Department of Metabolism, Digestion and Reproduction, Institute of Reproductive and Developmental Biology, Imperial College London, London, UK.
Faculty of Medicine, University of Southampton, Southampton, UK.
RNA Biol. 2022;19(1):256-265. doi: 10.1080/15476286.2021.2024031. Epub 2021 Dec 31.
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.
剪接位点、辅助剪接元件和剪接机制的突变导致了广泛的遗传疾病。在这里，我们报告说，许多剪接突变的复杂影响可以从背景剪接信息中预测，重点是 BRCA1、BRCA2 和 DMD。背景剪接源于很少使用的背景剪接位点之间的低水平剪接，以及内含子剪接位点之间的低水平外显子跳跃。我们展示了如何从剪接 RNA 的 Snaptron 数据库中下载这些信息，然后将其与人类剪接位点突变数据库进行比较。我们报告说，在内含子剪接位点的失活突变中，在超过 90%的情况下，非突变的伴侣剪接位点与已知的背景剪接位点剪接，在绝大多数情况下与最强的背景剪接位点剪接。因此，背景剪接信息可以有效地预测剪接位点突变的影响，包括隐蔽剪接激活和单个或多个外显子跳跃。此外，新生剪接位点和涉及假外显子形成、递归剪接和癌症中异常剪接的剪接位点与背景剪接位点有 90%的匹配，因此可以确定背景剪接的增强导致了广泛的剪接异常。我们还讨论了如何利用背景剪接信息识别可能被反义寡核苷酸（ASO）靶向的隐蔽剪接位点，以及如何指示旨在诱导单个外显子跳跃的 ASO 可能产生的多个外显子跳跃副作用。
