When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis
When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis
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DOI：
10.1002/bies.20749
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发表时间：
2008-06-01
期刊：
影响因子：
4
通讯作者：
Irimia, Manuel
中科院分区：
文献类型：
--
作者：
Roy, Scott William;Irimia, Manuel
基因和内含子的预测对于精确推断基因组进化是必不可少的。最近，两项全基因组研究寻找人类最近的内含子增益，得出了非常不同的结论：自早期哺乳动物进化以来完全没有内含子增益，或者通过重复区域的基因组复制产生大量内含子。我们讨论了一个可能的解释：“模板转换”，逆转录酶可能会创建人为的剪接样事件在制备的cDNA/EST库，可能会导致复杂的搜索新获得的内含子中的重复区域的未被充分认识的现象。我们报告了大量的明显的模板转换转录序列的内含子穷人原生生物阴道毛滴虫和贾第鞭毛虫。这篇文章的补充材料可以在BioEssays网站上找到（http：//www.mrw.interscience. wiley.com/jpages/0265-9247/suppmat/index.htmi).
Gene and intron prediction are essential for accurate inferences about genome evolution. Recently, two genome-wide studies searched for recent intron gains in humans, reaching very different conclusions: either of a complete absence of intron gain since early mammalian evolution, or of creation of numerous introns by genomic duplication in repetitive regions. We discuss one possible explanation: the underappreciated phenomenon of "template switching", by which reverse transcriptase may create artifactual splicing-like events in the preparation of cDNA/EST libraries, may cause complications in searches for newly gained introns in repetitive regions. We report large numbers of apparent template switching in transcript sequences from the intron-poor protists Trichomonas vaginalis and Giardia lamblia. Supplementary material for this article can be found on the BioEssays website (http://www.mrw.interscience. wiley.com/jpages/0265-9247/suppmat/index.htmi).