Genome Wide Manipulation of Transcription by CRISPR-Cas9 Transcription Factors in Saccharomyces cerevisiae

Bacterial type II CRISPR-Cas9 systems have been widely adapted for RNA-guided genome editing and transcription regulation in eukaryotic cells. We have optimized different activator and repressor fusions, and assessed the effects of guide position, to optimize Cas9-mediated transcriptional regulation in yeast. Using these data we developed a computational method that uses published data to select guides that activate or repress genes with superior specificity and potency. As a proof of concept we activated and repressed several known drug targets, investigated the effects of transcriptional changes on the protein-protein interaction network, and investigated the effects of guides targeting bidirectional promoters. We are currently applying these methods to answer a variety of questions on a genome-wide scale using competitive assays involving pools of strains expressing individual guide RNAs.