LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
- Shengjun Tan1,
- Margarida Cardoso-Moreira2,6,
- Wenwen Shi1,
- Dan Zhang1,3,
- Jiawei Huang1,3,
- Yanan Mao1,
- Hangxing Jia1,3,
- Yaqiong Zhang1,
- Chunyan Chen1,3,
- Yi Shao1,3,
- Liang Leng1,
- Zhonghua Liu4,
- Xun Huang4,
- Manyuan Long5 and
- Yong E. Zhang1,3
- 1Key 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;
- 2Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland;
- 3University of Chinese Academy of Sciences, Beijing 100049, China;
- 4State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- 5Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
- Corresponding author: zhangyong{at}ioz.ac.cn
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.204925.116.
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Freely available online through the Genome Research Open Access option.
- Received January 29, 2016.
- Accepted October 18, 2016.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
