Fig. 6: Validation of genomic S segment RNA accessibility in RVFV MP-12 vRNPs.

Antisense oligonucleotide (ASO)-targeted RNase H digestion was performed using vRNP preparations or isolated RNA from RVFV MP-12 virions. A IGV tracks representing N binding profiles in the IGR-proximal region of the MP-12 vS segment (~650–1050), obtained for virions. iCLIP-derived crosslink sites for the genomic-sense RNA are shown here in 3′–5′ orientation and nucleotide positions are numbered as in the reference genome. Binding positions of targeting ASOs (“1–8”) are illustrated, as well as the areas covered by the IGR (positions 777-858; black line) and the exposed vS region (EvSR, positions ~800-900; solid red line) derived from the iCLIP2 data. The region of the EvSR as inferred from the accessibility experiment (from B) is shown as a dashed red line (positions 777-911). B, C RNase H digestion was performed in the presence of ASOs targeting the genomic S segment, or, as controls, without any ASO (“-“ lanes) or in the presence of a scrambled oligonucleotide (“scr” lanes); vRNP preparations were used in (B), and isolated RNA from RVFV MP-12 virions in (C). Resulting RNA fragments were visualized by northern blot using the DIG-labelled probe 3′ end vS. The intact genomic segment (“vS”) is indicated with an arrowhead. D RNA minimal free energy secondary structure by RNAfold for the proposed exposed vS region (core EvSR; corresponding to the solid red line in A). Source data are provided as a Source Data file. The experiments were performed 3 times independently with similar results.