Formation of Complex and Unstable Chromosomal Translocations in Yeast

Genome instability, associated with chromosome breakage syndromes and most humancancers, is still poorly understood. In the yeast Saccharomycescerevisiae, numerous genes with roles in the preservation of genomeintegrity have been identified. DNA-damage-checkpoint-deficient yeast cells thatlack Sgs1, a RecQ-like DNA helicase related to the humanBloom''s-syndrome-associated helicase BLM, show an increased rate ofgenome instability, and we have previously shown that they accumulate recurringchromosomal translocations between three similar genes, CAN1,LYP1 and ALP1. Here, the chromosomallocation, copy number and sequence similarity of the translocation targetsALP1 and LYP1 were altered to gain insightinto the formation of complex translocations. Among 844 clones with chromosomalrearrangements, 93 with various types of simple and complex translocationsinvolving CAN1, LYP1 and ALP1were identified. Breakpoint sequencing and mapping showed that the formation ofcomplex translocation types is strictly dependent on the location of theinitiating DNA break and revealed that complex translocations arise via acombination of interchromosomal translocation and template-switching, as well asfrom unstable dicentric intermediates. Template-switching occurred betweensequences on the same chromosome, but was inhibited if the genes weretransferred to different chromosomes. Unstable dicentric translocationscontinuously gave rise to clones with multiple translocations in variouscombinations, reminiscent of intratumor heterogeneity in human cancers. Basesubstitutions and evidence of DNA slippage near rearrangement breakpointsrevealed that translocation formation can be accompanied by point mutations, andtheir presence in different translocation types within the same clone providesevidence that some of the different translocation types are derived from eachother rather than being formed de novo. These findings provideinsight into eukaryotic genome instability, especially the formation oftranslocations and the sources of intraclonal heterogeneity, both of which areoften associated with human cancers.