The folding of the hepatitis C virus internal ribosome entry site depends on the 3'-end of the viral genome

Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3'-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility u...

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Bibliographic Details
Published in:Nucleic acids research 2012-12, Vol.40 (22), p.11697-11713
Main Authors: Romero-López, Cristina, Barroso-Deljesus, Alicia, García-Sacristán, Ana, Briones, Carlos, Berzal-Herranz, Alfredo
Format: Article
Language:English
Subjects:
5' Untranslated Regions
Antisense oligonucleotides
Base Sequence
dimethyl sulfate
Genome, Viral
Genomes
genomics
Hepacivirus - genetics
Hepacivirus - physiology
Hepatitis C virus
Internal ribosome entry site
Molecular Sequence Data
Nucleic Acid Conformation
Oligonucleotide Array Sequence Analysis
Protein structure
Replication
RNA
RNA Folding
RNA, Viral - chemistry
Translation initiation
Virus Replication
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Summary:Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3'-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility using antisense oligonucleotide microarrays, here, we show that HCV IRES folding is fine-tuned by the genomic 3'-end. The essential IRES subdomains IIIb and IIId, and domain IV, adopted a different conformation in the presence of the cis-acting replication element and/or the 3'-untranslatable region compared to that taken up in their absence. Importantly, many of the observed changes involved significant decreases in the dimethyl sulfate or N-methyl-isatoic anhydride reactivity profiles at subdomains IIIb and IIId, while domain IV appeared as a more flexible element. These observations were additionally confirmed in a replication-competent RNA molecule. Significantly, protein factors are not required for these conformational differences to be made manifest. Our results suggest that a complex, direct and long-distance RNA-RNA interaction network plays an important role in the regulation of HCV translation and replication, as well as in the switching between different steps of the viral cycle.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gks927