Codon occupancy for individual codon identity in the A-site and its surrounding codon positions in carboxy-terminally FLAG-tagged UPF1 libraries. (A) Mean relative occupancy values were calculated as described in Materials and Methods. Briefly, read count of major footprint size (M in this case) at each codon position relative to the codon of interest in the A-site was normalized by the average count in the 60-codon window. Thus, mean relative occupancy of 1 (white) indicates that A-site occupancy at that position is no different from the window average. Mean relative occupancy >1 (red) and <1 (blue), respectively, indicate enrichment and depletion of ribosomal A-site at that position compared to window average. Only codons −10 to 10 were plotted. (B) Differences in mean relative occupancy between IP and total libraries. Ratios of mean relative occupancy (from A) of IP to Total, log2-transformed. Thus, log2(IP/Total) of 0 (white) indicates no difference in mean relative occupancy between IP and Total at that codon position, while positive (orange) and negative (purple) log2(IP/Total) indicate, respectively, higher and lower occupancy in IP compared to total at that codon position.
