A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data
Fig 6
Molecular factors shaping the variability of individual codon translation rates.
(A-B) Median translation times of codon types are negatively correlated with cognate tRNA abundance estimated by (A) gene copy number and (B) RNA-Seq gene expression. (C) Probability distribution of translation times of codons in the A-site either when a proline is present in the P-site (green) or when a proline is not present in the P-site (blue). (D-E) Percentage difference in median translation times when mRNA structure is present relative to when it is not present is plotted as a function of codon position after the A-site. Grey bars indicate results that are not statistically significant. Error bars are the 95% C.I. calculated using 104 bootstrap cycles; significance is assessed using the Mann-Whitney U test corrected with the Benjamini Hochberg FDR method for multiple-hypothesis correction. mRNA structure information used in (D) and (E) are provided by in vivo DMS and in vitro PARS data, respectively. (F) Scatter plot of the median translation times of pairs of codon types that are decoded by the same tRNA molecule. The red line is the identity line. The list of tRNA molecule names and decoded codon types were taken from Ref. [54]. Error bars are standard error about the median translation time calculated with 104 bootstrap cycles.