Hotspot ofde novotelomere addition stabilizes linear amplicons in yeast grown in sulfate-limiting conditions

Abstract

AbstractEvolution is driven by the accumulation of competing mutations that influence survival. A broad form of genetic variation is the amplification or deletion of DNA (≥50 bp) referred to as copy number variation. In humans, copy number variation may be inconsequential, contribute to minor phenotypic differences, or cause conditions such as birth defects, neurodevelopmental disorders, and cancers. To identify mechanisms that drive copy number variation, we monitored the experimental evolution ofSaccharomyces cerevisiaepopulations grown under sulfate-limiting conditions. Cells with increased copy number of the geneSUL1, which encodes a primary sulfate transporter, exhibit a fitness advantage. Previously, we reported interstitial inverted triplications ofSUL1as the dominant rearrangement in a haploid population. Here, in a diploid population, we find instead that small linear fragments containingSUL1form and are sustained over several generations. Many of the linear fragments are stabilized byde novotelomere addition within a telomere-like sequence nearSUL1(within theSNF5gene). Using an assay that monitors telomerase action following an induced chromosome break, we show that this region acts as a hotspot ofde novotelomere addition and that required sequences map to a region of <250 base pairs. Consistent with previous work showing that association of the telomere-binding protein Cdc13 with internal sequences stimulates telomerase recruitment, mutation of a four-nucleotide motif predicted to associate with Cdc13 abolishesde novotelomere addition. Our study suggests that internal telomere-like sequences that stimulatede novotelomere addition can contribute to adaptation by promoting genomic plasticity.