Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping

Abstract

The recent identification of compounds that interact the spliceosome (sudemycins, spliceostatin A, and meamycin) indicate that these molecules modulate alternative splicing via SF3B1 inhibition. Through whole transcriptome sequencing, we have demonstrated that treatment of Rh18 cells with sudemycin leads to exon skipping as the predominant aberrant splicing event. This was also observed following reanalysis of published RNAseq datasets derived from Hela cells after spliceostatin A exposure. These results are in contrast to previous reports that indicate that intron retention was the major consequence of SF3B1 inhibition. Analysis of the exon junctions up-regulated by these small molecules indicated that these sequences were absent in annotated human genes, suggesting that aberrant splicing events yielded novel RNA transcripts. Despite the fact that aberrant exon skipping was observed in both Rh18 and Hela cells, the number of commonly differentially expressed genes was surprisingly small. Interestingly, the length of preferred downstream exons was significantly longer than the skipped exons, although there was no bias towards the generation of out-of-frame mRNAs. However, genes involved in nonsense mediated decay and RNAs encoding proteins involved in the splicing process were enriched in both datasets. Our findings establish the fundamental mechanism by which SF3B1 inhibition modulates pre-mRNA splicing.