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Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses
Published on: December 29, 2015
Comparative analysis of flavivirus sfRNA dynamics and secondary structure
Camden R Bair1, David VanInsberghe1, Anice C Lowen1
1Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.
Journal of Virology
|July 10, 2026
Summary
Subgenomic flavivirus RNAs (sfRNAs) are crucial for viral pathogenicity. This study reveals that sfRNA structures largely resemble in vitro models but show transient interactions within infected cells, common across multiple flaviviruses.
Area of Science:
- Virology
- Molecular Biology
- RNA Structure and Function
Background:
- Subgenomic flavivirus RNAs (sfRNAs) are noncoding RNAs essential for flavivirus fitness and pathogenicity.
- sfRNAs are generated by incomplete digestion of viral RNA by the cellular exoribonuclease XRN1, mediated by RNA structural elements (RSEs) in the 3'-untranslated region (3'-UTR).
- The structural dynamics of sfRNAs within infected cells remain understudied despite their importance.
Purpose of the Study:
- To quantify sfRNA levels during infection for a panel of mosquito-borne flaviviruses.
- To determine the secondary structures of sfRNAs in infected cells and compare them to in vitro models.
- To investigate potential interactions of sfRNAs with viral or host factors during infection.
Main Methods:
- Digital droplet PCR was used to quantify sfRNA levels in infected cells.
- Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) was performed on in vitro transcribed and cell-derived sfRNAs.
- Comparison of SHAPE-MaP reactivity profiles between in vitro and in-cell conditions to infer structural differences and potential interactions.
Main Results:
- sfRNA levels were quantified for dengue virus serotypes 1, 2, and 4, and Zika virus.
- In-cell and in vitro sfRNA secondary structures were largely similar, validating previous models.
- Specific regions, including the dumbbell, upstream hairpin, and 3'-stem loop, showed differential nucleotide reactivity in cells versus in vitro, suggesting transient interactions with cellular components.
Conclusions:
- The secondary structures of sfRNAs are generally maintained within infected cells.
- Differences in reactivity suggest that sfRNAs engage in limited, transient interactions with viral or host factors, possibly via base-paired regions.
- These transient interactions may play a functional role in sfRNA activity during flavivirus infection.
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