Genetics and Molecular Biology Department, Biology Institute, State University of Campinas, 13083-862 Campinas, SP, Brazil.
Brief Bioinform. 2010 Mar;11(2):198-209. doi: 10.1093/bib/bbp041. Epub 2009 Dec 2.
Trans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, 'Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence?', we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent study has reported that trans-splicing may occur not only in malignant tissues, but in normal tissues as well. Our methodology can be applied to 5'-UTR, coding sequences and 3'-UTR in order to find new candidates for a posteriori experimental confirmation.
转剪接是线虫和动基体生物中的一种常见现象，也在其他生物体中有所报道，包括人类。到目前为止，所有在计算机上寻找人类中转剪接证据的策略都要求候选序列遵循一致的剪接位点规则（核酶介导的机制）。然而，这一标准并不符合人类最佳实验证据，除了一个单一的例子外，这些证据都不遵循规范的剪接位点。此外，最近的研究结果描述了一种新的替代 tRNA 介导的转剪接机制，该机制不依赖于核酶机制。为了回答“在序列数据库中是否存在混合 mRNA，其特征类似于人类最佳实验证据？”这一问题，我们开发了一种方法，成功鉴定了 16 种可能是染色体间转剪接实例的混合 mRNA。每个杂交 mRNA 都是由一个转剪接区（TSR）组成的，该转剪接区成功地映射到已知基因或人类内源性逆转录病毒（HERV-K）转录本上，这些转录本支持它们的转录。这些混合 mRNA 的存在表明，转剪接可能比人们想象的更为普遍。此外，非规范的剪接位点模式表明，不常见的剪接位点可能在特殊条件下发生，或者涉及替代的转剪接机制。最后，我们的候选者来自正常组织，最近的一项研究报告称，转剪接不仅可能发生在恶性组织中，也可能发生在正常组织中。我们的方法可以应用于 5'UTR、编码序列和 3'UTR，以找到新的候选者，供后续的实验验证。
