Fig. 1: Profiling ZIKV vRNA–host protein interactomes identified ILF3 and DHX9 forming a protein complex bound to ZIKV SLB.

A RNA-pull-down efficiency at ZIKV genome in mock, ZIKV MR766 or PRVABC.59-infected SK-N-BE(2) cells (Multiplicity of infection, MOI = 1, 48 hpi) were assessed by RT-qPCR. Target viral RNA was pull-down by biotin-labeled scramble oligo or SLB oligo. Four primer pairs were used to assess the enrichment across ZIKV vRNA. The position of each PCR amplicon is presented as below diagram. Bars, mean ± SD, n = 3 biological replicates/group, two-tailed Student’s t-test. *p < 0.05, **p < 0.01. B Venn diagram illustrates the identification of human proteins interacting with ZIKV SLB vRNA in mock, ZIKV MR766, or PRVABC.59-infected cells. C Gene Ontology (GO) analysis shows the enriched signal pathways among common SLB-interacting proteins for MR766 and PRVABC.59 strains. The size of the dot represents enriched gene numbers. And dots are colored according to p values calculated by hypergeometric test. GO terms with p value adjust <0.05 are plotted. D Venn diagram illustrates the intersecting results of ZIKV SLB-interacting proteins in SK-N-BE(2) and Huh7 cells. E Western blot analysis of ILF3 and DHX9 protein pull-downed by biotin-labeled scramble oligo or SLB oligo in mock, ZIKV MR766, or PRVABC.59-infected SK-N-BE(2) cells (MOI = 1, 48 hpi). GAPDH was applied as a loading control. n = 4 biological replicates/group. F Venn diagram illustrates ILF3-interacting proteins in mock or ZIKV MR766-infected cells. G Western blot detection of ILF3 and DHX9, NS5, E protein in ILF3 endogenous IP samples from mock, ZIKV MR766 or PRVABC.59-infected SK-N-BE(2) cells (MOI = 1, 48 hpi). GAPDH was applied as a loading control. n = 3 biological replicates/group. H Western blot detection of ILF3 and DHX9 interactions in ILF3 endogenous IP samples from mock or PRVABC.59-infected SK-N-BE(2) cells (MOI = 1, 48 hpi) with or without RNase A (20 μg/ml) treatment. n = 3 biological replicates/group. I Western blot analysis of ILF3, NS5, E, and GAPDH protein expressions in ZIKV-infected SK-N-BE(2) cells at indicated time points (MOI = 1). n = 3 biological replicates/group. J Western blot showing the distribution of ILF3, NS5, E, and Histone H3 in the nuclear or cytoplasmic fraction from ZIKV-infected SK-N-BE(2) cells at indicated time points (MOI = 1). n = 3 biological replicates/group. K Immunofluorescence showing the localization of ILF3 among mock, ZIKV MR766 or PRVABC.59-infected SK-N-BE(2) cells (MOI = 1) at 48 hpi (scale bar, 7.5 μm). Bars, mean ± SD, n = 3 biological replicates/group, two-tailed Student’s t-test. **p < 0.01, ***p < 0.001. Source data are provided as a Source Data file.