Fig 6. Endogenous mRNAs with stall sequences show signatures of inefficient translation initiation.

(A) Mean ribosome density around stall-encoding sequences in S. cerevisiae mRNAs using data from Weinberg and colleagues [62]. Stall-encoding sequences are defined as 10-codon windows that have either a minimum of 6 lysine and arginine codons or a minimum of 6 proline codons. The first nucleotide of the 10-codon window is at distance 1 nt. In total, 1,251 S. cerevisiae mRNAs have at least one stall-encoding sequence. Arrow indicates peak in ribosome density at +24 nt that is consistent with Brandman and colleagues [16]. (B) Effect of endogenous stalls on protein expression from reporter mRNAs. Protein levels measured by flow cytometry and their mean and standard error quantified as in Fig 1. ***, *, N.S. indicate P < 0.001, P < 0.05, P > 0.05 (one-tailed t test) for higher ΔASC1/WT protein-level ratio of the stall-encoding reporters in comparison with the no-stall control. (C) TE of S. cerevisiae mRNAs that either contain or do not contain stall-encoding sequences. TE is defined as the normalized ratio of ribosome footprint counts to total mRNA counts as measured by Weinberg and colleagues [62]. (D) Fold change in mRNA levels [57] between both ΔHEL2 and ΔASC1 strains and WT strain. (C, D) Box plots shows mean and standard deviation within each gene group; violin plot shows the gene density at each y-axis value; P values calculated using the two-sided Wilcoxon rank-sum test. The underlying data for panels A, B, C, and D can be found at https://github.com/rasilab/ribosome_collisions_yeast. a.u., arbitrary unit; nt, nucleotide; N.S., not significant; TE, translation efficiency; WT, wild-type.