Fig. 3

JEV infection influences the m6A methylome of host cell. A Analysis of m6A peak enrichment in mock (gray line) and JEV-infected neuro2a cells (red line) via metagene analysis reveals annotation of 5' UTR, 3' UTR, and CDS at 24 hpi and 48 hpi, respectively. B A pie chart illustrates the relative proportions of total m6A peaks in the 5' UTR, CDS, 3' UTR and ncRNA of host cell RNA transcripts. C The top consensus sequences for m6A methylation in mock and JEV-infected neuro2a cells at 24 hpi and 48 hpi. D The total number of m6A peaks that were classified as gained, retained, or lost after 24-h or 48-h infection with JEV in comparison to neuro2a cells was determined. E Bar plots are used to depict the quantity of genes that have gained, retained, or lost m6A in neuro2a cells after 24 hpi and 48 hpi. F A bar graph illustrating the percentages of up- or down-regulated genes that overlap with either gained or lost m6A genes. G KEGG analysis of genes which were up-regulated and gained m6A peak upon JEV infection at 24 hpi and 48 hpi revealed the top 20 enriched pathways. The size of the dots indicates the gene enrichment ratio, while their color reflects the log10 level of significance. H A nine-quadrant graph was generated to evaluate the correlation between transcriptome and m6A modification between mock and JEV-infected neuro2a cells. The abscissa of the graph is the fold change of the m6A peak (taken log2) while the ordinate is the fold change of the transcriptome (taken log2). The red dots signify genes that are both up-regulated in the transcriptome and m6A peaks, the orange dots represent genes that are down-regulated in both the transcriptome and m6A peaks, the blue dots identify genes that are up-regulated in the transcriptome but down-regulated in m6A peaks, and the green dots indicate genes that are down-regulated in the transcriptome but up-regulated in m6A peaks. Meanwhile, the gray dots signify genes and m6A peaks that are not differentially expressed. DiffBind was employed to assess the rate of RNA methylation while DESeq2 was utilized to analyze the differential expression of RNAs between different groups. Genes/peaks with a false discovery rate (FDR) below 0.05 and an absolute fold change ≥ 2 were considered to be significantly differential. The most differentially expressed genes were also labeled