Efficient, specific and combinatorial control of endogenous exon splicing with dCasRx-RBM25

Efficient targeted control of exon splicing is a major goal of functional genomic and therapeutic applications. Guide RNA-directed, deactivated (d)Cas CRISPR enzymes fused to splicing effectors represent a promising strategy due to the flexibility and presumed specificity of these systems. However, efficient, selective, and generalizable activation of targeted endogenous exons using this approach has not been reported. Here, we identify dCasRx-RBM25 as a potent activator of exons by screening over 300 dCasRx splicing factor fusions tethered to splicing reporters. dCasRx-RBM25 also strongly activates splicing of endogenous alternative exons, when recruited to downstream intron sequences using single guide RNAs. In transcriptome wide analyses we observe a high degree of specificity of dCasRx-RBM25 for endogenous exon targeting. We further leverage the guide array-processing activity of dCasRx to simultaneously target multiple endogenous exons for activation and repression by dCasRx-RBM25. Our results pave the way for versatile exon-resolution functional assays and splicing-directed therapeutic applications. This dataset consists of 12 RNA-seq files associated with the manuscript "Efficient, specific and combinatorial control of endogenous exon splicing with dCasRx-RBM25" characterizing the effect of dCasRx-RBM25, RBFOX1N-dCasRx-C, or dCasRx overexpression by co-transfection either with a non-targeting guide RNA, a gRNA targeting MAPT exon 10 for activation, or a gRNA targeting CD46 exon 13 for repression (for dCasRx-RBM25 only) on global gene expression and alternative splicing patterns in HEK293T cells. Each treatment was performed in two biological replicates.