References
- Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L. Natural selection has driven population differentiation in modern humans. Nat Genet 2008;40:340-345. https://doi.org/10.1038/ng.78
- Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 2003;31:3812-3814. https://doi.org/10.1093/nar/gkg509
- Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986;3:418-426.
- King JL, Jukes TH. Non-Darwinian evolution. Science 1969;164:788-798. https://doi.org/10.1126/science.164.3881.788
- Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007;24:1586-1591. https://doi.org/10.1093/molbev/msm088
- Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 2002;30:3894-3900. https://doi.org/10.1093/nar/gkf493
- Thomas RK, Baker AC, Debiasi RM, Winckler W, Laframboise T, Lin WM, et al. High-throughput oncogene mutation profiling in human cancer. Nat Genet 2007;39:347-351. https://doi.org/10.1038/ng1975
- Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 2007;39:207-211. https://doi.org/10.1038/ng1954
- Romeo S, Kozlitina J, Xing C, Pertsemlidis A, Cox D, Pennacchio LA, et al. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet 2008;40:1461-1465. https://doi.org/10.1038/ng.257
- Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum Mutat 2009;30:1237-1244. https://doi.org/10.1002/humu.21047
- Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010;42:30-35. https://doi.org/10.1038/ng.499
- Li MX, Kwan JS, Bao SY, Yang W, Ho SL, Song YQ, et al. Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS Genet 2013;9:e1003143. https://doi.org/10.1371/journal.pgen.1003143
- Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 2011;12:32-42. https://doi.org/10.1038/nrg2899
- Doherty A, McInerney JO. Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates. Mol Biol Evol 2013;30:2263-2267. https://doi.org/10.1093/molbev/mst128
- Komar AA. The Yin and Yang of codon usage. Hum Mol Genet 2016;25:R77-R85. https://doi.org/10.1093/hmg/ddw207
- Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 1985;2:13-34.
- Chamary JV, Parmley JL, Hurst LD. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 2006;7:98-108. https://doi.org/10.1038/nrg1770
- Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH. Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci U S A 2004;101:3480-3485. https://doi.org/10.1073/pnas.0307827100
- Nabiyouni M, Prakash A, Fedorov A. Vertebrate codon bias indicates a highly GC-rich ancestral genome. Gene 2013;519:113-119. https://doi.org/10.1016/j.gene.2013.01.033
- Lavner Y, Kotlar D. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 2005;345:127-138. https://doi.org/10.1016/j.gene.2004.11.035
- Quax TE, Claassens NJ, Soll D, van der Oost J. Codon bias as a means to fine-tune gene expression. Mol Cell 2015;59:149-161. https://doi.org/10.1016/j.molcel.2015.05.035
- Zhou Z, Dang Y, Zhou M, Li L, Yu CH, Fu J, et al. Codon usage is an important determinant of gene expression levels largely through its effects on transcription. Proc Natl Acad Sci U S A 2016;113:E6117-E6125. https://doi.org/10.1073/pnas.1606724113
- Tuller T, Carmi A, Vestsigian K, Navon S, Dorfan Y, Zaborske J, et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 2010;141:344-354. https://doi.org/10.1016/j.cell.2010.03.031
- Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol 2001;53:290-298. https://doi.org/10.1007/s002390010219
- Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, et al. Codon optimality is a major determinant of mRNA stability. Cell 2015;160:1111-1124. https://doi.org/10.1016/j.cell.2015.02.029
- Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008;134:341-352. https://doi.org/10.1016/j.cell.2008.05.042
- Comeron JM, Kreitman M, Aguade M. Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 1999;151:239-249.
- Marais G, Mouchiroud D, Duret L. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci U S A 2001;98:5688-5692. https://doi.org/10.1073/pnas.091427698
- Zhou T, Lu ZH, Sun X. The correlation between recombination rate and codon bias in yeast mainly results from mutational bias associated with recombination rather than Hill-Robertson Interference. Conf Proc IEEE Eng Med Biol Soc 2005;5:4787-4790.
- Novoa EM, Pavon-Eternod M, Pan T, Ribas de Pouplana L. A role for tRNA modifications in genome structure and codon usage. Cell 2012;149:202-213. https://doi.org/10.1016/j.cell.2012.01.050
- Zalucki YM, Beacham IR, Jennings MP. Biased codon usage in signal peptides: a role in protein export. Trends Microbiol 2009;17:146-150. https://doi.org/10.1016/j.tim.2009.01.005
- Clarke TF 4th, Clark PL. Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. BMC Genomics 2010;11:118. https://doi.org/10.1186/1471-2164-11-118
- Zhou M, Guo J, Cha J, Chae M, Chen S, Barral JM, et al. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 2013;495:111-115. https://doi.org/10.1038/nature11833
- Michel F, Dujon B. Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplastand nuclear-encoded members. EMBO J 1983;2:33-38.
- Takahashi A. Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam. BMC Evol Biol 2009;9:214. https://doi.org/10.1186/1471-2148-9-214
- Sharp PM, Tuohy TM, Mosurski KR. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 1986;14:5125-5143. https://doi.org/10.1093/nar/14.13.5125
- Warnecke T, Hurst LD. Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster. Mol Biol Evol 2007;24:2755-2762. https://doi.org/10.1093/molbev/msm210
- Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, et al. Exonic transcription factor binding directs codon choice and affects protein evolution. Science 2013;342:1367-1372. https://doi.org/10.1126/science.1243490
- Kepes F. The “+70 pause”: hypothesis of a translational control of membrane protein assembly. J Mol Biol 1996;262:77-86. https://doi.org/10.1006/jmbi.1996.0500
- Zhou T, Weems M, Wilke CO. Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol 2009;26:1571-1580. https://doi.org/10.1093/molbev/msp070
- Zhang G, Hubalewska M, Ignatova Z. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol 2009;16:274-280. https://doi.org/10.1038/nsmb.1554
- Saunders R, Deane CM. Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res 2010; 38:6719-6728. https://doi.org/10.1093/nar/gkq495