A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast

BackgroundCRISPR/Cas9-mediated transcriptional interference (CRISPRi) enables programmable gene knock-down, yielding loss-of-function phenotypes for nearly any gene. Effective, inducible CRISPRi has been demonstrated in budding yeast, and genome-scale guide libraries enable systematic, genome-wide genetic analysis.ResultsWe present a comprehensive yeast CRISPRi library, based on empirical design rules, containing 10 distinct guides for most genes. Competitive growth after pooled transformation revealed strong fitness defects for most essential genes, verifying that the library provides comprehensive genome coverage. We used the relative growth defects caused by different guides targeting essential genes to further refine yeast CRISPRi design rules. In order to obtain more accurate and robust guide abundance measurements in pooled screens, we link guides with random nucleotide barcodes and carry out linear amplification by in vitro transcription.ConclusionsTaken together, we demonstrate a broadly useful platform for comprehensive, high-precision CRISPRi screening in yeast.

Automated summary

This study introduces a comprehensive yeast CRISPRi library based on empirical design rules, which has been validated to provide comprehensive genome coverage through competitive growth experiments. The fitness defects of essential genes caused by different guides targeting them were used to refine yeast CRISPRi design rules, and guide abundance measurements in pooled screens were improved by linking guides with random nucleotide barcodes and carrying out linear amplification.