Yeast genetics on microarrays

The recent completion of the set of “molecular-barcoded” yeast knockout mutants (referred to as YKO mutants) of essentially all ORFs in Saccharomyces cerevisiae by the Saccharomyces genome deletion project permits parallel quantitative functional profiling of all YKO mutants using high-density oligonucleotide arrays. Each YKO mutant was assigned two unique “molecular barcodes”-20-mer oligonucleotides as strain identifiers. The “molecular barcode”, serving as the matchmaker, marries the awesome power of yeast genetics and high throughput capabilities of microarray technology.; Many of the ∼4860 non-essential yeast genes still have unknown functions. Genome-wide synthetic lethality provides a means to reveal the functions of these genes and to study their interrelationships. Synthetic lethality describes a phenomenon in which the combination of two separately non-essential mutations leads to lethality. We developed a microarray-based synthetic lethality screen in which a “query mutation” of interest was introduced into the haploid YKO pools to generate a haploid YKO library containing mutation in the “query gene” in combination with each non-essential mutation in the yeast genome. The query mutation was generated by direct transformation of a PCR-generated query construct to disrupt the gene encoding the “query mutation”. The query construct contains a URA3 marker that replaces part or all of the query gene, and 2 kb genomic fragments flanking the query gene to facilitate integrative transformation. Such microarray-based synthetic lethality screen was performed for SGS1, a member of the RecQ-like DNA helicase family. Known synthetic fitness interactors for SGS1 as well as new synthetic fitness interactors for SGS1, such as RNH35, YLR154C and HST3 were identified.; A genome-wide microarray-based genetic screen was also developed to identify components of the nonhomologous end-joining (NHEJ) pathway. Known components of the pathway as well as a new gene, NEJ1, were identified. Nej1 protein interacts with the N-terminus of LIF1/XRCC4, a recently recognized “guardian of the genome” against cancer.; We showed that functional profiling is efficient, sensitive and quantitative, and can be applied on a genome-wide level. As the YKO mutants continue to be screened for additional phenotypes, the functional profiling data can be used to determine the function of every yeast gene and to generate a genetic interaction map for the yeast genome. Since most cellular pathways are highly conserved between yeast and higher eukaryotes, results from genome-wide analyses of yeast will significantly advance our understanding of biological processes and the basis of human diseases.