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Figure 3 | Genome Biology

Figure 3

From: Composite effects of gene determinants on the translation speed and density of ribosomes

Figure 3

Genomic profiles of robustness to transcription error demonstrate that there is an increased selection for robustness at the beginning of genes in S. cerevisiae. (a) An illustration of the robustness computation: for each sliding window (length 13 codons) and in every coding sequence we computed the mean distance (in terms of folding energy (FE), tAI, and charge) from all its single nucleotide point mutations. In the next stage, the genomic profiles of robustness were plotted and analyzed (see more details in the Materials and methods). (b) The genomic profiles of robustness to transcription error (mean number of mutations that do not change the mRNA folding). The number of transcription errors (point mutations) that change the folding energy is lower at the beginning of genes (P = 1.4 × 10-100, Kolmogorov-Smirnov (KS) test). (c) The profiles of robustness to transcription error for five bins of equal size corresponding to the folding energy of the windows (Materials and methods; the boundaries of each bin are reported in the figures). The increased robustness at the beginning of genes remains significant even when controlling for local folding energy of the mRNA sequences. (d) The robustness to transcriptional errors in terms of folding energy is stronger than in randomized sequences (that maintain the codon bias and amino acid content of the original sequences; Materials and methods) at the beginning of genes (P = 6.5 × 10-5, KS test). (e, f) Profile of the robustness to transcriptional errors in terms of charge (e) and tAI (f). There is increased robustness at the beginning of genes in terms of the charge (e) as well as in terms of tAI (f). Ramp length and corresponding P-values are reported in the figures.

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