Analysis of ~10,000 CRISPR interference perturbations in a yeast cross
Authors: Joseph Hale 1; Ilan Goldstein 1; Takeshi Matsui 2,3,4; Martin Mullis 1; Kevin Roy 5,6; Lars Steinmetz 5,6,7; Sasha Levy 2,3,4; Ian Ehrenreich 1
Affiliations: 1) Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; 2) Joint Initiative for Metrology in Biology, Stanford, CA 94305, USA; 3) SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; 4) Department of Genetics, Stanford University, Stanford, CA 94305, USA; 5) Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA; 6) Department of Genetics, Stanford University School of Medicine, Stanford, California, USA; 7) Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
Keywords: Genetic interactions
Genetic perturbations can show different phenotypic effects across individuals due to epistasis with segregating loci. To achieve a broader understanding of the extent and genetic basis of these background effects, we developed a yeast cross amenable to high-throughput integration and efficient phenotyping of CRISPR interference libraries. In our initial experiment, we examined ~200 segregants, each containing a library of ~10,000 gRNAs targeting primarily essential genes. The relative fitnesses of all segregant-gRNA combinations were measured in a common pool using a double-barcode sequencing strategy, with one barcode denoting a segregant genotype and a second barcode denoting a gRNA. While analysis is ongoing, we expect these data will enable a broad, systems-level understanding of how genetic differences among individuals cause background effects.