Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing
Altered splicing is a frequent mechanism by which genetic variants cause disease. However, the regulatory architecture of human exons remains poorly understood, making the therapeutic modulation of splicing in disease challenging. Here we show that deep indel mutagenesis (DIM) provides an efficient strategy to chart the regulatory landscape of human exons and to rapidly identify effective splice-modulating oligonucleotides. DIM defines a minimal exon length, uncovers a mechanism for the evolutionary birth of unusually short microexons and the repression of transmembrane domain-encoding exons, and reveals a checkerboard architecture of sequential enhancers and silencers in a model alternatively spliced exon. Accurate prediction of the effects of deletions using deep learning provides a resource, DANGO, that maps the splicing regulatory landscape of all human exons and predicts effective splice-altering antisense oligonucleotides genome-wide. Overall design: Deep insertion-deletion mutagenesis of a model human alternatively-spliced exon (FAS exon 6).