Figure 3. Single codon occupancy changes may be insufficient to affect protein output.

(A) Fold changes for all single codons in uba4Δ are plotted against their read density in grey. Colored lines are the mean fold changes for the specified codons over read-coverage bins of width 0.2 (log₂ scaled). “Other” is a pool of all non-VAA codons. (B) Metaplot of ribosome footprint density around all AAA and CAA codons with ≥2-fold change in uba4Δ, and ≥32 reads in both datasets. Reads at each position were normalized by the total number of reads for the parent gene, and averaged across all host genes that overlap that position. The plot is offset such that 0 corresponds to having the codon in the A site. The expected location of a ribosome queuing event is indicated, and a diagram of such an event is shown below. The dip in ribosome footprint density at −10 is a computational artifact, due to an inability to determine read lengths of poly-adenylated fragments when they end in one or more adenosines.