Background splicing as a predictor of aberrant splicing in genetic disease

Abstract

Mutations of splice sites, auxiliary splicing elements and the splicing machinery cause a wide range of genetic disease. Here we report that many of the complex effects of splicing mutations can be predicted from background splicing information, with emphasis on BRCA1, BRCA2 and DMD. Background splicing arises from very low level splicing between rarely used background splice sites and from low-level exon skipping between intron splice sites. We show how this information can be downloaded from the Snaptron database of spliced RNA, which we then compared with databases of human splice site mutations. We report that inactivating mutations of intron splice sites typically caused the non-mutated partner splice site to splice to a known background splice site in over 90% of cases and to the strongest background splice site in the large majority of cases. Consequently, background splicing information can usefully predict the effects of splice site mutations, which include cryptic splice activation and single or multiple exon skipping. In addition, de novo splice sites and splice sites involved in pseudoexon formation, recursive splicing and aberrant splicing in cancer show a 90% match to background splice sites, so establishing that the enhancement of background splicing causes a wide range of splicing aberrations. We also discuss how background splicing information can identify cryptic splice sites that might be usefully targeted by antisense oligonucleotides (ASOs) and how it might indicate possible multiple exon skipping side effects of ASOs designed to induce single exon skipping.

Treatability of the KMT2-Associated Neurodevelopmental Disorders Using Antisense Oligonucleotide-Based Treatments

“…Their inclusion in the transcript will lead to nonsense-mediated decay, as the poison exon contains a premature termination codon [102]. In recent years, there has been an increase in the identification of such transcripts and background splicing events in general, and more of these events may be uncovered in the future [103]. Forgoing the nonproductive AS events through the use of ssASOs generally leads to higher levels of protein-coding transcripts (Figure 4).…”

Alternative RNA splicing in cancer: what about adult T-cell leukemia?

“…SFs such as SR (serine/arginine-rich) proteins and hnRNPs (heterogeneous nuclear ribonucleoproteins) are RNA-binding proteins and are considered as enhancers ( 50 , 51 ) and silencers ( 52 , 53 ) respectively since SR proteins are typically recruited to ISEs and ESEs (respectively intronic & exonic splicing enhancers) while hnRNPs usually bind to ISSs and ESSs ( Figure 3B ). Disruptions of the splicing mechanism and regulation have been documented in many pathologies, ranging from genetic ( 54 – 56 ) and autoimmune ( 57 , 58 ) diseases, to cancers; the latter being the center of discussion in the following sections.…”