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(1996) Engineering a mini-herpesvirus as a general strategy to transduce up to 180 kb of functional self- replicating human mini-chromosomes. Gene Ther. 3, 1081–1088 38 Wang, S. and Vos, J.M. (1996) A hybrid herpesvirus infectious vector based on Epstein–Barr virus and herpes simplex virus type 1 for gene transfer into human cells in vitro and in vivo. J. Virol. 70, 8422–8430 39 Suter, M. et al. (1999) BAC-VAC, a novel generation of (DNA) vaccines: a bacterial artificial chromosome (BAC) containing a replication-competent, packaging-defective virus genome induces protective immunity against herpes simplex virus 1. Proc. Natl. Acad. Sci. U. S. A. 96, 12697–12702 B roken chromosomes pose a serious threat to cell sur- vival. The presence of an unrepaired double-strand break (DSB) will trigger the DNA-damage response sys- tems of a cell to arrest its progression through the cell cycle and, sometimes, to cause apoptotic cell death. But even if a cell with an unrepaired DSB continues to divide, the broken chromosome fragments will mis-segregate and be degraded, producing aneuploidy. In response to this threat, cells have elaborated an impressive arsenal of DNA-repair pathways. There are two general types of repair: homologous recombination (HR) and nonhomologous end-joining (NHEJ). These two processes are in competition with each other and one focus of this review is to examine the way that this compe- tition is regulated. But the cell’s options are far more com- plex than simply electing to employ HR or NHEJ. There are several types of homologous repair: gene conversion, break-induced replication and single-strand annealing (reviewed in Ref. 1). Similarly, there are also several alter- native end-joining mechanisms 2,3 . Moreover, even once a process such as gene conversion is initiated, there are additional genetically regulated decisions in choosing among alternative homologous templates to carry out repair. How does the cell decide to use a template on a sister chromatid, on a homologous chromosome or at an ectopic site? Moreover, how are these choices tied to the cell’s DNA damage-sensing checkpoints? This review surveys the impressive recent progress in delineating the different mechanisms of homologous and nonhomologous repair and the way in which they all com- pete in repairing DSBs. The emphasis will be on what has been learned in the best-studied organism, Saccharomyces cerevisiae, but I also discuss studies in other model eukary- otic systems and in mammalian cells. Homologous recombination mechanisms The three major types of HR all begin in the same way, as the ends of the DSB are resected by 5' to 3' exonucleases or by a helicase coupled to an endonuclease, to produce long, 3'-ended single-stranded DNA tails (Fig. 1). Single-strand annealing In the simplest process (Fig. 1d), resection exposes com- plementary regions of homologous sequences originally flanking the DSB, creating a deletion by single-strand annealing (SSA). SSA will occur with as little as 30 bp of homology, although it is much more efficient with 200–400 bp (Ref. 44). Double-strand chromosome breaks can arise in a number of ways, by ionizing radiation, by spontaneous chromosome breaks during DNA replication, or by the programmed action of endonucleases, such as in meiosis. Broken chromosomes can be repaired either by one of several homologous recombination mechanisms, or by a number of nonhomologous repair processes. Many of these pathways compete actively for the repair of a double-strand break. Which of these repair pathways is used appears to be regulated developmentally, genetically and during the cell cycle. Partners and pathways repairing a double-strand break James E. Haber haber@brandeis.edu Rosentiel Basic Medical Sciences Research Center, MS 029 Brandeis University, 415 South Street, Waltham, MA 02454-9110, USA. 0168-9525/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S0168-9525(00)02022-9