Marquez Yamile, Höpfler Markus, Ayatollahi Zahra, Barta Andrea, Kalyna Maria
Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria;
Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria; Department of Applied Genetics and Cell Biology, BOKU - University of Natural Resources and Life Sciences, Vienna A-1190, Austria.
Genome Res. 2015 Jul;25(7):995-1007. doi: 10.1101/gr.186585.114. Epub 2015 May 1.
Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also identify such AS events in human and use these two sets to analyse their features, regulation, functional impact, and evolutionary origin. As these events involve introns with features of both introns and protein-coding exons, we name them exitrons (exonic introns). Though exitrons were detected as a subset of retained introns, they are clearly distinguishable, and their splicing results in transcripts with different fates. About half of the 1002 Arabidopsis and 923 human exitrons have sizes of multiples of 3 nucleotides (nt). Splicing of these exitrons results in internally deleted proteins and affects protein domains, disordered regions, and various post-translational modification sites, thus broadly impacting protein function. Exitron splicing is regulated across tissues, in response to stress and in carcinogenesis. Intriguingly, annotated intronless genes can be also alternatively spliced via exitron usage. We demonstrate that at least some exitrons originate from ancestral coding exons. Based on our findings, we propose a "splicing memory" hypothesis whereby upon intron loss imprints of former exon borders defined by vestigial splicing regulatory elements could drive the evolution of exitron splicing. Altogether, our studies show that exitron splicing is a conserved strategy for increasing proteome plasticity in plants and animals, complementing the repertoire of AS events.
可变剪接（Alternative splicing，AS）使转录组和蛋白质组多样化，被广泛认为是调节基因表达的关键机制。此前，在对拟南芥内含子保留事件的分析中，我们在注释的蛋白质编码外显子内部发现了异常的可变剪接事件。在此，我们也在人类中鉴定出此类可变剪接事件，并利用这两组数据来分析它们的特征、调控、功能影响及进化起源。由于这些事件涉及具有内含子和蛋白质编码外显子特征的内含子，我们将它们命名为外显子内内含子（exitrons）。尽管外显子内内含子被检测为保留内含子的一个子集，但它们明显可区分，并且其剪接会产生具有不同命运的转录本。在1002个拟南芥和923个人类外显子内内含子中，约一半的长度为3个核苷酸（nt）的倍数。这些外显子内内含子的剪接会导致蛋白质内部缺失，并影响蛋白质结构域、无序区域和各种翻译后修饰位点，从而广泛影响蛋白质功能。外显子内内含子的剪接在不同组织中受到调控，对应激和癌症发生有响应。有趣的是，注释的无内含子基因也可以通过外显子内内含子的使用进行可变剪接。我们证明至少一些外显子内内含子起源于祖先编码外显子。基于我们的发现，我们提出了一个“剪接记忆”假说，即在内含子丢失时，由残留剪接调控元件定义的前外显子边界印记可能驱动外显子内内含子剪接的进化。总之，我们的研究表明，外显子内内含子剪接是动植物中增加蛋白质组可塑性的一种保守策略，补充了可变剪接事件的库。
