Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages.

Nucleic Acids Research
Yedael Y WaldmanEytan Ruppin

Abstract

Various studies in unicellular and multicellular organisms have shown that codon bias plays a significant role in translation efficiency (TE) by co-adaptation to the tRNA pool. Yet, in humans and other mammals the role of codon bias is still an open question, with contradictory results from different studies. Here we address this question, performing a large-scale tissue-specific analysis of TE in humans, using the tRNA Adaptation Index (tAI) as a direct measure for TE. We find tAI to significantly correlate with expression levels both in tissue-specific and in global expression measures, testifying to the TE of human tissues. Interestingly, we find significantly higher correlations in adult tissues as opposed to fetal tissues, suggesting that the tRNA pool is more adjusted to the adult period. Optimization based analysis suggests that the tRNA pool-codon bias co-adaptation is globally (and not tissue-specific) driven. Additionally, we find that tAI correlates with several measures related to the protein functionally importance, including gene essentiality. Using inferred tissue-specific tRNA pools lead to similar results and shows that tissue-specific genes are more adapted to their tRNA pool than other genes and that related ...Continue Reading

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Citations

Aug 2, 2011·Genome Biology and Evolution·Yedael Y WaldmanEytan Ruppin
Dec 2, 2010·Human Molecular Genetics·Elisa DominguezMartine Barkats
Sep 13, 2011·PLoS Computational Biology·Shlomi ReuveniTamir Tuller
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Sep 30, 2021·Oncogene·Sarah L GillenMartin Bushell

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Methods Mentioned

BETA
chip
GTPase

Software Mentioned

BioMart
DAVID
DAVID bioinformatics Functional Annotation tool

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