Fig. 8: eCLIP reveals NS3 binding to defined RNA elements in viral (+) and (−) RNA.

A Alignment of NS3 eCLIP data for neoJFH1 wt/D1467G replicons to the corresponding neoJFH1 subgenomic replicon reference sequence. Location in subgenomic and full-length RNA is indicated. Relative coverage information in IP vs. SMI is calculated at each position and displayed for positive-strand RNA (blue) and negative-strand RNA (pink). One-sided Fisher’s exact test was performed and Benjamini–Yekutieli¹²¹ procedure was applied to correct for multiple testing. NS3 binding sites significantly enriched relative to SMI (adjusted P value < 0.05, log₂-fold change > 2) are displayed below the tracks. For each significantly enriched NS3 binding site, crosslinking events are extracted and shown in black (relative information in IP vs. SMI). B Zoomed-in view of NS3 eCLIP signal at the 3’ end of the viral genome. Blue and pink boxes indicate significantly enriched NS3 binding sites overlapping known RNA secondary structures in (+) strand RNA (blue) and (−) strand RNA (pink). C Illustration of known RNA secondary structures at regulatory regions overlapping indicated NS3 binding sites.