Genome-scale exon perturbation screens uncover exons critical for cell fitness
Mei‐Sheng Xiao, Arun Prasath Damodaran, Bandana Kumari, Ethan Dickson, Kun Xing, Tyler A. On, Nikhil Parab, Helen E. King, Alexendar R. Perez, Wilfried M. Guiblet, Gerard Duncan, Anney Che, Raj Chari, Þorkell Andrésson, Joana A. Vidigal, Robert J. Weatheritt, Michael Aregger, Thomas Gonatopoulos-Pournatzis
Abstract
CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.