Transcriptome sequencing suggests that pre-mRNA splicing counteracts premature intronic polyadenylation

Alternative splicing (AS) and alternative polyadenylation (APA) are two crucial steps in the post-transcriptional regulation of eukaryotic gene expression. Protocols capturing and sequencing RNA 3’-ends have uncovered widespread intronic polyadenylation (IPA) in physiological and disease conditions, where it is currently attributed to stochastic variations in pre-mRNA processing. Here, we took advantage of the massive amount of RNA-seq data generated by the Genotype Tissue Expression project (GTEx) to simultaneously identify and match tissue-specific usage of intronic polyadenylation sites with tissue-specific splicing. A combination of computational methods including the analysis of short reads with non-templated adenines confirmed highly abundant IPA events. Among them, composite terminal exons and skipped terminal exons expectedly correlate with splicing, however we also observed a considerable fraction of IPA events that lack AS support and can be attributed to lariat polyadenylation (LPA). We hypothesize that LPA originates from a dynamic coupling between APA and AS, in which the spliceosome removes an intron after CPA have already occurred in it. Taken together, these results suggest that co-transcriptional pre-mRNA splicing could serve as a natural mechanism of suppression of premature transcription termination.