Fig. 4: Ribosome heterogeneity with dysregulated rRNP associations in SARS-CoV-2-infected tissues.

a Relative proportions of the Ribo-seq reads aligned to host mRNAs, rRNAs, tRNAs, and 7SL RNAs. b The prediction of ribosome heterogeneity in SARS-CoV-2-infected tissues. Each panel corresponds to a dripARF prediction for each indicated time point. All statistical indices were obtained based on dripARF enrichment tests. An enrichment score of 1 represents the normalized enrichment score (NES) of every RP contact point. An enrichment score of 2 corresponds to the deviation of the NES from the background level. An enrichment score 3 indicates whether rRNA positions where rRNA fragment abundance was significantly changed are included in predicted RP contact regions. See also Supplementary Fig. 4a for results obtained 1 dpi and 5 dpi. c The crystal structure of the 60 S ribosome large subunit (LSU), wherein 5 S RNP and tRNA are highlighted by different colors. Yellow represents the region in which rRNAs are close to uL5 and uL18 (within 27.4 Å). The coordinates (start and end positions) of the proximal region in rRNA genome sequences (orange: 5 S, cyan: 18 S, and pink: 28 S) are shown in the top square bracket. In heatmaps, white‒black represents distances between RP and rRNA at individual coordinates. The other heatmap with red‒white shows the fold changes in the Ribo-seq reads 7 dpi versus the uninfected controls at the corresponding coordinates. d Box plot depicting RPF and RNA level changes in TP53 in lung tissue following SARS-CoV-2 infection.