Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication

Area of Science:

• Virology
• Molecular Biology
• Genomics

Background:

• Viral RNA genomes contain both linear sequence and higher-order structures essential for replication.
• While some conserved RNA structures are known, many functional elements remain undetected by sequence analysis alone.
• The role of sequence-independent RNA structures in viral fitness is largely unexplored.

Purpose of the Study:

• To develop and apply a structure-first strategy to identify functional RNA structural motifs within viral coding sequences.
• To investigate the extent of RNA structure-mediated regulation in viral genomes, particularly for dengue virus.
• To explore the potential of these RNA structures as targets for antiviral interventions.

Main Methods:

• Devised a structure-first experimental approach to identify RNA structural motifs.
• Analyzed the coding sequences of the four dengue virus serotypes.
• Validated the functional impact of identified motifs on viral fitness.

Main Results:

• Identified 22 structure-similar motifs across the coding sequences of all four dengue virus serotypes.
• Demonstrated that at least 10 of these motifs significantly modulate viral fitness.
• Revealed that these viral RNA structures contribute to genome compactness, protein interactions, and replication regulation.

Conclusions:

• A significant, previously unrecognized layer of RNA structure-mediated regulation exists within viral coding sequences.
• These conserved RNA structural motifs are constrained by both RNA structure and protein sequence.
• Identified motifs represent potential targets for developing resistance-refractory antivirals and live-attenuated vaccines.