Fig. 2.
Structures of GCRs isolated in strains with defects in MRC1 and SWR1. a Copy number analysis of chrV L (left) and the target chromosomes (right) for representative GCRs based on whole-genome sequencing. The thick hashed blue arrow indicates sequences within the GCR; the thin dashed blue arrow indicates connectivity between portions of the GCR that map to different regions of the reference chromosome(s). Filled triangles are Ty-related (red) multi-copy sequences involved in GCR-related HR events. Junction sequences are displayed for rearrangements not associated with copy number increases. Telomere addition GCRs had deletion of the terminal region of chromosome V, including the CAN1-URA3 cassette, and addition of a de novo telomere to the broken end; the junctions involved short telomere-like sequences on chromosome V. Interstitial deletions spanned the CAN1-URA3 cassette and contained microhomology at the deletion junctions. Hairpin-mediated GCRs had deletion of the terminal region of chromosome V and hairpin formation, followed by inverted duplication of a region of chromosome V ending in a region of homology, either a Ty delta sequence or PAU gene, and a subsequent secondary translocation with a homologous target elsewhere in the genome. In all hairpin-mediated inverted duplication GCRs, subsequent rearrangements involved a non-reciprocal translocation with a target chromosome, involving duplication of the target chromosome from the targeted homology to the telomere. Homology-mediated inverted duplications are similar to hairpin-mediated inverted duplications except that the fold-back loop is formed by HR between the YCLWdelta5 fragment in can1::PLEU2-NAT and other Ty delta sequences on the left arm of chromosome V, leading to inverted duplication of the flanking sequence. b Distribution of the microhomology lengths at the junctions in the 35 microhomology-mediated translocations and interstitial deletions observed in the uGCR and sGCR products from the wild-type strain, the mrc1Δ, swr1Δ, and mrc1-1-843 single mutants, and the mrc1Δ swr1Δ and mrc1-1-843 swr1Δ double mutants. c. Distribution of the breakpoint junction lengths for randomly generated translocations scaled so that the total number of events was 35