A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data
Fig 3
Eq (12) accurately determines codon translation times from simulated ribosome profiles.
(A) Average translation time of a codon in YER009W S. cerevisiae transcript is plotted as a function of its position within the transcript. The true codon translation times in the simulations are plotted as green boxes, blue and black data points are the translation times measured using Eq (12). Blue data points were calculated using the average protein synthesis time measured from the simulations and relative ribosome density calculated using a large number of in silico ribosome profiling reads. Black data points were calculated using the average protein synthesis time estimated from the scaling relationship (Eq. (S10)) and the relative ribosome density calculated from the in silico reads which were equal to the reads aligned to the same transcript in the experiment [16]. (B) Measured codon translation times, plotted with black and blue data points in (A), are plotted against true codon translation times in the simulations in the top and bottom panel, respectively. (C) Probability distribution of the R2 correlation between the true and calculated codon translation times for the 85 S. cerevisiae transcripts. (D) Probability distribution of the slope of the best-fit lines between the estimated and true codon translation times for the 85 S. cerevisiae transcripts. The high R2 in (C) and median slope of 1.00 in (D) indicate that Eq (12) can, in principle, accurately measure absolute rates.