Widespread 3′ UTR splicing regulates expression of oncogene transcripts through multiple mechanisms

Splicing in 3′ untranslated regions (3′ UTRs) is generally expected to elicit degradation via nonsense-mediated decay (NMD) due to the presence of an exon junction complex (EJC) downstream of the stop codon. However, 3′ UTR intron (3UI)-containing transcripts are widespread and highly expressed in both normal tissues and cancers. We present a transcriptome assembly built from 7897 solid tumour and normal samples from The Cancer Genome Atlas. We identify thousands of 3UI-containing transcripts, many expressed across multiple cancer types. Expression of NMD component UPF1 negatively correlates with 3UI-splicing in normal, but not colon cancer, samples. 3UIs found exclusively within 3′ UTRs (bona-fide 3UIs) are not predominantly NMD-sensitizing, unlike introns found in 3′ UTRs due to the presence of an early premature termination codon (PTC). We identify 3UI-splicing that rescues the transcript from NMD. Bona-fide 3UI-transcripts are over-spliced in cancer samples. In colon cancer, differentially-spliced 3UI transcripts are enriched in the Wnt signalling pathway, with CTNNB1 showing the greatest increase in splicing. Manipulating Wnt signalling can further regulate 3UI-splicing of Wnt components. Our results indicate that 3′ UTR splicing is not a rare occurrence and 3UI-splicing can regulate transcript expression in multiple ways, some of which are likely to be EJC-independent.