Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families

Alexis S. Chasseur; Maxime Bellefroid; Mathilde Galais; Meijiao Gong; Pierre Lombard; Sarah Mathieu; Amandine Pecquet; Estelle Plant; Camille Ponsard; Laure Vreux; Carlo Yague-Sanz; Benjamin G. Dewals; Nicolas A. Gillet; Benoît Muylkens; Carine M. Van Lint; Damien Coupeau

doi:10.1371/journal.ppat.1013448

Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families

Alexis S. Chasseur, Maxime Bellefroid, Mathilde Galais, Meijiao Gong, Pierre Lombard, Sarah Mathieu, Amandine Pecquet, Estelle Plant, Camille Ponsard, Laure Vreux, Carlo Yague-Sanz, Benjamin G. Dewals, Nicolas A. Gillet, Benoît Muylkens, Carine M. Van Lint, Damien Coupeau

Namur Research Institute for Life Sciences

Research output: Contribution to journal › Article › peer-review

3 Downloads (Pure)

Abstract

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.

Original language	English
Article number	e1013448
Journal	Plos Pathogens
Volume	21
Issue number	9 September
DOIs	https://doi.org/10.1371/journal.ppat.1013448
Publication status	Published - Sept 2025

Funding

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 Télévie program of the F.R.S.-FNRS, the International Brachet Stiftung (IBS), the French INSERM agency “ANRS/Maladies infectieuses émer-gentes”, and the University of Brussels (ULB -Action de Recherche Concertée (ARC) grant). Four Fonds pour la Recherche dans l’Indus-trie et l’Agriculture (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 “Fondation Rose et Jean Hoguet”. EP was a fellow of the Télévie program (F.R.S-FNRS) [grant number 7653019F]. A “Chargé de Recherches” 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 Télévie program of the F.R.S.-FNRS, the International Brachet Stiftung (IBS), the French INSERM agency “ANRS/Maladies infectieuses émergentes”, and the University of Brussels (ULB - Action de Recherche Concertée (ARC) grant). Four Fonds pour la Recherche dans l’Industrie et l’Agriculture (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 “Fondation Rose et Jean Hoguet”. EP was a fellow of the Télévie program (F.R.S-FNRS) [grant number 7653019F]. A “Chargé de Recherches” 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.

Funders	Funder number
International Brachet Stiftung
Institut National de la Santé et de la Recherche Médicale
Action de Recherche Concertée
ARC
University of Brussels
Four Fonds pour la Recherche dans l’Indus-trie et l’Agriculture
Fondation Rose et Jean Hoguet	FC5555, 7653019F
Fonds De La Recherche Scientifique - FNRS	T.0160.23
EU Marie Sklodowska-Curie	801505
Fonds pour la Formation à la Recherche dans l’Industrie et dans l’Agriculture	35484055, 40014728, 40021558, 40004528

Access to Document

10.1371/journal.ppat.1013448

2025 Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families

Cite this

Chasseur, A. S., Bellefroid, M., Galais, M., Gong, M., Lombard, P., Mathieu, S., Pecquet, A., Plant, E., Ponsard, C., Vreux, L., Yague-Sanz, C., Dewals, B. G., Gillet, N. A., Muylkens, B., Van Lint, C. M., & Coupeau, D. (2025). Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families. Plos Pathogens, 21(9 September), Article e1013448. https://doi.org/10.1371/journal.ppat.1013448

@article{819316581ae543d6b05cb10740d65329,

title = "Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families",

abstract = "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.",

author = "Chasseur, \{Alexis S.\} and Maxime Bellefroid and Mathilde Galais and Meijiao Gong and Pierre Lombard and Sarah Mathieu and Amandine Pecquet and Estelle Plant and Camille Ponsard and Laure Vreux and Carlo Yague-Sanz and Dewals, \{Benjamin G.\} and Gillet, \{Nicolas A.\} and Beno{\^i}t Muylkens and \{Van Lint\}, \{Carine M.\} and Damien Coupeau",

note = "Publisher Copyright: {\textcopyright} 2025 Chasseur et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2025",

month = sep,

doi = "10.1371/journal.ppat.1013448",

language = "English",

volume = "21",

journal = "Plos Pathogens",

issn = "1553-7366",

publisher = "Public Library of Science",

number = "9 September",

}

Chasseur, AS, Bellefroid, M, Galais, M, Gong, M, Lombard, P , Mathieu, S, Pecquet, A, Plant, E, Ponsard, C, Vreux, L, Yague-Sanz, C, Dewals, BG, Gillet, NA , Muylkens, B, Van Lint, CM & Coupeau, D 2025, 'Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families', Plos Pathogens, vol. 21, no. 9 September, e1013448. https://doi.org/10.1371/journal.ppat.1013448

TY - JOUR

T1 - Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families

AU - Chasseur, Alexis S.

AU - Bellefroid, Maxime

AU - Galais, Mathilde

AU - Gong, Meijiao

AU - Lombard, Pierre

AU - Mathieu, Sarah

AU - Pecquet, Amandine

AU - Plant, Estelle

AU - Ponsard, Camille

AU - Vreux, Laure

AU - Yague-Sanz, Carlo

AU - Dewals, Benjamin G.

AU - Gillet, Nicolas A.

AU - Muylkens, Benoît

AU - Van Lint, Carine M.

AU - Coupeau, Damien

N1 - Publisher Copyright: © 2025 Chasseur et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2025/9

Y1 - 2025/9

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/105015702140

U2 - 10.1371/journal.ppat.1013448

DO - 10.1371/journal.ppat.1013448

M3 - Article

C2 - 40934191

AN - SCOPUS:105015702140

SN - 1553-7366

VL - 21

JO - Plos Pathogens

JF - Plos Pathogens

IS - 9 September

M1 - e1013448

ER -

Unbiased and comprehensive identification of virus-derived circular RNAs in a large range of viral species and families

Abstract

Funding

Access to Document

Other files and links

Fingerprint

Cite this