Data from: Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments

Segmented RNA viruses are ubiquitous pathogens, which include influenza
viruses and rotaviruses. A major challenge in understanding their assembly
is the combinatorial problem of a non-random selection of a full genomic
set of distinct RNAs. This process involves complex RNA-RNA and
protein-RNA interactions, which are often obscured by non-specific binding
at concentrations approaching in vivo assembly conditions. Here, we
present direct experimental evidence of sequence-specific inter-segment
interactions between rotavirus RNAs, taking place in a complex RNA- and
protein-rich milieu. We show that binding of the rotavirus-encoded
non-structural protein NSP2 to viral ssRNAs results in the remodeling of
RNA, which is conducive to formation of stable inter-segment contacts. To
identify the sites of these interactions, we have developed an RNA-RNA
SELEX approach for mapping the sequences involved in inter-segment
base-pairing. Our findings elucidate the molecular basis underlying
inter-segment interactions in rotaviruses, paving the way for delineating
similar RNA-RNA interactions that govern assembly of other segmented RNA
viruses.