Effect of high copy retrotransposon insertions on yeast genome stability

Abstract

Retrotransposons are dispersed sequences that are able to copy themselves and reinsert throughout the genome. These mobile elements display preferences for the positions in the genome at which they insert and over 90% of retrotransposon insertions in Saccharomyces cerevisiae are within 2 kb upstream of tRNA genes. The yeast genome is comprised of only 3% retrotransposons as compared with 44% in humans; to use the yeast genome as a model to study insertion preferences in retrotransposon‐dense genomes, Retrotransposon Overdose (RO) strains were made by inserting a large number of Ty1 retrotransposons within the yeast genome. Our first goal was to analyze the genome sequences of these strains to determine the sites of Ty1 insertion. Analysis of the sequenced genomes revealed that as the number of retrotransposons increased, the number of insertions into less preferred target sites increased, including a significant number of insertions within essential genes, which may decrease either the quantity or size of transcription products. Our second goal was to analyze the targeting of Ty1 retrotransposons once all preferred sites in the genome were saturated. We have found that pairs of retrotransposons are frequently formed. Retrotransposons that are adjacent to each other in the genome are hypothesized to form fragile sites, which are sites of chromosome breakage that are associated with tumor formation in humans. RO strains contain numerous pairs of retrotransposons as well as higher order Ty1 multimers, despite the genome instability that might result from these retrotransposon arrangements.