Competitive Repair by Naturally Dispersed Repetitive DNA during Non-Allelic Homologous Recombination

Abstract

Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR–dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR–dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer.

Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae

“…Assuming that such lesion originated at a putative fragile site distal to YMRCTy1-5, this resection would have to span at least an additional 370 kb to reach YMRCTy1-4. Chromosomal rearrangements that involve long-range processing of a distally located DSB up to a Ty element have also been observed previously (Hoang et al 2010).Another interesting observation in the strain with the deletion of YMRCTy1-5 was the appearance of a different recurrent rearrangement. Five of 10 CFRs had the same 925-kb chr7/chr5 translocation that comigrated with chr16 and chr13 in PFGE (e.g., CFR501; Figure 4A).…”

“…Assuming that such lesion originated at a putative fragile site distal to YMRCTy1-5, this resection would have to span at least an additional 370 kb to reach YMRCTy1-4. Chromosomal rearrangements that involve long-range processing of a distally located DSB up to a Ty element have also been observed previously (Hoang et al 2010).…”

“…Chromosomal rearrangements involving similarly long resection tracts (break-distal recombination, BDR) have been recently reported (Hoang et al 2010;Tan et al 2012). While the DSB at chr13R explanation is attractive, it is unlikely to be the only factor involved.…”

“…For example, growth of yeast cells in medium with low levels of phosphate result in duplication of the linked PHO3 and PHO5 genes (Hansche et al 1978), cells grown in limited glucose have duplications of the hexose transporter encoded by HXT6 (Brown et al 1998;Dunham et al 2002), and cells selected in medium with low sulfur concentrations amplified the SUL1 gene (Gresham et al 2008). Amplification of the HTA2-HTB2 histone genes has also been identified as a dosage compensation mechanism for the deletion of HTA1-HTB1 ( arm associated with a terminal deletion of another chromosome (Dunham et al 2002;Umezu et al 2002;Kim et al 2008;Vernon et al 2008;Hoang et al 2010;McCulley and Petes 2010; Kolodner 2011, 2012); (5) linear extrachromosomal plasmids with the amplified copies in inverted orientation (Dorsey et al 1992;Narayanan et al 2006); and, (6) interstitial triplications of a genomic segment containing an origin of replication flanked by short inverted repeats (Brewer et al 2011). Class 1 duplications can be generated by unequal crossovers ( Figure 1B) or by break-induced replication (BIR) in which a double-strand break (DSB) in one repeat is repaired using a nonallelic repeat on a sister chromatid or a homolog.…”

“…However, it is important to note that the fragile nature may not be entirely dependent on replication stress. For example, the same yeast fragile sites have also been detected as hotspots for NAHR even under normal growth conditions (Hoang et al 2010;Chan and Kolodner 2012).We tested the candidate chr13R fragile site in two ways. We deleted the YMRCTy1-5 element and observed that in some cases the rearrangements recovered involved a proximal Ty element on the right arm of chr13.…”