High-resolution genome-wide analysis of irradiated (UV and γ-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events

• Published in: Genetics (Austin) 2012-04, Vol.190 (4), p.1267-1284
• Main Authors: St Charles, Jordan, Hazkani-Covo, Einat, Yin, Yi, Andersen, Sabrina L, Dietrich, Fred S, Greenwell, Patricia W, Malc, Ewa, Mieczkowski, Piotr, Petes, Thomas D
• Format: Article
• Language: English
• Subjects: Chromatids - genetics; Chromatids - radiation effects; Chromosome Mapping; Chromosomes, Fungal - genetics; Chromosomes, Fungal - radiation effects; Crossing Over, Genetic; Deoxyribonucleic acid; Diploidy; DNA; DNA Damage; DNA, Fungal - genetics; Gamma Rays; Genome, Fungal; Genomics; High-Throughput Nucleotide Sequencing; Investigations; Loss of Heterozygosity; Meiosis; Mitosis; Oligonucleotide Array Sequence Analysis - methods; Polymorphism, Single Nucleotide; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - radiation effects; Studies; Ultraviolet radiation; Ultraviolet Rays; Yeast
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1534/genetics.111.137927

In diploid eukaryotes, repair of double-stranded DNA breaks by homologous recombination often leads to loss of heterozygosity (LOH). Most previous studies of mitotic recombination in Saccharomyces cerevisiae have focused on a single chromosome or a single region of one chromosome at which LOH events can be selected. In this study, we used two techniques (single-nucleotide polymorphism microarrays and high-throughput DNA sequencing) to examine genome-wide LOH in a diploid yeast strain at a resolution averaging 1 kb. We examined both selected LOH events on chromosome V and unselected events throughout the genome in untreated cells and in cells treated with either γ-radiation or ultraviolet (UV) radiation. Our analysis shows the following: (1) spontaneous and damage-induced mitotic gene conversion tracts are more than three times larger than meiotic conversion tracts, and conversion tracts associated with crossovers are usually longer and more complex than those unassociated with crossovers; (2) most of the crossovers and conversions reflect the repair of two sister chromatids broken at the same position; and (3) both UV and γ-radiation efficiently induce LOH at doses of radiation that cause no significant loss of viability. Using high-throughput DNA sequencing, we also detected new mutations induced by γ-rays and UV. To our knowledge, our study represents the first high-resolution genome-wide analysis of DNA damage-induced LOH events performed in any eukaryote.