Splicing-dependent transcriptional activation

Abstract

Transcription and splicing are intrinsically coupled. Transcription dynamics regulate splicing, and splicing feeds back to transcription initiation to jointly determine gene expression profiles. A recently described phenomenon called exon-mediated activation of transcription starts (EMATS) shows that splicing of internal exons can regulate transcription initiation and activate cryptic promoters. Here, we present the first complete catalog of human EMATS genes that have a weak alternative promoter located upstream and proximate to an efficiently spliced internal skipped exon. We found that EMATS genes are associated with Mendelian genetic diseases --specifically intellectual development disorders, cardiomyopathy, and immunodeficiency-- and provide a list of EMATS genes with pathological variants. EMATS was originally described as a natural mechanism used during evolution to fine-tune gene expression through punctual genomic mutations that affect splicing. Here, we show that EMATS can be used to manipulate gene expression with therapeutic purposes. We constructed stable cell lines expressing a splicing reporter based on the alternative splicing of exon 7 of SMN2 gene under the regulation of different promoters. Using a small molecule (Risdiplam) and an antisense oligonucleotide (ASO) modeled after Spinraza, we promoted the inclusion of SMN2 exon 7 which triggered an increase in gene expression up to 40-folds by activating transcription initiation. We observed the strongest effects in reporters under the regulation of weak human promoters, where the highest drug doses dramatically increased exon inclusion. Overall, our findings present evidence to develop the first therapeutic strategy to use EMATS to activate gene expression using small molecules and ASOs that affect splicing.