title: Identification of Chemical-Genetic Interactions via Parallel Analysis of Barcoded Yeast Strains.
abstract: The Yeast Knockout Collection is a complete set of gene deletion strains for the budding yeast, Saccharomyces cerevisiae In each strain, one of approximately 6000 open-reading frames is replaced with a dominant selectable marker flanked by two DNA barcodes. These barcodes, which are unique to each gene, allow the growth of thousands of strains to be individually measured from a single pooled culture. The collection, and other resources that followed, has ushered in a new era in chemical biology, enabling unbiased and systematic identification of chemical-genetic interactions (CGIs) with remarkable ease. CGIs link bioactive compounds to biological processes, and hence can reveal the mechanism of action of growth-inhibitory compounds in vivo, including those of antifungal, antibiotic, and anticancer drugs. The chemogenomic profiling method described here measures the sensitivity induced in yeast heterozygous and homozygous deletion strains in the presence of a chemical inhibitor of growth (termed haploinsufficiency profiling and homozygous profiling, respectively, or HIPHOP). The protocol is both scalable and amenable to automation. After competitive growth of yeast knockout collection cultures, with and without chemical inhibitors, CGIs can be identified and quantified using either array- or sequencing-based approaches as described here.
authors: Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304;
authors: Sundari
authors: S
authors: Suresh
authors: Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304;
authors: Ulrich
authors: U
authors: Schlecht
authors: Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304;
authors: Weihong
authors: W
authors: Xu
authors: Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304;
authors: Molly
authors: M
authors: Miranda
authors: Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304;
authors: Ronald W
authors: RW
authors: Davis
authors: Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
authors: Corey
authors: C
authors: Nislow
authors: Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
authors: Guri
authors: G
authors: Giaever
authors: Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304;
authors: Robert P
authors: RP
authors: St Onge
mesh_terms: D000935:Antifungal Agents / Q000494:pharmacology*; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D017353:Gene Deletion; D015723:Gene Library; D005800:Genes, Fungal; D005820:Genetic Testing; D006131:Growth Inhibitors / Q000494:pharmacology*; D012441:Saccharomyces cerevisiae / Q000187:drug effects* / Q000235:genetics / Q000254:growth & development*
chemical_list: D000935:Antifungal Agents; D006131:Growth Inhibitors