Systematic profiling of cellular phenotypes with spotted cell microarrays reveals new mating pheromone response genes

Abstract

We describe a technology for measuring cell morphology and subcellular localization phenotypes—spotted cell microarrays—applied to a model system in which yeast change morphology in response to mating pheromone. Cells are robotically printed on microscope slides, stained for subcellular features, then imaged via automated, high‐throughput microscopy, allowing systematic phenotypic characterization of thousands of genetically distinct cells in parallel. We constructed cell microarrays from ~4,800 yeast gene deletion mutants and assayed each gene's role in determining cellular morphology. From arrays constructed after treating the strains with mating pheromone, we identified 30 genes whose deletion disrupted pheromone response, independently validating the genes’ involvement through growth assays. Half of the known and expected pheromone response genes were recapitulated, including the MAP kinase signal transduction cascade; 15 new genes are implicated in the pathway, including genes from vesicular protein sorting and membrane structure; additional genes were implicated in shmoo morphology. Besides morphology assays, we expect spotted cell microarrays will be valuable for high‐throughput in situ hybridization and immunoassays, enabling a new class of genetic assays based on cell imaging.