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MBE Advance Access originally published online on November 9, 2005
Molecular Biology and Evolution 2006 23(3):523-529; doi:10.1093/molbev/msj053
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

Marie Sémon, Jean R. Lobry and Laurent Duret

Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Villeurbanne, France

E-mail: duret{at}biomserv.univ-lyon1.fr.

It has been proposed that the synonymous codon usage of human tissue-specific genes was under selective pressure to modulate the expression of proteins by codon-mediated translational control (Plotkin, J. B., H. Robins, and A. J. Levine. 2004. Tissue-specific codon usage and the expression of human genes. Proc. Natl. Acad. Sci. USA 101:12588–12591.) To test this model, we analyzed by internal correspondence analysis the codon usage of 2,126 human tissue-specific genes expressed in 18 different tissues. We confirm that synonymous codon usage differs significantly between the tissues. However, the effect is very weak: the variability of synonymous codon usage between tissues represents only 2.3% of the total codon usage variability. Moreover, this variability is directly linked to isochore-scale (>100 kb) variability of GC-content that affect both coding and introns or intergenic regions. This demonstrates that variations of synonymous codon usage between tissue-specific genes expressed in different tissues are due to regional variations of substitution patterns and not to translational selection.

Key Words: codon usage • tissue specific • expression • GC-content • multivariate analysis • correspondence analysis


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