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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.

SUBMITTER: Paulet D 

PROVIDER: S-EPMC5499818 | biostudies-other | 2017 Jun

REPOSITORIES: biostudies-other

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Ribo-seq enlightens codon usage bias.

Paulet Damien D   David Alexandre A   Rivals Eric E  

DNA research : an international journal for rapid publication of reports on genes and genomes 20170601 3


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 spe  ...[more]