Summary
Codon usage and context are biased in open reading frames (ORFs) of most genomes. Codon usage is largely influenced by biased genome G+C pressure, in particular in prokaryotes, but the general rules that govern the evolution of codon context remain largely elusive. To shed new light into this question, we have developed computational, statistical, and graphical tools for analysis of codon context on an ORFeome wide scale. Here, we describe these methodologies in detail and show how they can be used for analysis of ORFs of any genome sequenced.
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References
Ogle, J. M. and Ramakrishnan, V. (2005) Structural insights into translational fidelity. Annu. Rev. Biochem. 74, 129–177.
Irwin, B., Heck, J. D., and Hatfields, W. G. (1995) Codon pair utilization biases influence translational elongation step times. J. Biol. Chem. 270, 22, 801–22, 806.
Young, E. T., Sloan, J. S., and Riper, K. V. (2000) Trinucleotide repeats are clustered in regulatory genes in Saccharomyces cerevisiae. Genetics 154, 1053–1068.
Borstnik, B. and Pumpernik, D. (2002) Tandem repeats in protein coding regions of primate genes. Genome Res. 12, 909–915.
Karlin, S., Brocchieri, L., Bergman, A., Mrazek, J., and Gentles, A. J. (2002) Amino acid runs in eukaryotic proteomes and disease associations. PNAS 99, 333–338.
Flis, K., Hinzpeter, A., Edelman, A., and Kurlandzka, A. (2005) The functioning of mammalian CIC-2 chloride channel in Saccharomyces cerevisiae cells requires an increased level of Kha1p. Biochem. J. 390, 655–664.
Folley, L. S. and Yarus, M. (1989) Codon contexts from weakly expressed genes reduce expression in vivo. J. Mol. Biol. 209, 359–378.
Cliften, P., Fulton, R., Wilson, R., and Johnston, M. (2006) After the duplication: gene loss and adaptation in Saccharomyces genomes. Genetics 172, 863–872.
Van de Lagemaat, L. N., Gagnier, L., Medstrand, P., and Mager, D. L. (2005) Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res. 15, 1243–1249.
Lin, Y. W., Thi, D. A. D., Kuo, P. L., et al. (2005) Polymorphisms associated with the DAZ genes on the human Y chromosome. Genomics 86, 431–438.
Chen, S. L., Lee, W., Hottes, A. K., and McAdams, H. H. (2004) Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. USA 101, 3480–3485.
Berg, O. G. and Silva, P. J. (1997) Codon bias in Escherichia coli: the influence of codon context on mutation and selection. Nucleic Acids Res. 25, 1397–1404.
Akashi, H. (1994) Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136, 927–935.
Percudani, R. and Ottonello, S. (1999) Selection at the wobble position of codons read by the same tRNA in Saccharomyces cerevisiae. Mol. Biol. Evol. 16, 1752–1762.
Boycheva, S., Chkodrov, G., and Ivanov, I. (2003) Codon pairs in the genome of Escherichia coli. Bioinformatic 19, 987–998.
Shah, A. A., Giddings, M. C., Parvaz, J. B., Gesteland, R. F., Atkins, J. F., and Ivanov, I. P. (2002) Computational identification of putative programmed translational frameshift sites. Bioinformatics 18, 1046–1053.
Fedorov, A., Saxonov, S., and Gilbert, W. (2002) Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res. 30, 1192–1197.
Duan, J. and Antezana, M. A. (2003) Mammalial mutation pressure, synonymous codon choice, and mRNA degradation. J. Mol. Evol. 57, 649–701.
Sharp, P. M. and Li, W. H. (1987) The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281–1295.
Haberman, S. J. (1973) The analysis of residuals in cross-classified tables. Biometrics 29, 205–220.
Simonoff, J. (2003) Analyzing Categorical Data. Springer-Verlag, New York.
Everitt, B. S., Landau, S., and Leese, M. (2001) Cluster Analysis. Hodder Arnold, London, UK.
Moura, G., Pinheiro, M., Silva, R., et al. (2005) Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol. 6, R28.
Wright, F. (1990) The ‘effective number of codons’ used in a gene. Gene 87, 23–29.
Acknowledgments
This study was supported by FCT/FEDER project grant REF: POCI/BIA-MIC/55466/04. GM is supported by FCT (SFRH/BPD/7195/2001). MASS is an EMBO YIP and his work is supported by the FCT/POCI program and the Human Frontier Science Program (Grant RGP45/2005). AVF is member of the R&D Unit “Matemática e Aplicações,” University of Aveiro (through POCTI/FCT, cofinanced by FEDER).
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Moura, G., Pinheiro, M., Freitas, A.V., Oliveira, J.L., Santos, M.A.S. (2007). Computational and Statistical Methodologies for ORFeome Primary Structure Analysis. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_28
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DOI: https://doi.org/10.1007/978-1-59745-514-5_28
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