In the yeast Saccharomyces cerevisiae, reduced levels of the replicative alpha DNA polymerase result in greatly elevated frequencies of chromosome translocations and chromosome loss. We selected translocations in a small region of chromosome III and found that they involve homologous recombination events between yeast retrotransposons (Ty elements) on chromosome III and retrotransposons located on other chromosomes. One of the two preferred sites of these translocations on chromosome III involve two Ty elements arrayed head-to-head; disruption of this site substantially reduces the rate of translocations. We demonstrate that this pair of Ty elements constitutes a preferred site for double-strand DNA breaks when DNA replication is compromised, analogous to the fragile sites observed in mammalian chromosomes.

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 ...

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Specific regions of genomes (fragile sites) are hot spots for the chromosome rearrangements that are associated with many types of cancer cells. Understanding the molecular mechanisms regulating the stability of chromosome fragile sites, therefore, has important implications in cancer biology. We previously identified two chromosome fragile sites in Saccharomyces cerevisiae that were induced in response to the reduced expression of Pol1p, the catalytic subunit of DNA polymerase ␣. In the study presented here, we show that reduced levels of Pol3p, the catalytic subunit of DNA polymerase ␦, induce instability at these same sites and lead to the generation of a variety of chromosomal aberrations. These findings demonstrate that a change in the stoichiometry of replicative DNA polymerases results in recombinogenic DNA lesions, presumably doublestrand DNA breaks.