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Global mRNA Stability Is Not Associated with Levels of Gene Expression in Drosophila melanogaster But Shows a Negative Correlation with Codon Bias

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Abstract

A multitude of factors contribute to the regulation of gene expression in living cells. The relationship between codon usage bias and gene expression has been extensively studied, and it has been shown that codon bias may have adaptive significance in many unicellular and multicellular organisms. Given the central role of mRNA in post-transcriptional regulation, we hypothesize that mRNA stability is another important factor associated either with positive or negative regulation of gene expression. We have conducted genome-wide studies of the association between gene expression (measured as transcript abundance in public EST databases), mRNA stability, codon bias, GC content, and gene length in Drosophila melanogaster. To remove potential bias of gene length inherently present in EST libraries, gene expression is measured as normalized transcript abundance. It is demonstrated that codon bias and GC content in second codon position are positively associated with transcript abundance. Gene length is negatively associated with transcript abundance. The stability of thermodynamically predicted mRNA secondary structures is not associated with transcript abundance, but there is a negative correlation between mRNA stability and codon bias. This finding does not support the hypothesis that codon bias has evolved as an indirect consequence of selection favoring thermodynamically stable mRNA molecules.

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Acknowledgments

We thank John Parsch, Martin Kreitman, and anonymous reviewers for helpful comments. This work has been partly supported by the Norwegian Research Council grant no. 134800/410, and partly by the Swedish Research Council grant no. 621-2002-5896.

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  1. Hans K. Stenøien

    Present address: Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway

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  1. Plant Ecology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden

    Hans K. Stenøien

  2. Section of Evolutionary Biology, Biocenter, University of Munich, D-82152, Planegg-Martinsried, Germany

    Wolfgang Stephan

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Correspondence to Wolfgang Stephan.

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Stenøien, H.K., Stephan, W. Global mRNA Stability Is Not Associated with Levels of Gene Expression in Drosophila melanogaster But Shows a Negative Correlation with Codon Bias. J Mol Evol 61, 306–314 (2005). https://doi.org/10.1007/s00239-004-0271-9

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