TIBS 24 – JULY 1999 271 0968 – 0004/99/$ – See front matter © 1999, Elsevier Science. All rights reserved. PII: S0968-0004(99)01413-9 CELLS DEVOTE SIGNIFICANT resources to the repair of double-strand DNA breaks (DSBs). If left unrepaired, such damage re- sults in the loss of chromosomes and/or the induction of cell death. If imprecisely repaired, the damage leads to mutations and chromosomal rearrangements. Here, I focus on the repair of DNA breaks by the homologous-recombination process known as gene conversion, in which the broken chromosome is patched up by copying information from a homologous chromosome or from a sister chromatid. Gene conversion is the most conservative type of repair; it is much less likely to in- troduce a mutation at the site of damage than is a process such as non-homologous end-joining, in which various deletions or small insertions are created at the site of the DSB. However, gene conversions are sometimes accompanied by crossing over of the interacting sequences, which can lead to a loss of heterozygosity in mitotic cells. Very similar events occur in meiosis, and again are initiated by DSBs, but, in this case, crossovers are the desired outcome. In mammalian cells, because of the dif- ficulties of obtaining accurate gene target- ing and the high frequency of end-fusions of transfected DNA, it has been supposed that illegitimate recombination mecha- nisms are much more efficient than are homologous-repair pathways – the oppo- site of what one finds in yeast. However, recently, Liang and co-workers 1 have shown that vertebrate cells are quite proficient at homologous recombination, when DSBs are created within chromo- somes as opposed to when a DNA frag- ment is transfected into cells. Recom- bination is also enhanced when there are no base-pair differences between the transforming linear DNA and the target, chromosomal site: the cell’s mismatch- repair machinery does not provoke rejec- tion of the incoming DNA in the absence of such differences 2 . Moreover, some spe- cialized cells seem very yeast-like in their ability to carry our accurate gene target- ing. The best-studied type is chicken DT40 cells, which are derived from im- mune cells that rely on gene conversion to generate immunoglobulin diversity. DT40 cells have become an ideal system to analyse the consequences of knock- ing out genes that encode recombination proteins – in the same way that their homologs have been studied in yeast and bacteria 3,4 . The origins of double-strand breaks In the laboratory, DSBs have classically been created by X-rays. More recently, re- pair of DSBs has been studied after their induction by endonucleases during such natural processes as meiosis or during programmed chromosome rearrange- ments such as V(D)J joining of mammalian immunoglobulin genes or switching of yeast mating-type genes. DSB repair after excision of transposable elements from a chromosome has also been analysed. Although these repair events are impor- tant in the specialized cells that experi- ence programmed DSBs, multiple path- ways of recombinational repair almost certainly arose in response to a more prevalent source of such DNA damage: the process of DNA replication itself. Al- though DNA replication is a remarkably accurate process, human cells are esti- mated to suffer ~10 such lesions every time a cell divides; this figure is based on the incidence of sister-chromatid ex- changes. Consequently, vertebrate cells that lack the Rad51 recombination protein are inviable, presumably because they cannot repair these lesions; many broken chromosomes are present in such cells 4 . Homologous recombination could play a second, important role at the replication REVIEWS DNA recombination: the replication connection James E. Haber Chromosomal double-strand breaks (DSBs) arise after exposure to ionizing radiation or enzymatic cleavage, but especially during the process of DNA replication itself. Homologous recombination plays a critical role in repair of such DSBs. There has been significant progress in our understanding of two processes that occur in DSB repair: gene conversion and recombination- dependent DNA replication. Recent evidence suggests that gene conversion and break-induced replication are related processes that both begin with the establishment of a replication fork in which both leading- and lagging- strand synthesis occur. There has also been much progress in characteriz- ation of the biochemical roles of recombination proteins that are highly conserved from yeast to humans. J. E. Haber is at Brandeis University, Waltham, MA 02454-9110, USA. (a) (b) Gene conversion Break-induced replication DSB DSB Figure 1 Repair of double-strand breaks (DSBs) that arise during DNA replication. DSBs can be produced by replication across a single-stranded nick or by rupture of a DNA strand at a stalled replication fork. Newly synthesized DNA is shown in light blue. (a) If the DSB leaves sufficient duplex DNA on either side, the ends can participate in repair by gene conversion, which patches up the broken chromosome. In this process, the ends of the broken DNA molecule invade an intact template (here, the upper sister chromatid). The process involves DNA-strand-exchange proteins such as Rad51. New DNA synthesis can be initiated from the 3' ends and fills in the missing sequences. (b) If the DSB occurs near the replication fork, exonucleases can resect the broken end so that the resulting 3' end can invade the upper, intact template to re-establish a replication fork that can proceed either to the chromosome terminus or until it meets a converging replication fork.