CRISPRi-TnSeq: A tool for genetic interaction mapping

Genetic interaction networks highlight the mechanistic and functional connections between genes, which can be leveraged to identify drug targets, gene functions, regulatory networks, and to fill the gaps in pathways. Transposon sequencing (TnSeq) can be used to map genetic interaction networks by constructing transposon mutant libraries in the background of a deletion mutant, however such networks lack essential genes, since knockout mutants of essential genes are inviable. We develop CRISPRi-TnSeq, a genome-wide tool that maps bacterial genetic interactions including essential genes in high-throughput. We performed TnSeq analysis (van Opijnen et al. 2009) of 13 CRISPRi strains of Streptococcus pneumoniae D39 with and without knockdown of the target gene and in the absence and presence of target specific antibiotic. This project content sequencing files used to measure the abundance of transposon insertion mutants to determine the fitness-importance of individual nonessential genes in the given condition. The fitness change due to the CRISPRi target knockdown identify genetic interactions between target and corresponding nonessential genes.