Comparing experimental methodologies to estimate ribosome elongation rates.

Elongation rate estimate experiments were simulated for 2,647 human genes, using (A) Fluorescence Correlation Spectroscopy (FCS), (B) Run-Off Assays (ROA), and (C) Fluorescence Recovery After Photobleaching (FRAP). Top panels show the distributions of estimated for long genes (> 1000 codons, n = 658, purple), medium length genes (500 − 1000 codons, n = 1719, blue), and short genes (< 500 codons, n = 270, orange) using 100 mRNA spots for 300 frames at 1/3 FPS. The true elongation rate is denoted by a vertical dashed line. Bottom panels show the RMSE in elongation rate estimation as a function of the number of mRNA spots and the sampling rate. Red boxes highlight all experimental designs that yield a RMSE < 2.0. Asterisks represent the frame rate and number of repetitions used in panel (A). The ‘true’ elongation rate was set at , and the initiation rate was fixed at k_i = 0.03 sec⁻¹ for all simulations.