Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone.
Bottom Line: We also observe strong agreement between our parameter estimates and those derived from alternative data sets.Our estimates of codon-specific translational inefficiencies and tRNA copy number-based estimates of ribosome pausing time ([Formula: see text]), and mRNA and ribosome profiling footprint-based estimates of gene expression ([Formula: see text]) are also highly correlated, thus supporting the hypothesis that selection against translational inefficiency is an important force driving the evolution of CUB.In conclusion, our method demonstrates that an enormous amount of biologically important information is encoded within genome scale patterns of codon usage, accessing this information does not require gene expression measurements, but instead carefully formulated biologically interpretable models.
Affiliation: Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee email@example.com.Show MeSH
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Mentions: Briefly, when fitted to the S. cerevisiae S288c genome, we findnearly perfect agreement between ROC SEMPPR’s with andwithout estimates for codon-specific protein synthesistranslational inefficiencies, Δη, and mutation bias,ΔM (Pearson correlation for both sets of parameters, see figs. 1 and 2).We note that, with the exception Arginine’s , the central 95% credibility intervals (CIs)for ROC SEMPPR’s Δη and ΔM parameters do notoverlap with zero (see supplementary tables S1–S4, Supplementary Material online). These results indicate thatinformation on the genome scale parameters, and are robustly encoded and estimable from CUB patternsand that provides little additional information. Fig. 1.—
Affiliation: Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville National Institute for Mathematical and Biological Synthesis, Knoxville, Tennessee firstname.lastname@example.org.