Targeting the other genetic information coded by the viral RNA genomes

In addition of the protein coding information viral RNA genomes code functional information in structurally conserved units termed functional RNA domains. These RNA domains play essential roles in the viral cycle. Members of the Flaviviridae family are responsible of important worldwide human diseases (e.g. hepatitis C, dengue, zika, west Nile fever, among others). Their genome consists in a (+) single stranded RNA molecule, which contains numerous highly structurally conserved RNA domains. They represent a good model to study and characterize the functional roles of RNA domains in the regulation of essential viral processes (e.g. translation, replication). Understanding the molecular mechanisms behind their function is essential to understand the viral infective cycle. Interfering with the function of the genomic RNA domains offers a potential means of developing antiviral strategies. Nucleic acids tools and in particular aptamers are good candidates for targeting structural RNA domains. Besides its potential as therapeutics, aptamers also provides an excellent means for investigating the functionality of RNA domains in viral genomes.


Abstract:
In addition to the protein coding information viral RNA genomes code functional information in structurally conserved units termed functional RNA domains. These RNA domains play essential roles in the viral cycle. Members of the Flaviviridae family are responsible of important worldwide human diseases (e.g. hepatitis C, dengue, zika, West Nile fever, among others). Their genome consists in a (+) single stranded RNA molecule, which contains numerous highly structurally conserved RNA domains. They represent a good model to study and characterize the functional roles of RNA domains in the regulation of essential viral processes (e.g. translation, replication). Understanding the molecular mechanisms behind their function is essential to understand the viral infective cycle. Interfering with the function of the genomic RNA domains offers a potential means of developing antiviral strategies. Nucleic acids tools and in particular aptamers are good candidates for targeting structural RNA domains. Besides its potential as therapeutics, aptamers also provide an excellent means for investigating the functionality of RNA domains in viral genomes.

Picornavirus
-This system uses discrete RNA units that fold into a specific structure for coding information that is essential for the completion of the viral cycle. These structural units are considered functional genomic RNA domains.
-These units can be grouped in complex folded RNA regions that are conserved among the viral isolates.
-More than the sequence the structure of the entire genome has to be preserved in order to achieve an efficient viral propagation. The structure of the RNA domains determines their function.

Introduction: HCV genome
Conserved structural domains are also distributed all throughout the protein-coding region (indicated by grey color bars) Conserved domains represented by their predicted secondary structure.
The high structural conservation within a highly variable genome indicates that each structural unit plays an important function for the virus.

5'UTR nM
Long-range RNA-RNA interaction between the esential domains IIId within the IRES at the 5'UTR and the 5BSL3.2 within the CRE at the 3' end.
Network of RNA-RNA interactions that govern the essential viral processes (replication, translation) and the switch between them. The 5BSL3.2 domain is at the core of this network that governs the progression of the HCV propagation

HCV RNA genome: Network of RNA-RNA interactions
A detailed structural analysis providing information at nucleotide level allowed us to conclude: • The modulation of the activity of the 5' genomic end (translation efficiency) by the 3' end is achieved by promoting the conformational fine-tuning of the IRES essential domains III and IV • The 5' genomic end promotes significant structural changes at the 3' genomic end, mainly at the 3'X-tail region.
•This mutual structural influence may govern the regulation of the essential viral processes.
Nucleotides whose conformation is modified by the presence of the other genomic end are shown with red figures The 3'X-tail promotes the HCV genomic dimerization The efficiency of genomic dimerization is controlled by structural elements outside the 3'X tail domain.

Confirms the existence of functional RNA-RNA interactions involving CRE-3'X tail and IRES-3'X tail. These interactions modulate the structure and determine the function of the 3'X tail.
D=Dimer; M= Monomer C=CRE; U=3'UTR; I=IRES

Genomic structural RNA domains play essential roles in the regulation of the viral cycle
Interfering with the function of these domains (impeding the interactions they are involved in, or modifying their structure) offers a potential means of treating HCV infection Relative HCV RNA amount The RNA16(+) inhibits up to 80% HIV-1 viral particles production in a cell culture assay

Anti-HCV activity of Aptamers targeting the HCV IRES in cell culture
The RNA16(+) is the smaller aptamer molecule ever described • Viral RNA genomes have developed a storing information system that complements the protein coding one.
• This system codes essential information for the viral cycle.
• The information is coded in defined structural units. This units can be grouped in complex folded RNA regions that are highly conserved among the viral isolates. These structural domains play essential functions in the progression of infection. • The functional RNA domains establish a dynamic complex network of RNA-RNA interactions and recruit specific cellular and/or viral factors for their functioning. • In the case of HCV the CRE domain seems to play a central role in the regulation of the RNA-RNA interactions network, regulating the viral processes. • Interfering with the activity (structure/function) of the functional genomic RNA domains offers a potential means of treating viral infections. • RNA Aptamers targeting specific functional RNA domains are efficient antiviral agents.