sui1-L96P broadly decreases discrimination against poor Kozak context of main CDS AUG codons genome-wide. (A–C) RPFs and mRNA reads for the FIT3 (A), TEN1 (B) and SWT1 (C) genes in WT and L96P cells, as described in Figure 1A. (D) Notched box-plot of the distributions and medians of log2ΔTEL96P values for the CDSs of groups of genes with perfect or poor AUG context (as defined below the plot), preferred (A/G), or nonpreferred (C/U) bases at −3, and all 3650 genes with ≥10 RPF reads and ≥32 mRNA reads (average of four samples, two replicates of WT and two replicates of sui1-L96P) in the main CDS, and 5′UTR length >5 nt. (E) Logos of AUG context sequences for the 3650 genes in B, and the 100 genes showing the largest increase (TE_up) or decrease (TE_down) in CDS TE values in L96P versusWT. (F) Notched box-plot analysis of AUG context scores calculated for positions −6 to −1 and +4 to +6 for the “TE_up” and “TE_down” groups of genes defined in E. (G) Box-plot analysis of AUG context scores for the groups of genes exhibiting significantly increased (RPF_up) or decreased (RPF_down) RPFs in CDSs in L96P versus WT cells (FDR < 0.05), and for all 4035 genes. Before identifying the RPF_up and RPF_down groups, 258 mRNAs transcriptionally activated by Gcn4 were removed because sui1 alleles typically derepress GCN4 mRNA translation (Martin-Marcos et al. 2013), and we wished to exclude mRNAs with elevated RPFs owing to increased transcription. (H) Notched box-plot analysis of CDS ΔTEL96P values for the 3650 genes analyzed in D divided into deciles of equal size binned according to AUG context scores calculated as in F.
