Elsevier

Genomics

Volume 83, Issue 3, March 2004, Pages 502-507
Genomics

Short communication
Amino acids runs and genomic compositional biases in vertebrates

https://doi.org/10.1016/j.ygeno.2003.09.004Get rights and content

Abstract

A compositional analysis of a sample of 50 zebrafish proteins containing at least one alanine run and of their open reading frames (ORFs) has been performed. The sample of poly(Ala) proteins showed a tendency to have runs of other amino acids (His/H, Gln/Q, Ser/S, Pro/P). Their ORFs and the first and second codon positions had higher GC contents than a reference gene set. The “universal” correlation between the GC content of the first+second and third codon positions (GC1+2 vs GC3) does not hold, but I provide an explanation in terms of genomic heterogeneity. Significant correlation between AHQS content and GC3 was obtained, reflecting codon bias favoring G/C at the third codon position of these amino acids. A correspondence analysis (COA) of relative synonymous codon usage showed that the poly(Ala) proteins have a biased distribution according to the second axis of the COA, which correlates with gene expression in zebrafish. A comparison with human is undertaken.

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Acknowledgements

My work is supported by the Université Denis Diderot/Paris VII and the INSERM. I thank S. Caburet and J. Cocquet for helpful comments and H. Musto for sharing in-press data. Thanks to P. Sharp for helpful discussions about COA.

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Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.ygeno.2003.09.004.

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