Engineering artificial splicing factors with designed specificities

Abstract

The majority of human genes undergo alternative splicing to produce multiple isoforms with distinct functions. This process is tightly regulated by trans‐acting splicing factors that bind specifically to exons or introns to promote or inhibit their splicing. Here we report the engineering of novel artificial splicing factors that can be designed to specifically modulate alternative splicing of target genes. Sequence‐specific RNA‐binding domains of human Pumilio1 were fused with splicing regulatory motifs to produce artificial splicing factors with diverse activities in regulating different types of alternative splicing in several reporter systems. Because disruption of splicing regulation is closely associated with various human diseases, a new method to modulate disease‐associated splicing events provides therapeutic potential. We demonstrated such potential by engineering a splicing factor to modulate alternative splicing of the endogenous Bcl‐x gene, a target of anti‐cancer therapy. This engineered splicing factor shifted splicing toward the pro‐apoptotic Bcl‐xS isoform, promoted apoptosis, and increased chemosensitivity of several cancer cell lines to common anti‐tumor drugs. The ability to design the RNA sequence specificity of Pumilio1 permits creation of artificial splicing factors that can target virtually any pre‐mRNA.