Flavivirus RNA structures
Flaviviruses (dengue, Zika, West Nile, tick-borne encephalitis virus and many viruses without a known vector or vertebrate host) carry a positive-strand RNA genome of about 11 kb whose untranslated regions are densely structured. The 3′UTR in particular is a succession of conserved elements: exoribonuclease-resistant RNAs, dumbbells, stem-loops and the cyclization sequences that pair with the 5′ end of the genome.
Most of the work collected here is comparative: structures predicted and checked across hundreds of genomes, which shows what is conserved in a lineage and what is specific to a host or a vector. Other posts look at single elements in detail (the G-quadruplex at the Zika 3′ end, RNA–RNA interactions in Japanese encephalitis virus) or connect structure conservation with molecular epidemiology. See flavivirus and 3′ UTR in the glossary.
RNAplfold tutorial: accessibility in long RNAs
How to compute the accessibility of a region with RNAplfold in the ViennaRNA Package, i.e. the probability that a stretch of nucleotides is unpaired, how to read the _lunp file, how to choose the...
Functional RNAs in Virology Special Issue
A Viruses Special Issue on functional RNAs in virology, covering structured RNAs, RNA-protein interactions, and RNA-based regulation in viral infection.
3' UTR-biased siRNA production in an insect-specific flavivirus
A comparative analysis of vsiRNA profiles across insect-specific flaviviruses reveals unusually strong 3' UTR-biased siRNA production that is independent of sfRNA formation.
Xinyang flavivirus and a likely tick-only orthoflavivirus clade
Xinyang flavivirus defines a basal, likely tick-only orthoflavivirus clade and expands the comparative picture of vertebrate-independent flavivirus evolution.
A conserved G-quadruplex in the Zika virus 3' terminal region
This study examines evidence for a conserved G-quadruplex in the Zika virus 3' terminal region and discusses what the observed DDX17 interaction does, and does not, imply.