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Synonymous codon massive reporter library in zebrafish embryos

ABSTRACT: Synonymous codon massive reporter library in zebrafish embryos

PROVIDER: PRJNA856272 | ENA |

REPOSITORIES: ENA

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Synonymous codon massive reporter library in zebrafish embryos

Project description:Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability 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 both mRNA stability using a massive reporter library and expression levels using fluorescent reporters and analysis of endogenous gene expression in zebrafish embryos and/or human cells. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.

2022-07-09 | GSE207584 | GEO

Synonymous codon usage regulates translation initiation

Project description:Synonymous codon usage regulates translation initiation

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mRNA sequence analysis of zebrafish embryos injected with the codon tag reporter library

Project description:mRNA sequence analysis of zebrafish embryos injected with the codon tag reporter library

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Ribosome profiling analysis of zebrafish embryos injected with the codon tag reporter library

Project description:Ribosome profiling analysis of zebrafish embryos injected with the codon tag reporter library

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mRNA sequence analysis of zebrafish embryos injected with the codon tag reporter library [AnsB]

Project description:mRNA sequence analysis of zebrafish embryos injected with the codon tag reporter library [AnsB]

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Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe.

Project description:Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans, but was not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution. Relative amounts of mRNA for each ORF were measured by DNA microarray using genomic DNA as a reference, and the copy number of mRNA was calculated using an estimate of the total mRNA number in the cell as 100,000 copies.

2010-06-20 | E-GEOD-13554 | biostudies-arrayexpress

Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe.

2009-04-01 | GSE13554 | GEO

mRNA sequence analysis of zebrafish embryos injected with the codon tag reporter library

Project description:We measured the effect of codons on mRNA stability in zebrafish embryos using reporter mRNAs. We showed that slow decoding of codons by the ribosome promoted mRNA degradation in zebrafish.

2021-12-03 | GSE173179 | GEO

Ribosome profiling analysis of zebrafish embryos injected with the codon tag reporter library

2021-12-06 | GSE173604 | GEO

mRNA sequence analysis of zebrafish embryos injected with the codon tag reporter library [AnsB]

2021-12-03 | GSE185915 | GEO