The study of double-strand chromosome break repair by homologous and nonhomologous recombination is a growth industry. In the past year, there have been important advances both in understanding the connection between recombination and DNA replication and in linking recombination with origins of human cancer. At the same time, a combination of biochemical, genetic, molecular biological, and cytological approaches have provided a clearer vision of the specific functions of a variety of recombination proteins. Address MS029 Rosentiel Center, 415 South Street, Brandeis University, Waltham, MA 02454-9110, USA Current Opinion in Cell Biology 2000, 12:286–292 0955-0674/00/$ — see front matter © 2000 Elsevier Science Ltd. All rights reserved. Abbreviations ATM ataxia telangiectasia mutation DSB double-strand break HR homologous recombination NHEJ nonhomologous end-joining Sir silent information regulator Introduction Much progress in our understanding of recombination has been associated with the impressive and rapid develop- ment of specific recombination assays in vertebrate cells that permit a direct comparison between yeast and verte- brates. Site-specific rare-cutting endonucleases, such as HO and I-SceI, are making it possible to create double- strand breaks (DSBs) in chromosomes, producing results that are quite different from those obtained on the basis of the transfection of ‘naked’ DNA into cells. One important realization is that homologous recombination (HR) and nonhomologous end-joining (NHEJ) compete with each other and take place at comparable frequencies. Although budding yeast favors HR over NHEJ and mouse cells pre- fer NHEJ, the differences are much less than an order of magnitude [1 •• ,2 • ]. The idea that the ratio of HR to NHEJ is developmentally has recently received support from a study of Ku DNA end-binding proteins during meiosis in mouse cells [3 • ]. Ku proteins participate in NHEJ. Goedecke et al. [3 • ] found that the level of Ku proteins decreases during mouse cell meiosis, so that presumably HR becomes favored over NHEJ. HR proteins HR in Saccharomyces requires the RecA-homologous strand exchange proteins Rad51p (and the two Rad51-related pro- teins Rad55p and Rad57p), Rad52p, Rad54p and Rad59p. Rad50p, Mre11p and Xrs2p are also important. All these proteins have vertebrate homologues [4,5]. Investigation of the functions of these proteins has produced much new information and has provided further evidence that these proteins are important in preventing cancer. The roles of these recombination proteins are discussed below. Rad51p In vertebrates, the absence of Rad51p is lethal. When it is depleted from chicken DT40 cells, it causes an accumulation of chromosome breaks. Takeda and colleagues [6 • ], using chicken DT40 cells, created a mutation in Rad51p that pre- vents ATP hydrolysis but allows ATP binding; this mutated Rad51p rescues lethality in Rad51p null cells. However, recombination is surprisingly robust in this Rad51p mutant, showing that the essential functions of Rad51p are indepen- dent of ATP. By depleting Rad51p, or eliminating Rad54p (another recombination protein), Takeda and colleagues have also shown that sister chromatids in mammalian cells undergo exchange through HR [7]. In addition to Rad51p, vertebrates have five Rad51 homologues (Rad51B, Rad51C, Rad51D, XRCC1 and XRCC2) whereas yeast has only two. It now seems that all of them play important roles in recom- bination, although none of them is essential for cell viability. For example, Jasin and colleagues [8,9] have shown that XRCC2 and XRCC3 deletions reduce I-SceI-induced recombination in mouse cells. Rad54p Rad54p facilitates Rad51p’s strand exchange activity in vitro [10]. The importance of Rad54 homologues in HR has been demonstrated in fruit flies [11], chicken DT40 cells [7] and mice [12]; although, unlike Rad51p, Rad54p is not essential. In addition, rad54 –/– yeast cells are not as severely defective in recombination as rad51 –/– mutants [13]. In fact, from yeast to humans, there are only two Rad54-like proteins: Rad54p and Rad54Bp. In yeast, they apparently participate in different pathways, with Rad54p playing the key role in sister-chromatid recombination [14], and Rad54Bp (known in yeast as Tid1p or Rdh54p) being more important for inter-chromosomal transactions. (How cells know which recombination machinery to use, depending on the homologous partner chosen, is an endur- ing mystery). However, much of the increased interest in Rad54p and Rad54Bp has come from the demonstration that these genes are often mutated in primary cancers [15,16]. Loss of heterozygosity near other human recombi- nation genes has also been noted, suggesting that when a mutant allele is homozygous, cells have an elevated prob- ability of developing cancer [17]. BRCA1p and BRCA2p The connection between HR and cancer has been strengthened by the demonstration that a mutation in the breast cancer gene BRCA1 reduces recombination in mouse cells [18 •• ]. BRCA1p interacts with Rad51p, as well as with the Mre11–Rad50 complex [19], which has been implicated both in HR and in NHEJ. Whether another Recombination: a frank view of exchanges and vice versa James E Haber