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A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data
Fig 2
Measuring average elongation rate by applying Eq (7) to in silico and in vivo ribosome run-off data.
(A) Normalized average ribosome read density (
), Eq. (S15), calculated from simulated ribosome run-off experiment is plotted as a function of codon position for run-off times of 0, 5, 10, 15, 20, 25 and 30 s−1 with black, red, blue, cyan, pink, yellow and green data points, respectively. (B) The average time taken to fully deplete the normalized average ribosome read density within a window of the most 5′ codons positions in S. cerevisiae transcripts are plotted against the most 3′ codon position of the window. (C) Normalized average ribosome read density, calculated from in vivo run-off experimental data reported in Ref. [26], are plotted as a function of codon position for the run-off times of 0, 90, 120 and 150 seconds with black, red, blue and cyan data points, respectively. (D) The average time taken to fully deplete the normalized average ribosome read density within a window of the most 5′ codons positions in mouse stem cells transcripts are plotted against the most 3′ codon position of the window. The negative intercept reflects the time taken by harringtonine to engage with ribosomes.
doi: https://doi.org/10.1371/journal.pcbi.1007070.g002