Break-induced replication (BIR) is an important process of DNA metabolism that has been implicated in the restart of collapsed replication forks, as well as in various chromosomal instabilities, including loss of heterozygosity, translocations, and alternative telomere lengthening. Therefore, knowledge of how BIR is carried out and regulated is important for better understanding the maintenance of genomic stability in eukaryotes. Here we present a new yeast experimental system that enables the genetic control of BIR to be investigated. Analysis of mutations selected on the basis of their sensitivity to various DNA-damaging agents demonstrated that deletion of POL32, which encodes a third, nonessential subunit of polymerase d, significantly reduced the efficiency of BIR, although some POL32-independent BIR was still observed. Importantly, the BIR defect in pol32D cells was associated with the formation of half-crossovers. We propose that these half-crossovers resulted from aberrant processing of BIR intermediates. Furthermore, we suggest that the half-crossovers observed in our system are analogous to nonreciprocal translocations (NRTs) described in mammalian tumor cells and, thus, our system could represent an opportunity to further study the NRT mechanism in yeast.

Inverted DNA repeats are known to cause genomic instabilities. Here we demonstrate that double-strand DNA breaks (DSBs) introduced a large distance from inverted repeats in the yeast (Saccharomyces cerevisiae) chromosome lead to a burst of genomic instability. Inverted repeats located as far as 21 kb from each other caused chromosome rearrangements in response to a single DSB. We demonstrate that the DSB initiates a pairing interaction between inverted repeats, resulting in the formation of large dicentric inverted dimers. Furthermore, we observed that propagation of cells containing inverted dimers led to gross chromosomal rearrangements, including translocations, truncations, and amplifications. Finally, our data suggest that break-induced replication is responsible for the formation of translocations resulting from anaphase breakage of inverted dimers. We propose a model explaining the formation of inverted dicentric dimers by intermolecular single-strand annealing (SSA) between inverted DNA repeats. According to this model, anaphase breakage of inverted dicentric dimers leads to gross chromosomal rearrangements (GCR). This "SSA-GCR" pathway is likely to be important in the repair of isochromatid breaks resulting from collapsed replication forks, certain types of radiation, or telomere aberrations that mimic isochromatid breaks.Genetic instability is associated with most tumor cells, and fusions between chromosomes or chromatids is a common source of chromosome aberrations found in such cells. Fusions between chromatids can be initiated by simultaneous breakage of the two chromatids or by the loss of telomere capping (13,35). The outcome of fusions depends on the location of the fusion site. Thus, fusions between acentric fragments lead to gene amplifications due to missegregation (21,36). Fusions between fragments containing centromeres lead to the formation of dicentric chromosomes that break during anaphase, when the two centromeres are pulled in opposite directions (breakage-fusion bridge [BFB] events). BFB events often lead to BFB cycles characterized by continued breakages and fusions. The BFB cycle, which was originally described by McClintock for maize (32), is repeated until newly acquired telomeres stabilize the broken chromosomes (13, 35). The process of broken chromosomes acquiring telomeres (the exit from BFB) creates different chromosomal rearrangements, including translocations, deletions, and amplifications (25,35,39,46).The mechanisms responsible for initiating chromosome or chromatid fusions are not clear. Although several studies indicate an important role for nonhomologous end joining in this process (33, 41), fusions can efficiently occur in a number of nonhomologous end joining-defective mutants (11), implicating the involvement of alternative mechanisms. Junctions of chromatid fusions sometimes have short regions of homology (26), suggesting the possible involvement of a homology-driven repair mechanism. Our present knowledge of fusions is based mainly on cells with defects in telomere ...

DNA double-strand breaks (DSBs) are critical lesions that can lead to cell death or chromosomal rearrangements. Rad51 is necessary for most mitotic and meiotic DSB repair events, although a number of RAD51-independent pathways exist. Previously, we described DSB repair in rad51Δ yeast diploids that was stimulated by a DNA region termed “facilitator of break-induced replication” (FBI) located approximately 30 kb from the site of an HO-induced DSB. Here, we demonstrate that FBI is a large inverted DNA repeat that channels repair of DSBs into the singlestrand annealing-gross chromosomal rearrangements (SSA-GCR) pathway. Further, analysis of DSB repair in rad54Δ cells allowed us to propose that the SSA-GCR repair pathway is suppressed in the presence of Rad51p. Therefore, an additional role of Rad51 might be to protect eukaryotic genomes from instabilities by preventing chromosomal rearrangements.