[en] Non-coding RNAs play a significant role in viral infection cycles, with recent attention focused on circular RNAs (circRNAs) originating from various viral families. Notably, these circRNAs have been associated with oncogenesis and alterations in viral fitness. However, identifying their expression has proven more challenging than initially anticipated due to unique viral characteristics. This challenge has the potential to impede progress in our understanding of viral circRNAs. Key hurdles in working with viral genomes include: (1) the presence of repetitive regions that can lead to misalignment of sequencing reads, and (2) unconventional splicing mechanisms that deviate from conserved eukaryotic patterns. To address these challenges, we developed vCircTrappist, a bioinformatic pipeline tailored to identify backsplicing events and pinpoint loci expressing circRNAs in RNA sequencing data. Applying this pipeline, we obtained novel insights from both new and existing datasets encompassing a range of animal and human pathogens belonging to Herpesviridae, Retroviridae, Adenoviridae, Flaviviridae and Orthomyxoviridae families. Subsequent RT-PCR and Sanger sequencings validated the accuracy of the developed bioinformatic tool for a selection of new candidate virus-derived circRNAs. These findings demonstrate that vCircTrappist is an open and unbiased approach for comprehensive identification of virus-derived circRNAs.
Disciplines :
Microbiology
Author, co-author :
Chasseur, Alexis S ; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
Bellefroid, Maxime; Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
Galais, Mathilde; Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
Gong, Meijiao ; Université de Liège - ULiège > Fundamental and Applied Research for Animals and Health (FARAH)
Lombard, Pierre; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
Mathieu, Sarah; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
Pecquet, Amandine; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
Plant, Estelle; Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
Ponsard, Camille; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
Vreux, Laure; Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
Yague-Sanz, Carlo; Namur Research Institute for Life Sciences (NARILIS), Molecular Physiology Research Unit (URPhyM), University of Namur, Namur, Belgium
Dewals, Benjamin G ; Université de Liège - ULiège > Département des maladies infectieuses et parasitaires (DMI) > Immunologie vétérinaire ; Walloon Excellence in Life Sciences and Biotechnology (WELBIO) Department, WEL Research Institute, Wavre, Belgium
Gillet, Nicolas A; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
Muylkens, Benoît; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
Van Lint, Carine M ; Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
Coupeau, Damien; Namur Research Institute for Life Sciences (NARILIS), Integrated Veterinary Research Unit (URVI), University of Namur, Namur, Belgium
F.R.S.-FNRS - Fonds de la Recherche Scientifique Télévie INSERM - French Institute of Health and Medical Research ULB - Université Libre de Bruxelles FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture Fondation Rose et Jean Hoguet Marie Skłodowska-Curie Actions
Funding text :
Funding: This study was funded by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium) through the Projet de Recherche (PDR) program awarded to BM, BD and CVL [grant number T.0160.23]. This latter PDR program supported PL scholarship. Work in CVL lab was also funded by the T\u00E9l\u00E9vie program of the F.R.S.-FNRS, the International Brachet Stiftung (IBS), the French INSERM agency \u201CANRS/Maladies infectieuses \u00E9mer-gentes\u201D, and the University of Brussels (ULB -Action de Recherche Concert\u00E9e (ARC) grant). Four Fonds pour la Recherche dans l\u2019Indus-trie et l\u2019Agriculture (FRIA) scholarships were awarded to AC [grant number 40014728], MB [grant number 35484055], SM [grant number 40021558], and LV [grant number 40004528], respectively. LV and EP were also supported by a PhD candidate scholarship from the \u201CFondation Rose et Jean Hoguet\u201D. EP was a fellow of the T\u00E9l\u00E9vie program (F.R.S-FNRS) [grant number 7653019F]. A \u201CCharg\u00E9 de Recherches\u201D fellowship was awarded to CY [grant number FC5555]. MG was funded by a post-doctoral fellowship from the EU Marie Sklodowska-Curie COFUND Action [Grant number 801505]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This study was funded by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium) through the Projet de Recherche (PDR) program awarded to BM, BD and CVL [grant number T.0160.23]. This latter PDR program supported PL scholarship. Work in CVL lab was also funded by the T\u00E9l\u00E9vie program of the F.R.S.-FNRS, the International Brachet Stiftung (IBS), the French INSERM agency \u201CANRS/Maladies infectieuses \u00E9mergentes\u201D, and the University of Brussels (ULB - Action de Recherche Concert\u00E9e (ARC) grant). Four Fonds pour la Recherche dans l\u2019Industrie et l\u2019Agriculture (FRIA) scholarships were awarded to AC [grant number 40014728], MB [grant number 35484055], SM [grant number 40021558], and LV [grant number 40004528], respectively. LV and EP were also supported by a PhD candidate scholarship from the \u201CFondation Rose et Jean Hoguet\u201D. EP was a fellow of the T\u00E9l\u00E9vie program (F.R.S-FNRS) [grant number 7653019F]. A \u201CCharg\u00E9 de Recherches\u201D fellowship was awarded to CY [grant number FC5555]. MG was funded by a post-doctoral fellowship from the EU Marie Sklodowska-Curie COFUND Action [Grant number 801505]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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