4.7 Article

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans

Journal

GENOME RESEARCH
Volume 26, Issue 12, Pages 1663-1675

Publisher

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.204925.116

Keywords

-

Funding

  1. Strategic Priority Research Program of Chinese Academy of Sciences [XDB13010400]
  2. National Key Basic Research Program of China (Ministry of Science and Technology) [2015CB943001, 2013CB531202]
  3. National Natural Science Foundation of China [91331114, 31322050]
  4. 1000 Young Talents Program
  5. Marie Curie incoming postdoctoral fellowship
  6. HPC Platform in BIG, CAS
  7. HPC Platform, Scientific Information Center, Institute of Zoology, CAS, China
  8. Direct For Biological Sciences
  9. Div Of Molecular and Cellular Bioscience [1051826] Funding Source: National Science Foundation

Ask authors/readers for more resources

In a broad range of taxa, genes can duplicate through an RNA intermediate in a process mediated by retrotransposons (retroposition). In mammals, Ll 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.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available