Fig. 5
From: Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding
Ribosome collisions are enriched at polylysine in the exit tunnel. a The schematic of calculating the exit-tunnel pausing score. For each gene, we counted the numbers of the concerning amino-acid 3-mer (KKK as an example here) or the other 3-mers (non-KKK) in the 20 amino-acid region upstream of the P-site of the paused ribosome. mRNA-seq data were used as the background. The exit-tunnel pausing score was defined as the common odds ratio among genes, and the P value was given by the Mantel-Haenszel test. b The volcano plots show the exit-tunnel pausing score (based on disome or monosome footprints) of each of the 8000 amino-acid 3-mers and the corresponding Q value. Some 3-mers of consecutive positively charged amino acids are labeled in orange. c Determination of elongation rate with the dual-luciferase assay, in which the variants of different codon combinations for triple-lysine were inserted between Renilla and firefly-luciferase. Data are shown as the mean ± standard error (N = 11 biological replicates for each variant). ANOVA stands for the analysis of variance. d Similar to Fig. 5b, the volcano plot shows the exit-tunnel pausing score for disome footprints of each of the 613 codon 3-mers and the corresponding Q value. The eight codon combinations for triple-lysine are highlighted. The pie chart shows the relative abundance of the eight codon combinations for triple-lysine in the yeast transcriptome. e A putative pausing signal inducing ribosome collisions (KKRKKK) was conserved in the linker region between two domains of Rps31p, across the eukaryotic kingdom (top). The ribosome collision with the putative pausing signal located within the exit tunnel was also conserved between yeast and human (bottom). The footprint abundance at a site was normalized by the total footprints of RPS31 in the corresponding species