Journal Article

Weak 5′-mRNA Secondary Structures in Short Eukaryotic Genes

Yang Ding, Premal Shah and Joshua B. Plotkin

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 4, issue 10, pages 1046-1053
Published in print January 2012 |
Published online October 2012 | e-ISSN: 1759-6653 | DOI:

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  • Bioinformatics and Computational Biology
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Experimental studies of translation have found that short genes tend to exhibit greater densities of ribosomes than long genes in eukaryotic species. It remains an open question whether the elevated ribosome density on short genes is due to faster initiation or slower elongation dynamics. Here, we address this question computationally using 5′-mRNA folding energy as a proxy for translation initiation rates and codon bias as a proxy for elongation rates. We report a significant trend toward reduced 5′-secondary structure in shorter coding sequences, suggesting that short genes initiate faster during translation. We also find a trend toward higher 5′-codon bias in short genes, suggesting that short genes elongate faster than long genes. Both of these trends hold across a diverse set of eukaryotic taxa. Thus, the elevated ribosome density on short eukaryotic genes is likely caused by differential rates of initiation, rather than differential rates of elongation.

Keywords: translation initiation; ribosome density; codon bias; gene length

Journal Article.  4751 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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