Tan Shengjun, Cardoso-Moreira Margarida, Shi Wenwen, Zhang Dan, Huang Jiawei, Mao Yanan, Jia Hangxing, Zhang Yaqiong, Chen Chunyan, Shao Yi, Leng Liang, Liu Zhonghua, Huang Xun, Long Manyuan, Zhang Yong E
Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
Genome Res. 2016 Dec;26(12):1663-1675. doi: 10.1101/gr.204925.116. Epub 2016 Oct 20.
In a broad range of taxa, genes can duplicate through an RNA intermediate in a process mediated by retrotransposons (retroposition). In mammals, L1 retrotransposons drive retroposition, but the elements responsible for retroposition in other animals have yet to be identified. Here, we examined young retrocopies from various animals that still retain the sequence features indicative of the underlying retroposition mechanism. In Drosophila melanogaster, we identified and de novo assembled 15 polymorphic retrocopies and found that all retroposed loci are chimeras of internal retrocopies flanked by discontinuous LTR retrotransposons. At the fusion points between the mRNAs and the LTR retrotransposons, we identified shared short similar sequences that suggest the involvement of microsimilarity-dependent template switches. By expanding our approach to mosquito, zebrafish, chicken, and mammals, we identified in all these species recently originated retrocopies with a similar chimeric structure and shared microsimilarities at the fusion points. We also identified several retrocopies that combine the sequences of two or more parental genes, demonstrating LTR-retroposition as a novel mechanism of exon shuffling. Finally, we found that LTR-mediated retrocopies are immediately cotranscribed with their flanking LTR retrotransposons. Transcriptional profiling coupled with sequence analyses revealed that the sense-strand transcription of the retrocopies often lead to the origination of in-frame proteins relative to the parental genes. Overall, our data show that LTR-mediated retroposition is highly conserved across a wide range of animal taxa; combined with previous work from plants and yeast, it represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes.
在广泛的分类群中，基因可通过逆转座子介导的过程经RNA中间体进行复制（逆转座）。在哺乳动物中，L1逆转座子驱动逆转座，但其他动物中负责逆转座的元件尚未确定。在这里，我们研究了来自各种动物的年轻逆转录拷贝，这些拷贝仍保留着指示潜在逆转座机制的序列特征。在黑腹果蝇中，我们鉴定并从头组装了15个多态性逆转录拷贝，发现所有逆转座位点都是由不连续的LTR逆转座子侧翼的内部逆转录拷贝的嵌合体。在mRNA与LTR逆转座子之间的融合点，我们鉴定出了共享的短相似序列，这表明微相似性依赖的模板转换参与其中。通过将我们的方法扩展到蚊子、斑马鱼、鸡和哺乳动物，我们在所有这些物种中都鉴定出了最近起源的具有相似嵌合结构且在融合点具有共享微相似性的逆转录拷贝。我们还鉴定出了几个结合了两个或更多亲本基因序列的逆转录拷贝，证明LTR逆转座是外显子洗牌的一种新机制。最后，我们发现LTR介导的逆转录拷贝与其侧翼的LTR逆转座子立即共转录。转录谱分析与序列分析相结合表明，逆转录拷贝的有义链转录通常会导致相对于亲本基因产生符合读框的蛋白质。总体而言，我们的数据表明LTR介导的逆转座在广泛的动物分类群中高度保守；结合先前来自植物和酵母的研究工作，它代表了一种古老且持续存在的机制，不断塑造真核生物中的基因内容进化。
