Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
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...
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2024-09-01
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| author | Rebollo, Rita Gerenton, Pierre Cumunel, Eric Mary, Arnaud Sabot, François Burlet, Nelly Gillet, Benjamin Hughes, Sandrine S. Oliveira, Daniel Goubert, Clément Fablet, Marie Vieira, Cristina Lacroix, Vincent |
| author_facet | Rebollo, Rita Gerenton, Pierre Cumunel, Eric Mary, Arnaud Sabot, François Burlet, Nelly Gillet, Benjamin Hughes, Sandrine S. Oliveira, Daniel Goubert, Clément Fablet, Marie Vieira, Cristina Lacroix, Vincent |
| author_sort | Rebollo, Rita |
| collection | DOAJ |
| description | 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 RNA-seq 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 RNA-seq can be used to identify and quantify transcribed 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 (> 4.5 kb) 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 107 TE copies. Overall, this first comparison of TEs between testes and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level. |
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| institution | Kabale University |
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| language | English |
| publishDate | 2024-09-01 |
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| series | Peer Community Journal |
| spelling | doaj-art-c5e46ea8cc4643d29f5655ed672d825f2025-02-07T10:17:17ZengPeer Community InPeer Community Journal2804-38712024-09-01410.24072/pcjournal.45710.24072/pcjournal.457Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues Rebollo, Rita0https://orcid.org/0000-0002-8138-5082Gerenton, Pierre1Cumunel, Eric2Mary, Arnaud3Sabot, François4https://orcid.org/0000-0002-8522-7583Burlet, Nelly5Gillet, Benjamin6Hughes, Sandrine7https://orcid.org/0000-0003-3932-9180S. Oliveira, Daniel8https://orcid.org/0000-0001-5468-6640Goubert, Clément9https://orcid.org/0000-0001-8034-5559Fablet, Marie10Vieira, Cristina11https://orcid.org/0000-0003-3414-3993Lacroix, Vincent12INRAE, INSA Lyon, BF2I, UMR203, Villeurbanne, FranceUniversité Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.; ERABLE team, Inria, Lyon Rhone-Alpes, Villeurbanne, FranceUniversité Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.; ERABLE team, Inria, Lyon Rhone-Alpes, Villeurbanne, FranceUniversité Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.; ERABLE team, Inria, Lyon Rhone-Alpes, Villeurbanne, FranceDIADE unit, Univ Montpellier, Cirad, IRD, Montpellier, FranceUniversité Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242 , Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1 , Lyon, France.Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242 , Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1 , Lyon, France.Université Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.; São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil.Human Genetics, McGill University, Montreal, QC, CanadaUniversité Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.; Institut Universitaire de France (IUF), Paris, France.Université Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.; ERABLE team, Inria, Lyon Rhone-Alpes, Villeurbanne, FranceUniversité Claude Bernard Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR5558, Villeurbanne, France.; ERABLE team, Inria, Lyon Rhone-Alpes, Villeurbanne, FranceTransposable 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 RNA-seq 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 RNA-seq can be used to identify and quantify transcribed 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 (> 4.5 kb) 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 107 TE copies. Overall, this first comparison of TEs between testes and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level.https://peercommunityjournal.org/articles/10.24072/pcjournal.457/long-read sequencing, ONT, transposable elements, regulation, RNA-seq, full-length cDNA |
| spellingShingle | Rebollo, Rita Gerenton, Pierre Cumunel, Eric Mary, Arnaud Sabot, François Burlet, Nelly Gillet, Benjamin Hughes, Sandrine S. Oliveira, Daniel Goubert, Clément Fablet, Marie Vieira, Cristina Lacroix, Vincent Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues Peer Community Journal long-read sequencing, ONT, transposable elements, regulation, RNA-seq, full-length cDNA |
| title | Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
|
| title_full | Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
|
| title_fullStr | Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
|
| title_full_unstemmed | Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
|
| title_short | Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
|
| title_sort | identification and quantification of transposable element transcripts using long read rna seq in drosophila germline tissues |
| topic | long-read sequencing, ONT, transposable elements, regulation, RNA-seq, full-length cDNA |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.457/ |
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