Codon and amino acid content are associated with mRNA stability in mammalian cells
Fig 4
Codon-specific effects on stability are associated with tRNA and amino acid levels.
(A) Plot of tRNA adaptive indices (tAI) representing relative tRNA levels calculated from tRNA sequencing data in HeLa cells. Purple represents optimal codons, defined by tAI > median (0.1478). Green represents non-optimal codons, defined by tAI < median. Errorbars indicate standard deviation of three replicates. (B) Plot of HeLa tAI vs. HeLa CSC for all 61 codons. Purple represents optimal codons; green represents non-optimal codons (defined in Fig 4A). Red dotted line indicates linear regression trendline. rho (ρ) = 0.14, p = 0.29 (Spearman correlation test). (C) Boxplots comparing distribution of HeLa CSCs for optimal and non-optimal codons as defined in Fig 4A; p = 0.37 (Wilcoxon test). (D) Plot of relative free amino acid concentrations (versus glycine) determined from HeLa cell lysates. Errorbars indicate standard deviation of two replicates. (E) Plot of HeLa relative free amino acid concentration vs. HeLa CSC for all codons except those encoding Cys and Glu (n = 57). Red line indicates linear regression trendline. rho (ρ) = 0.079, p = 0.56 (Spearman correlation test). (F) Plot of HeLa tAI vs. HeLa CSC for all 61 codons. Blue dotted line indicates linear regression trendline. Gray indicates codons encoding amino acids with mild-moderate effect on stability; magenta indicates codons encoding amino acids with extreme effects on stability (AASC > 0.10 or < -0.10 and p < 1.0 x 10−30). Overall rho (ρ) = 0.14, p = 0.29 (Spearman correlation test). (G) Plot of HeLa tAI vs. HeLa CSC for the 42 codons encoding amino acids with mild-moderate effect on stability. Blue dotted line indicates linear regression trendline. rho (ρ) = 0.48, p = 0.0015 (Spearman correlation test). (H) Plot of HeLa relative intracellular amino acid concentration vs. HeLa CSC for the 19 codons encoding amino acids with extreme effects on stability as defined in Fig 4F. Blue dotted line indicates linear regression trendline. rho (ρ) = 0.43, p = 0.064 (Spearman correlation test). See also S2 Table for CSC, tAI, and free amino acid concentration values and statistical data.