Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus

The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Amo...

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Autores: Baquero Pérez, Belinda, Bortoletto, Enrico, Rosani, Umberto, Delgado-Tejedor, Anna, Medina, Rebeca, Novoa, Eva Maria, Venier, Paola, Díez Antón, Juana, 1962-
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2024
País:España
Recursos:Universitat Pompeu Fabra
Repositório:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/61147
Acesso em linha:http://hdl.handle.net/10230/61147
http://dx.doi.org/10.3390/v16060945
Access Level:Acceso aberto
Palavra-chave:ADAR1
RNA modifications
Alphaviruses
Chikungunya virus
Epitranscriptome
Inosine
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spelling Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya VirusBaquero Pérez, BelindaBortoletto, EnricoRosani, UmbertoDelgado-Tejedor, AnnaMedina, RebecaNovoa, Eva MariaVenier, PaolaDíez Antón, Juana, 1962-ADAR1RNA modificationsAlphavirusesChikungunya virusEpitranscriptomeInosineThe genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analysed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyse the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNA modifications in viral RNA genomes.This work was supported by funds from the Spanish Ministry of Science, Innovation and Universities (PID2022-136939OB-I00 funded by MICIU/AEI/10.13039/501100011033 and ERDF/EU and PID2019106959RB-I00/AEI/10.13039/50110001103), by the 2021 SGR 00176 grant from the Departament de Recerca i Universitats de la Generalitat de Catalunya and an institutional “María de Maeztu” Programme for Units of Excellence in R&D (CEX2018-000792-M). B.B.P. was the recipient of a Beatriu Pinós postdoctoral fellowship funded by the Secretary of Universities and Research (Generalitat de Catalunya) and by the Horizon 2020 programme of research and innovation of the European Union under the Marie Sklodowska-Curie grant agreement No. 801370. The mass spectrometric analyses were performed in the CRG/UPF Proteomics Unit, which is part of the Proteored, PRB3 and is supported by grant PT17/0019, of the PE I+D+i 2013–2016, funded by ISCIII and ERDF. The PhD scholarship to E.B. was granted by the Department of Biology, Univ. of Padova, on funds from the MIUR Project Departments of Excellence.MDPI202420242024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/61147http://dx.doi.org/10.3390/v16060945reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésViruses. 2024 Jun 12;16(6):945info:eu-repo/grantAgreement/EC/H2020/801370info:eu-repo/grantAgreement/ES/3PE/PID2022-136939OB-I00info:eu-repo/grantAgreement/ES/2PE/PID2019-106959RB-I00info:eu-repo/grantAgreement/ES/2PE/CEX2018-000792-M© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/611472026-06-12T07:21:37Z
dc.title.none.fl_str_mv Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
title Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
spellingShingle Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
Baquero Pérez, Belinda
ADAR1
RNA modifications
Alphaviruses
Chikungunya virus
Epitranscriptome
Inosine
title_short Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
title_full Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
title_fullStr Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
title_full_unstemmed Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
title_sort Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus
dc.creator.none.fl_str_mv Baquero Pérez, Belinda
Bortoletto, Enrico
Rosani, Umberto
Delgado-Tejedor, Anna
Medina, Rebeca
Novoa, Eva Maria
Venier, Paola
Díez Antón, Juana, 1962-
author Baquero Pérez, Belinda
author_facet Baquero Pérez, Belinda
Bortoletto, Enrico
Rosani, Umberto
Delgado-Tejedor, Anna
Medina, Rebeca
Novoa, Eva Maria
Venier, Paola
Díez Antón, Juana, 1962-
author_role author
author2 Bortoletto, Enrico
Rosani, Umberto
Delgado-Tejedor, Anna
Medina, Rebeca
Novoa, Eva Maria
Venier, Paola
Díez Antón, Juana, 1962-
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv ADAR1
RNA modifications
Alphaviruses
Chikungunya virus
Epitranscriptome
Inosine
topic ADAR1
RNA modifications
Alphaviruses
Chikungunya virus
Epitranscriptome
Inosine
description The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analysed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA. However, orthogonal validation by Illumina RNA-seq analyses did not identify any inosine modification along the CHIKV RNA genome. Moreover, CHIKV infection did not alter the expression of ADAR1 isoforms, the enzymes that catalyse the adenosine to inosine conversion. Together, this study highlights the importance of a multidisciplinary approach to assess the presence of RNA modifications in viral RNA genomes.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/61147
http://dx.doi.org/10.3390/v16060945
url http://hdl.handle.net/10230/61147
http://dx.doi.org/10.3390/v16060945
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Viruses. 2024 Jun 12;16(6):945
info:eu-repo/grantAgreement/EC/H2020/801370
info:eu-repo/grantAgreement/ES/3PE/PID2022-136939OB-I00
info:eu-repo/grantAgreement/ES/2PE/PID2019-106959RB-I00
info:eu-repo/grantAgreement/ES/2PE/CEX2018-000792-M
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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