Ribo-seq enlightens codon usage bias

Abstract : Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of ribosome protected mRNA fragments (Ribo-seq) allowed us to rank genes and compute codon usage bias with high precision for a great variety of species, including mammals. Genes ranking using Ribo-Seq data confirms the influence of the tRNA pool on codon usage bias and shows a decreasing bias in multicellular species. Ribo-Seq analysis also makes possible to detect preferred codons without information on genes function.
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Submitted on : Wednesday, October 4, 2017 - 12:22:35 PM
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Damien Paulet, Alexandre David, Eric Rivals. Ribo-seq enlightens codon usage bias. DNA Research, Oxford University Press (OUP), 2017, 24 (3), pp.303-210. ⟨https://academic.oup.com/⟩. ⟨10.1093/dnares/dsw062⟩. ⟨lirmm-01610054⟩

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