![]() A similar level of template switching is found in another DSB repair mechanism, gene conversion, which is not Pol32-dependent ( Hicks et al. The repair replication fork established by BIR is not as accurate as a normal replication fork consequently, BIR exhibits a highly elevated rate of mutation as well as evidence of template switching, in which a replicating strand jumps from copying one chromosome to begin copying a homologous chromosome ( Smith et al. BIR can also occur via a less efficient Rad51-independent mechanism ( Malkova et al. Recently, we showed that the mammalian homolog of Pol32, POLD3, is essential for cell viability when they are subjected to replication stress, presumably using a BIR mechanism to repair and restart stalled and broken replication forks ( Costantino et al. 2013), most BIR events depend on the recombination protein Rad51 and are substantially dependent on the nonessential DNA polymerase δ (Pol δ) subunit Pol32 ( Davis and Symington 2004 Malkova et al. 2013 Donnianni and Symington 2013 Saini et al. In budding yeast, where BIR has been most extensively studied ( Anand et al. BIR occurs when one end of DSB is able to strand-invade a homologous or divergent (homeologous) sequence and to initiate recombination-dependent DNA replication, which can proceed ≥100 kb to a chromosome end, creating nonreciprocal translocations. (2009a) proposed that these alterations occur via microhomology-mediated break-induced replication (MM-BIR) a similar mechanism has been suggested to explain the origin of some segmental duplications in budding yeast ( Payen et al. 2012), many others must have involved repair-mediated DNA replication to create genomes in which there are copy number increases ( Lee et al. Although some of these chromosome rearrangements can readily be explained by several nonhomologous end-joining mechanisms ( Shaw and Lupski 2005 Lieber et al. Many chromosomal rearrangements in mammalian cells, including translocations and segmental duplications, exhibit junctions that share only very few base pairs (i.e., microhomology). ![]() ![]() Regardless of the origins of the DSBs, it is clear that DNA ends are potent inducers of chromosome rearrangements that result in cancer and other diseases ( Elliott and Jasin 2002 Aguilera and Gomez-Gonzalez 2008 Halazonetis et al. Recent studies have suggested that precancerous cells show evidence of replication stress in the form of an increased amount of ssDNA, terminated replication forks, and DNA double-strand breaks (DSBs), suggesting replication-generated DNA breaks as the initial trigger for genome instability. A question of utmost importance is what makes normal cells, which have a remarkably stable genome, undergo such drastic genetic changes. ![]() In some cases, there are dramatic chromosome rearrangements known as chromothripsis or chromosome shattering in which, within a single chromosome, there are dozens of inversions, deletions, and duplications of sequences characterized by very small numbers of shared nucleotides at their junctions. Genome instability-commonly manifested as gain, loss, or translocation of chromosome segments and often involving entire chromosome arms-is a hallmark of cancer and other diseased cells ( Lupski 2007 Negrini et al. These results suggest that template switching among repeated genes is a potent driver of genome instability and evolution. BIR traversing repeated DNA sequences frequently results in complex translocations analogous to those seen in mammalian cells. In particular, such jumps are less constrained by sequence divergence and exhibit a different pattern of microhomology junctions. Template switches between highly divergent sequences appear to be mechanistically distinct from the initial strand invasions that establish BIR. Our data show that such template switches are robust mechanisms that give rise to complex rearrangements. We examined BIR and template switching between highly diverged sequences in Saccharomyces cerevisiae, induced during repair of a site-specific double-strand break (DSB). Models such as microhomology-mediated break-induced replication (MM-BIR) have been invoked to explain these rearrangements. Although some of these rearrangements appear to involve nonhomologous end-joining, many must have involved mechanisms requiring new DNA synthesis. Recent high-resolution genome analyses of cancer and other diseases have revealed the occurrence of microhomology-mediated chromosome rearrangements and copy number changes.
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