Figure 3.

Ribosomal density analysis. (a) Boxplots of the ORF length of all the RNA that peaked in each fraction. The plots include only the genes that have a clearly defined EDTA-releasable peak on their polysomal profiles and a signal intensity higher than the median of all the signals at each time point. Thus, 2,237 genes were included at 0-2 hours, 2,282 genes at 4-6 hours and 2,446 genes at 8-10 hours. x-axis, polysomal fractions 6-12; y-axis, transcript ORF length (amino acid). The box stretches from the ORF length at lower 25th percentile to that at the 75th percentile; the median of the ORF length is shown as a line across the box. The vertical dashed lines indicate the ORF length ranges of individual fractions. (b) The median ORF length of mRNAs peaking in each fraction versus the assigned number of associated ribosomes in each fraction. The assigned number of associated ribosomes of fractions 6-12 is in the order of 2, 3, 5, 7.5, 11, 17 and 26, respectively. x-axis, the assigned number of associated ribosomes; y-axis, ORF length (amino acids). The slope and the coefficient of determination (R²) are shown with each trend line. The data points for fractions 6, 7 and 12 are shown as diamonds, which are not included in the slope calculation. (c) Inverse correlation of the ribosomal density and ORF length. x-axis, ORF length (amino acids); y-axis, ribosomal density that is defined as the ratio of the estimated number of associated ribosomes to the ORF length of mRNA (amino acid).