Solving the riddle of codon usage preferences: a test for translational selection.

By Mario dos Reis, R. Savva, L. Wernisch. Nucleic Acids Research, 2004

738 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9e020ce12c1d7045ab6b93d6ef82300e09e6b434

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In Molecular Biology

Citations in the corpus

An evolutionarily conserved mechanism for controlling the efficiency of protein translation. (2010, methodology): “In particular, we used the tRNA-adaptation index (tAI) to evaluate translation efficiency (dos Reis et al., 2004 and Experimental Procedures) at each codon.”
Codon Bias as a Means to Fine-Tune Gene Expression (2015, methodology): “To better analyze the relation between codon frequency bias and tRNA abundance in multicellular organisms, the tRNA adaptation index (tAI) was developed (dos Reis et al., 2004).”
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes (2011, methodology): “Subsets of genes for elongation rate analysis were as follows: (1) lowest and highest quintile of tAI, computed according to dos Reis et al. (2004); (2) lowest and highest quintile of ribosome footprint density; (3) short Cell 147, 789–802, November 11, 2011 ª2011 Elsevier Inc. 799 genes, 750–1,000…”
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution (2008, neutral): “Selection on translational efficiency in mammals is viewed as weak and contentious (Chamary et al., 2006) or absent (dos Reis et al., 2004).”
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition (2016, positive): “…that optimal codons are more commonly used in the transcriptome (P = 2.4e-06, R = 0.57, Spearman) (Fig lG), suggesting that codon optimality may be in part related to tRNA availability and codon usage (dos Reis et al, 2004; Pechmann & Frydman, 2013; Presnyak et al, 2015; Richter & Coller, 2015).”
Codon optimality is a major determinant of mRNA stability (2015, methodology): “The rare codons used in our previous studies belong to a general class of codons defined as non-optimal (Pechmann and Frydman, 2013; dos Reis et al., 2004).”