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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

1
a Beijing Institutes of Life Science , Chinese Academy of Sciences , Beijing , China.
2
b State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology , Chinese Academy of Sciences , Beijing , China.
3
c Sino-Danish College , University of Chinese Academy of Sciences , Beijing , China.
4
d College of Life Sciences , University of Chinese Academy of Sciences , Beijing , China.

Abstract

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.

KEYWORDS:

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

PMID:
30982421
PMCID:
PMC6546357
DOI:
10.1080/15476286.2019.1602437
[Indexed for MEDLINE]
Free PMC Article

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