Widespread alternative and aberrant splicing revealed by lariat sequencing.
Widespread alternative and aberrant splicing revealed by lariat sequencing.
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DOI：
10.1093/nar/gkv763
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发表时间：
2015-09-30
影响因子：
14.9
通讯作者：
Pleiss JA
中科院分区：
文献类型：
--
作者：
Stepankiw N;Raghavan M;Fogarty EA;Grimson A;Pleiss JA
选择性剪接是真核基因结构的一个重要而古老的特征，它的存在可能促进了真核蛋白质组的扩增。在这里，我们使用内含子套索测序来生成庞氏裂殖酵母的剪接事件的全面概况，裂殖酵母是具有哺乳动物样剪接位点简并的最简单的生物之一。我们揭示了前所未有的选择性剪接水平，包括超过一半的注释内含子的选择性剪接位点选择，数百个新的外显子跳过事件，以及数千个新的内含子。此外，这些事件的发生频率远远高于先前的估计，选择性剪接位点的平均激活频率为∼标准位点的3%。虽然部分替代位点在相关物种中是保守的，这意味着功能潜力，但大多数都不是可检测到的保守。有趣的是，异常剪接率与表达水平成反比，低表达的基因更容易发生错误剪接。虽然我们用RNAseq验证了许多事件，但用套索测序发现的替代剪接的比例要大得多，我们将这种差异归因于异常剪接转录本的优先衰退。综上所述，这些数据表明，剪接体的保真度远低于之前所认识的水平，突显了选择性剪接在产生新基因结构方面的潜在贡献。
Alternative splicing is an important and ancient feature of eukaryotic gene structure, the existence of which has likely facilitated eukaryotic proteome expansions. Here, we have used intron lariat sequencing to generate a comprehensive profile of splicing events in Schizosaccharomyces pombe, amongst the simplest organisms that possess mammalian-like splice site degeneracy. We reveal an unprecedented level of alternative splicing, including alternative splice site selection for over half of all annotated introns, hundreds of novel exon-skipping events, and thousands of novel introns. Moreover, the frequency of these events is far higher than previous estimates, with alternative splice sites on average activated at ∼3% the rate of canonical sites. Although a subset of alternative sites are conserved in related species, implying functional potential, the majority are not detectably conserved. Interestingly, the rate of aberrant splicing is inversely related to expression level, with lowly expressed genes more prone to erroneous splicing. Although we validate many events with RNAseq, the proportion of alternative splicing discovered with lariat sequencing is far greater, a difference we attribute to preferential decay of aberrantly spliced transcripts. Together, these data suggest the spliceosome possesses far lower fidelity than previously appreciated, highlighting the potential contributions of alternative splicing in generating novel gene structures.