Epithelial-Mesenchymal Transition (EMT) is a tightly regulated cellular process that involves profound phenotypic change in cells critical for embryonic development, tissue repair, and cancer progression. The RNA binding protein Quaking (QKI) regulates widespread changes in Alternative Splicing (AS) during EMT that directly impact cellular processes such as cell migration and invasion. However, despite the importance of AS in EMT, the functions of most alternatively spliced proteins are unknown due to challenges in manipulating AS in a scalable manner. To address this gap in understanding, we have developed RNA-targeting CRISPR technology to precisely manipulate alternative splicing of individual genes and study their functions in high-throughput screening formats. We are utilizing catalytically inactive “dead” CasRx (dCasRx) that binds to target RNA sequences, blocks the access to splice machinery and causes exon skipping. In parallel, we have developed a dCasRx fusion protein with the RNA binding protein QKI to facilitate exon inclusion when targeted to QKI biding sites. As proof of principle, we have used dCasRx to effectively block the inclusion of exon 3 in the transcription factor NFYA and enhances cell proliferation. This strategy will be applied with pool single cell screening, to assess the functional consequences of hundreds of individual splicing alterations on cell proliferation, migration, EMT, and drug resistance.