In vivo secondary structural analysis of Influenza A virus genomic RNA.
Chemical mapping
Conserved RNA motifs
Influenza A virus (IAV)
Mutational profiling (MaP)
Next-generation sequencing (NGS)
RNA secondary structure
Journal
Cellular and molecular life sciences : CMLS
ISSN: 1420-9071
Titre abrégé: Cell Mol Life Sci
Pays: Switzerland
ID NLM: 9705402
Informations de publication
Date de publication:
02 May 2023
02 May 2023
Historique:
received:
28
10
2022
accepted:
19
03
2023
revised:
19
03
2023
medline:
4
5
2023
pubmed:
3
5
2023
entrez:
2
5
2023
Statut:
epublish
Résumé
Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.
Identifiants
pubmed: 37131079
doi: 10.1007/s00018-023-04764-1
pii: 10.1007/s00018-023-04764-1
pmc: PMC10153785
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
136Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM132185
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01GM132185
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01GM133810
Pays : United States
Informations de copyright
© 2023. The Author(s).
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