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iCodon: ideal codon design for customized gene expression

Santiago Gerardo Medina-Muñoz, Michay Diez, Luciana Andrea Castellano, Gabriel da Silva Pescador, View ORCID ProfileQiushuang Wu, View ORCID ProfileAriel Alejandro Bazzini
doi: https://doi.org/10.1101/2021.05.06.442969
Santiago Gerardo Medina-Muñoz
1Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
2National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, 36824 Irapuato, Mexico
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Michay Diez
1Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
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Luciana Andrea Castellano
1Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
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Gabriel da Silva Pescador
1Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
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Qiushuang Wu
1Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
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Ariel Alejandro Bazzini
1Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
3Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
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  • For correspondence: arb@stowers.org
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Abstract

Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability, in turn, is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon (www.iCodon.org), an algorithm for customizing mRNA expression through the introduction of synonymous codon substitutions into the coding sequence. iCodon is optimized for four vertebrate transcriptomes: mouse, human, frog, and fish. Users can predict the mRNA stability of any coding sequence based on its codon composition and subsequently generate more stable (optimized) or unstable (deoptimized) variants encoding for the same protein. Further, we show that codon optimality predictions correlate with expression levels using fluorescent reporters and endogenous genes in human cells and zebrafish embryos. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.

Competing Interest Statement

The authors have declared no competing interest.

  • Abbreviations

    mRNA
    messenger RNA
    miR
    microRNAs
    m6A
    N6-methyladenosine
    m5C
    5-methylcytosine
    P2A
    2A ribosome skipping sequence
    GFP
    green fluorescent protein
    EGFP
    enhanced green fluorescent protein
    AausFP1
    Aequorea. cf. australis fluorescent protein 1
    UTR
    untranslated regions
  • Copyright 
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    iCodon: ideal codon design for customized gene expression
    Santiago Gerardo Medina-Muñoz, Michay Diez, Luciana Andrea Castellano, Gabriel da Silva Pescador, Qiushuang Wu, Ariel Alejandro Bazzini
    bioRxiv 2021.05.06.442969; doi: https://doi.org/10.1101/2021.05.06.442969
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    iCodon: ideal codon design for customized gene expression
    Santiago Gerardo Medina-Muñoz, Michay Diez, Luciana Andrea Castellano, Gabriel da Silva Pescador, Qiushuang Wu, Ariel Alejandro Bazzini
    bioRxiv 2021.05.06.442969; doi: https://doi.org/10.1101/2021.05.06.442969

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