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MBE Advance Access published online on November 9, 2005
Molecular Biology and Evolution, 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
Accepted November 2, 2005

Research Article

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

Marie Sémon 1, Jean R. Lobry 1, and Laurent Duret 1*

1 Laboratoire de Biométrie et Biologie Evolutive (UMR 5558); CNRS; Univ. Lyon 1; 16 rue Raphaël Dubois, 69622 Villeurbanne Cedex, France

* To whom correspondence should be addressed.
Laurent Duret, E-mail: duret{at}biomserv.univ-lyon1.fr


  Abstract

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 et al 2004 Proc. Natl. Acad. Sci. 101:12588-12591). To test this model, we analysed 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.

Keywords: codon usage; tissue-specific; expression; GC-content; multivariate analysis; correspondence analysis.
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