Roy Scott William
Department of Biology, San Francisco State University , San Francisco , CA , United States.
PeerJ. 2017 Jan 5;5:e2861. doi: 10.7717/peerj.2861. eCollection 2017.
The mechanisms by which DNA sequences are expressed is the central preoccupation of molecular genetics. Recently, ourselves and others reported that in the diplomonad protist , the coding regions of several mRNAs are produced by ligation of independent RNA species expressed from distinct genomic loci. Such trans-splicing of introns was found to affect nearly as many genes in this organism as does classical cis-splicing of introns. These findings raised questions about the incidence of intron trans-splicing both across the transcriptome and across diplomonad diversity in general, however a dearth of transcriptomic data at the time prohibited systematic study of these questions.
I leverage newly available transcriptomic data from and the related diplomonad to search for trans-spliced introns. My computational pipeline recovers all four previously reported trans-spliced introns in , suggesting good sensitivity.
Scrutiny of thousands of potential cases revealed only a single additional trans-spliced intron in , in the p68 helicase gene, and no cases in . The p68 intron differs from the previously reported trans-spliced introns in its high degree of streamlining: the core features of trans-spliced introns are closely packed together, revealing striking economy in the implementation of a seemingly inherently uneconomical molecular mechanism.
These results serve to circumscribe the role of trans-splicing in diplomonads both in terms of the number of genes effected and taxonomically. Future work should focus on the molecular mechanisms, evolutionary origins and phenotypic implications of this intriguing phenomenon.
DNA序列的表达机制是分子遗传学的核心关注点。最近，我们和其他人报道，在双滴虫原生生物中，几种mRNA的编码区是由从不同基因组位点表达的独立RNA物种连接产生的。发现这种内含子的反式剪接在该生物体中影响的基因数量几乎与经典的内含子顺式剪接一样多。然而，这些发现引发了关于内含子反式剪接在整个转录组以及整个双滴虫多样性中的发生率的问题，不过当时转录组数据的匮乏阻碍了对这些问题的系统研究。
我利用来自[具体物种]和相关双滴虫新获得的转录组数据来搜索反式剪接的内含子。我的计算流程找回了[具体物种]中先前报道的所有四个反式剪接的内含子，表明具有良好的灵敏度。
对数千个潜在案例的仔细审查仅在[具体物种]的p68解旋酶基因中发现了另外一个反式剪接的内含子，而在[另一具体物种]中未发现此类案例。p68内含子与先前报道的反式剪接内含子的不同之处在于其高度精简：[具体物种]反式剪接内含子的核心特征紧密排列在一起，揭示了在实施一种看似本质上不经济的分子机制时的惊人经济性。
这些结果有助于从受影响的基因数量和分类学方面界定反式剪接在双滴虫中的作用。未来的工作应集中在这一有趣现象的分子机制、进化起源和表型影响上。
