RT Journal Article SR Electronic T1 iCodon: ideal codon design for customized gene expression JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.05.06.442969 DO 10.1101/2021.05.06.442969 A1 Medina-Muñoz, Santiago Gerardo A1 Diez, Michay A1 Castellano, Luciana Andrea A1 da Silva Pescador, Gabriel A1 Wu, Qiushuang A1 Bazzini, Ariel Alejandro YR 2021 UL http://biorxiv.org/content/early/2021/05/07/2021.05.06.442969.abstract AB 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 StatementThe authors have declared no competing interest.mRNAmessenger RNAmiRmicroRNAsm6AN6-methyladenosinem5C5-methylcytosineP2A2A ribosome skipping sequenceGFPgreen fluorescent proteinEGFPenhanced green fluorescent proteinAausFP1Aequorea. cf. australis fluorescent protein 1UTRuntranslated regions