Send to

Choose Destination
RNA Biol. 2019 Jul;16(7):950-959. doi: 10.1080/15476286.2019.1602437. Epub 2019 Apr 14.

Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts.

Author information

a Beijing Institutes of Life Science , Chinese Academy of Sciences , Beijing , China.
b State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology , Chinese Academy of Sciences , Beijing , China.
c Sino-Danish College , University of Chinese Academy of Sciences , Beijing , China.
d College of Life Sciences , University of Chinese Academy of Sciences , Beijing , China.


The large genome of the migratory locust (Locusta migratoria) genome accumulates massive amount of accumulated transposable elements (TEs), which show intrinsic transcriptional activities. Hampering the ability to precisely determine full-length RNA transcript sequences are exonized TEs, which produce numerous highly similar fragments that are difficult to resolve using short-read sequencing technology. Here, we applied a 5'-Cap capturing method using Nanopore long-read direct RNA sequencing to characterize full-length transcripts in their native RNA form and to analyze the TE exonization pattern in the locust transcriptome. Our results revealed the widespread establishment of TE exonization and a substantial contribution of TEs to RNA splicing in the locust transcriptome. The results of the transcriptomic spectrum influenced by Piwi expression indicated that TE-derived sequences were the main targets of Piwi-mediated repression. Furthermore, our study showed that Piwi expression regulates the length of RNA transcripts containing TE-derived sequences, creating an alternative UTR usage. Overall, our results reveal the transcriptomic characteristics of TE exonization in the species characterized by large and repetitive genomes.


Nanopore; direct RNA sequencing; insects; piwi; transposable element

[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Taylor & Francis Icon for PubMed Central
Loading ...
Support Center