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

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Autor(es): dc.contributorUMR203-
Autor(es): dc.contributorUMR5558-
Autor(es): dc.contributorLyon Rhone-Alpes-
Autor(es): dc.contributorIRD-
Autor(es): dc.contributorUniversité Claude Bernard Lyon 1-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorMcGill University-
Autor(es): dc.contributorInstitut Universitaire de France (IUF)-
Autor(es): dc.creatorRebollo, Rita-
Autor(es): dc.creatorGerenton, Pierre-
Autor(es): dc.creatorCumunel, Eric-
Autor(es): dc.creatorMary, Arnaud-
Autor(es): dc.creatorSabot, François-
Autor(es): dc.creatorBurlet, Nelly-
Autor(es): dc.creatorGillet, Benjamin-
Autor(es): dc.creatorHughes, Sandrine-
Autor(es): dc.creatorOliveira, Daniel S.-
Autor(es): dc.creatorGoubert, Clément-
Autor(es): dc.creatorFablet, Marie-
Autor(es): dc.creatorVieira, Cristina-
Autor(es): dc.creatorLacroix, Vincent-
Data de aceite: dc.date.accessioned2025-08-21T21:15:17Z-
Data de disponibilização: dc.date.available2025-08-21T21:15:17Z-
Data de envio: dc.date.issued2025-04-29-
Data de envio: dc.date.issued2023-12-31-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.24072/pcjournal.457-
Fonte completa do material: dc.identifierhttps://hdl.handle.net/11449/297594-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/297594-
Descrição: dc.descriptionTransposable 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 over-lapping 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 in-deed 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.-
Descrição: dc.descriptionAgence Nationale de la Recherche-
Descrição: dc.descriptionINRAE INSA Lyon BF2I UMR203-
Descrição: dc.descriptionUniversité Claude Bernard Lyon 1 Laboratoire de Biométrie et Biologie Evolutive CNRS UMR5558-
Descrição: dc.descriptionERABLE team Inria Lyon Rhone-Alpes-
Descrição: dc.descriptionDIADE unit Univ Montpellier Cirad IRD-
Descrição: dc.descriptionInstitut de Génomique Fonctionnelle de Lyon (IGFL) CNRS UMR 5242 Ecole Normale Supérieure de Lyon Université Claude Bernard Lyon 1-
Descrição: dc.descriptionSão Paulo State University (Unesp) Institute of Biosciences Humanities and Exact Sciences, SP-
Descrição: dc.descriptionHuman Genetics McGill University-
Descrição: dc.descriptionInstitut Universitaire de France (IUF)-
Descrição: dc.descriptionSão Paulo State University (Unesp) Institute of Biosciences Humanities and Exact Sciences, SP-
Descrição: dc.descriptionAgence Nationale de la Recherche: ANR-16-CE23-0001-
Descrição: dc.descriptionAgence Nationale de la Recherche: ANR-20-CE02-0015-
Idioma: dc.languageen-
Relação: dc.relationPeer Community Journal-
???dc.source???: dc.sourceScopus-
Título: dc.titleIdentification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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