Fig. 3
From: Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding
Ribosome collisions occur at stop codons. a Two genes (RPS14A and RPL15A) exemplify ribosome collisions at stop codons. b The schematic of the calculation of the A-site pausing score. We counted the numbers of disome (or monosome) footprints with the concerning codon (GAA as an example here) or the other codons (all 63 non-GAA codons) at their A-sites, respectively. The mRNA-seq reads were used to control for the codon frequency in the transcript. The A-site pausing score was defined as the common odds ratio among genes, and the P value was given by the Mantel-Haenszel test. c The scatter plot shows the A-site pausing scores estimated from cells treated with 3-AT or growing in the rich medium, for the 61 codons that encode amino acids. The dashed line shows y = x. d The scatter plot shows the A-site pausing scores estimated from disome-seq or monosome-seq, for cells growing in the rich medium. The dashed line shows y = x. e Aggregated profiles of footprint densities over 3527 (58, 59, 61, and 62-nt footprints in disome-seq, in orange) and 5230 (28 and 29-nt footprints in monosome-seq, in blue) genes, normalized against the CDS length, are shown