.
213. Koonin, E. V.,, S. F. Altschul, and, P. Bork. 1996. BRCA1 protein products: functional motifs. Nat. Genet. 13 :266– 268.
214. Kostriken, R.,, J. N. Strathern,, A. J. S. Klar,, J. B. Hicks, and, F. Heffron. 1983. A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae. Cell 35 :167– 174.
215. Kraakman-van der Zwet, M.,, W. J. I. Overkamp,, R. E. E. van Lange,, J. Essers,, A. van Duijn-Goedhart,, I. Wiggers,, S. Swaminathan,, P. P. W. van Buul,, A. Errami,, R. T. L. Tan,, N. G. J. Jaspers,, S. K. Sharan,, R. Kanaar, and, M. Z. Zdzienicka. 2002. Brca2 (XRCC11) deficiency results in radioresistant DNA synthesis and a higher frequency of spontaneous deletions. Mol. Cell. Biol. 22 :669– 679.
216. 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.
217. Kraus, E.,, W.-Y. Leung, and, J. E. Haber. 2001. Break-induced replication: a review and an example in budding yeast. Proc. Natl. Acad. Sci. USA 98 :8255– 8262.
218. Krejci, L.,, L. Chen,, S. Van Komen,, P. Sung, and, A. Tomkinson. 2003. Mending the break: two DNA double-strand break repair machines in eukaryotes. Prog. Nucleic Acid Res. Mol. Biol. 74 :159– 201.
219. Krejci, L.,, J. Damborsky,, B. Thomsen,, M. Duno, and, C. Bendixen. 2001. Molecular dissection of interactions between Rad51 and members of the recombination-repair group. Mol. Cell. Biol. 21 :966– 976.
220. Krejci, L.,, S. Van Komen,, Y. Li,, J. Villemain,, M. S. Reddy,, H. Klein,, T. Ellenberger, and, P. Sung. 2003. DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature 423 :305– 309.
221. Kunz, B. A., and, R. H. Haynes. 1981. Phenomenology and genetic control of mitotic recombination in yeast. Annu. Rev. Genet. 15 :57– 89.
222. Kupiec, M., 2000. Damage-induced recombination in the yeast Saccharomyces cerevisiae. Mutat. Res. 451 :91– 105.

References: V. 
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 V. 
 V. 
 V. 
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