Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues - Archive ouverte HAL Access content directly
Preprints, Working Papers, ... Year : 2023

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Eric Cumunel
  • Function : Author
Arnaud Mary
  • Function : Author
François Sabot
Nelly Burlet
  • Function : Author
Benjamin Gillet
  • Function : Author
Sandrine Hughes
Daniel Oliveira
Clément Goubert
Marie Fablet
  • Function : Author
Vincent Lacroix
  • Function : Author

Abstract

Abstract Transposable elements (TEs) are repeated DNA sequences potentially able to move throughout the genome. In addition to their inherent mutagenic effects, TEs can disrupt nearby genes by donating their intrinsic regulatory sequences, for instance, promoting the ectopic expression of a cellular gene. TE transcription is therefore not only necessary for TE transposition per se but can also be associated with TE-gene fusion transcripts, and in some cases, be the product of pervasive transcription. Hence, correctly determining the transcription state of a TE copy is essential to apprehend the impact of the TE in the host genome. Methods to identify and quantify TE transcription have mostly relied on short RNAseq reads to estimate TE expression at the family level while using specific algorithms to discriminate copy-specific transcription. However, assigning short reads to their correct genomic location, and genomic feature is not trivial. Here we retrieved full-length cDNA (TeloPrime, Lexogen) of Drosophila melanogaster gonads and sequenced them using Oxford Nanopore Technologies. We show that long-read RNAseq can be used to identify and quantify TEs at the copy level. In particular, TE insertions overlapping annotated genes are better estimated using long reads than short reads. Nevertheless, long TE transcripts (> 5kb) are not well captured. Most expressed TE insertions correspond to copies that have lost their ability to transpose, and within a family, only a few copies are indeed expressed. Long-read sequencing also allowed the identification of spliced transcripts for around 190 TE copies. Overall, this first comparison of TEs between testes and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level.

Dates and versions

hal-04285238 , version 1 (14-11-2023)

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Rita Rebollo, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet, et al.. Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues. 2023. ⟨hal-04285238⟩
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