RT Journal
A1 Tan, Shengjun
A1 Cardoso-Moreira, Margarida
A1 Shi, Wenwen
A1 Zhang, Dan
A1 Huang, Jiawei
A1 Mao, Yanan
A1 Jia, Hangxing
A1 Zhang, Yaqiong
A1 Chen, Chunyan
A1 Shao, Yi
A1 Leng, Liang
A1 Liu, Zhonghua
A1 Huang, Xun
A1 Long, Manyuan
A1 Zhang, Yong Edward
T1 LTR retrotransposons create transcribed retrocopies in metazoans
JF Genome Research 
JO Genome Research 
YR 2016 
FD October 20 
DO 10.1101/gr.204925.116 
SP gr.204925.116 
UL http://genome.cshlp.org/content/early/2016/10/20/gr.204925.116.abstract 
AB 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 which 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 co-transcribed 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 and combined with previous work from plants and yeast that it represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes.