N6-methyladenosine modification is not a general trait of viral RNA genomes

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• dc.contributor.author Baquero Pérez, Belinda
• dc.contributor.author Yonchev, Ivaylo D.
• dc.contributor.author Delgado-Tejedor, Anna
• dc.contributor.author Medina, Rebeca
• dc.contributor.author Puig-Torrents, Mireia
• dc.contributor.author Sudbery, Ian
• dc.contributor.author Begik, Oguzhan
• dc.contributor.author Wilson, Stuart A.
• dc.contributor.author Novoa, Eva Maria
• dc.contributor.author Díez Antón, Juana, 1962-
• dc.date.accessioned 2024-03-20T15:27:45Z
• dc.date.available 2024-03-20T15:27:45Z
• dc.date.issued 2024
• dc.description.abstract Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-Seq, an antibody-dependent technique with a high rate of false positives. Here, we address the presence of m6A in CHIKV and DENV RNAs. For this, we combine m6A-Seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we find no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery does not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection has no effect on the m6A machinery's localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.
• dc.description.sponsorship This work was supported by funds from the Spanish Ministry of Science and Innovation (PID2022-136939OB-I00 funded by MICIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe” and PID2019106959RB-I00/AEI/10.13039/50110001103 to J.D.), Spanish Ministry of Economy, Industry and Competitiveness (MEIC) (PID2021-128193NB-100 to E.M.N.), the European Research Council (ERC-StG-2021 No. 101042103 to E.M.N.), an institutional “María de Maeztu” Programme for Units of Excellence in R&D (CEX2018-000792-M) and by the 2021 SGR 00176 grant from the Departament de Recerca i Universitats de la Generalitat de Catalunya. 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. I.D.Y. and S.A.W. were supported by the Biotechnology and Biological Sciences Research Council, U.K. (BBSRC grant: BB/V00722X/1). A.D.T. and M.P.T. are supported by FPI Severo-Ochoa fellowships by the Spanish Ministry of Science and Innovation. We acknowledge the support of the MEIC to the EMBL partnership, Centro de Excelencia Severo Ochoa and CERCA Programme/Generalitat de Catalunya. We thank the Genomics Core Facility (UPF), in particular Núria Bonet Martín and Raquel Rasal Soteras for technical assistance with library preparation of m6A-Seq and plasmid DNA, and Marc Tormo for assisting with plasmid variant calling. 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. We also thank Dr. Matthew Seddon for technical assistance for producing the data graphs. Figures 1a, c, d, 3a, 6a, b and 7c, d were created using Biorender for which we own a full licence.
• dc.format.mimetype application/pdf
• dc.identifier.citation Baquero-Pérez B, Yonchev ID, Delgado-Tejedor A, Medina R, Puig-Torrents M, Sudbery I, et al. N6-methyladenosine modification is not a general trait of viral RNA genomes. Nat Commun. 2024 Mar 11;15(1):1964. DOI: 10.1038/s41467-024-46278-9
• dc.identifier.doi http://dx.doi.org/10.1038/s41467-024-46278-9
• dc.identifier.issn 2041-1723
• dc.identifier.uri http://hdl.handle.net/10230/59509
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Nat Commun. 2024 Mar 11;15(1):1964
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2022-136939OB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2019-106959RB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2021-128193NB-100
• dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101042103
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CEX2018-000792-M
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/801370
• dc.rights © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Alphaviruses
• dc.subject.keyword Microbiology
• dc.subject.keyword Virology
• dc.title N6-methyladenosine modification is not a general trait of viral RNA genomes
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion