Improved discovery of genetic interactions using CRISPRiSeq across multiple environments
Abstract
Large-scale Genetic Interaction (GI) screens in yeast have been invaluable for our understanding of molecular systems biology, and for characterizing novel gene function. Due in part to the high costs and long experiment times required, a preponderance of GI data has been generated in a single environmental condition. However, an unknown fraction of GIs may be specific to other conditions. Here, we developed a pooled-growth CRISPRi-based sequencing assay for genetic interactions, CRISPRiSeq, that increases throughput such that GIs can be easily assayed across multiple growth conditions. We assayed the fitness of ~17,000 strains encompassing ~7,700 pairwise interactions in five conditions and found that the additional conditions increased the number of GIs detected nearly 3-fold over the number detected in rich media alone In addition, we found that condition-specific GIs are prevalent and improved the power to functionally classify genes. Finally, we found new links during respiratory growth between members of the Ras-nutrient sensing pathway and both the COG complex and a gene of unknown function. Our results highlight the potential of conditional GI screens to improve our understanding of cellular genetic networks.
- Received November 19, 2018.
- Accepted February 13, 2019.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International license), as described at http://creativecommons.org/licenses/by/4.0/.
