Evidence of abundant stop codon readthrough in Drosophila and other metazoa
Evidence of abundant stop codon readthrough in Drosophila and other metazoa
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DOI：
10.1101/gr.119974.110
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发表时间：
2011-12-01
期刊：
影响因子：
7
通讯作者：
Kellis, Manolis
中科院分区：
文献类型：
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作者：
Jungreis, Irwin;Lin, Michael F.;Kellis, Manolis
虽然翻译终止密码子通读现象经常被病毒基因组使用，但在真核生物基因中仅在少数情况下被观察到。我们之前利用比较基因组学证据识别了12种果蝇的蛋白质编码区域，并表明对于149个基因，终止密码子之后的开放阅读框具有蛋白质编码保守特征，这暗示终止密码子通读在果蝇中可能很常见。我们借助来自modENCODE项目的深度RNA序列数据、一种用于检测蛋白质编码区域的改进的高分辨率比较基因组学指标、来自其他物种的比较序列信息以及定向实验证据，重新审视这一观察结果。我们报道了一组扩大的283个通读候选基因，包括16个双通读候选基因；对这些基因进行了人工筛选，以排除诸如A到I编辑、可变剪接、双顺反子翻译和硒代半胱氨酸掺入等其他可能性。我们报道了使用绿色荧光蛋白标记和质谱法对几个通读区域进行翻译的实验证据。我们发现通读候选基因集在长度、组成、保守性、终止密码子上下文以及在某些情况下的保守茎环等方面与其他基因不同，这为通读调控和潜在机制提供了线索。最后，我们将研究扩展到果蝇以外，并发现在其他几种昆虫物种和一种甲壳类动物中存在大量通读的证据，以及在线虫和人类中的几个通读候选基因，这表明具有功能重要性的翻译终止密码子通读在后生动物中的普遍性比之前所认识到的要高得多。
While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions in 12 species of Drosophila and showed that for 149 genes, the open reading frame following the stop codon has a protein-coding conservation signature, hinting that stop codon readthrough might be common in Drosophila. We return to this observation armed with deep RNA sequence data from the modENCODE project, an improved higher-resolution comparative genomics metric for detecting protein-coding regions, comparative sequence information from additional species, and directed experimental evidence. We report an expanded set of 283 readthrough candidates, including 16 double-readthrough candidates; these were manually curated to rule out alternatives such as A-to-I editing, alternative splicing, dicistronic translation, and selenocysteine incorporation. We report experimental evidence of translation using GFP tagging and mass spectrometry for several readthrough regions. We find that the set of readthrough candidates differs from other genes in length, composition, conservation, stop codon context, and in some cases, conserved stem-loops, providing clues about readthrough regulation and potential mechanisms. Lastly, we expand our studies beyond Drosophila and find evidence of abundant readthrough in several other insect species and one crustacean, and several readthrough candidates in nematode and human, suggesting that functionally important translational stop codon readthrough is significantly more prevalent in Metazoa than previously recognized.