Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus.
Full-genome alignment
Hepatitis C virus
RNA secondary structure prediction
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
02 07 2024
02 07 2024
Historique:
received:
19
12
2023
accepted:
22
05
2024
medline:
3
7
2024
pubmed:
3
7
2024
entrez:
2
7
2024
Statut:
epublish
Résumé
Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large 'cloud' of RNA genomes (quasispecies) which-by trial and error-comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement.
Identifiants
pubmed: 38956134
doi: 10.1038/s41598-024-62897-0
pii: 10.1038/s41598-024-62897-0
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
15145Subventions
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : EXC 2051-Project-ID 390713860
Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : "VIROINF"-Project-ID 955974
Organisme : Thüringer Aufbaubank (TAB)
ID : Project-ID 2021 FGI 0009
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : FOR 5151 QuaLiPerF-TP4: MA5082/15-1
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : SFB 1021-Project-ID 197785619
Informations de copyright
© 2024. The Author(s).
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