Fig. 3: Pseudoribosomal RNP interactions are associated with translational suppression of transcriptionally activated genes. | Experimental & Molecular Medicine

Fig. 3: Pseudoribosomal RNP interactions are associated with translational suppression of transcriptionally activated genes.

From: SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs

Fig. 3

a, b t-SNE visualization of host nuclear genes (n = 9255) embedded in a 2D plot based on RAIs of all the individual Ribo-seq libraries. Each coordinate is colored according to a the RAI at each time point and b protein localization annotated in the UniProt database. c Gene Ontology (GO) term enrichment analysis using EnrichR for the top 20% of genes with the highest RAIs in uninfected controls. The top 10 GO terms of cellular compartments that were significantly enriched (adjusted P value < 0.05) are presented. The color gradients and circle sizes represent the odds ratios and numbers of overlapping genes, respectively. d Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis based on the RAIs of the late phase samples (5 and 7 dpi) versus the respective controls. The top 10 significantly enriched terms with an FDR below 0.05 are displayed. The color gradients and circle sizes represent normalized enrichment scores (NESs) and the numbers of overlapping genes, respectively. e A scatter plot representing the changes in RPF (x-axis) versus RNA (y-axis) levels in the samples taken 5 and 7 dpi compared to the uninfected controls. The sky blue dots represent the genes associated with overrepresented KEGG terms, and the gray dots represent all other genes. f, g Scatter plots representing the changes in RAI (x axis) versus the changes in RPF (f) and mRNA (g) levels (y axis) of samples taken 5 and 7 dpi compared to uninfected controls. Each dot represents an individual gene. Linear regression analysis was performed to assess the correlation and significance between RPF level changes and RAI. h Box plot showing the relative proportions of stalled transcripts at each time point for the genes with high (top 25%) and low (bottom 25%) RAI fold changes (FCs). The rhombuses indicate the outliers of all replicates per condition. Mann‒Whitney U test P values are denoted by asterisks. Significant differences are indicated by [*] P < 0.05.

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