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

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.

Metadata

Item Type:	Article
Authors/Creators:	Baquero-Pérez, B. https://orcid.org/0000-0002-0956-7164 Yonchev, I.D. https://orcid.org/0000-0001-8486-7362 Delgado-Tejedor, A. https://orcid.org/0000-0002-3836-0293 Medina, R. Puig-Torrents, M. Sudbery, I. https://orcid.org/0000-0002-5038-0190 Begik, O. https://orcid.org/0000-0002-8663-4586 Wilson, S.A. https://orcid.org/0000-0003-3073-258X Novoa, E.M. https://orcid.org/0000-0002-9367-6311 Díez, J. https://orcid.org/0000-0002-9013-0751
Copyright, Publisher and Additional Information:	© 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/.
Keywords:	Alphaviruses; Microbiology; Virology
Dates:	Published: 11 March 2024 Published (online): 11 March 2024 Accepted: 16 February 2024 Submitted: 27 September 2023
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield)
Funding Information:	Funder Grant number BIOTECHNOLOGY AND BIOLOGICAL SCIENCES RESEARCH COUNCIL BB/V00722X/1
Depositing User:	Symplectic Sheffield
Date Deposited:	20 Mar 2024 10:45
Last Modified:	20 Mar 2024 10:45
Status:	Published
Publisher:	Springer Science and Business Media LLC
Refereed:	Yes
Identification Number:	10.1038/s41467-024-46278-9
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Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:210484