Figure 6.

mRNA features influence sensitivity to translation inhibition. (A) Volcano plot showing global translation efficiency (Riborex engine) changes of 6878 genes in SARS-CoV-2 infected Calu-3 cells with previously documented mRNA stability [22]. Log2FoldChange infected 24 h versus mock. 135 transcripts were differentially expressed (DE) in SARS-CoV-2 infected cells based on the cut-off of p-value < 0.05, log2fold change > 1. Genes were categorized as having half-life more or less than 5 h as indicated. (B) Log2 fold change as presented in (A) of unstable (<5 h mRNA half-life) and stable (>5 h mRNA half-life) genes presented using geom_boxplot function in the ggplot2 R package using the 25th and 75th percentiles to form the box and whiskers no larger than 1.5 times the interquartile range. Data points beyond the whiskers are outliers. *** indicates one-way analysis of variance [ANOVA], p < 0.001. (C) Volcano plot showing global translation efficiency changes of 9751 genes in SARS-CoV-2 infected Calu-3 cells, 2659 of which have one or more high-confidence upstream open reading frames (uORFS) obtained from [26]. (D) Log2 fold change for genes with no uORF or one or more uORF as presented in (C) using geom_boxplot as described in (B). *** indicates one-way analysis of variance [ANOVA], p < 0.001. (E) Venn diagram showing genes significantly decreased in translation efficiency by 24 h of SARS-CoV-2 infection in Calu-3 cells (blue), genes increased in translation during EIF2A repression [25] (yellow) and genes significantly increased in translation efficiency by 24 h of SARS-CoV-2 infection in Calu-3 cells (green).