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Codon usage optimization in pluripotent embryonic stem cells

ABSTRACT: Codon usage optimization in pluripotent embryonic stem cells

PROVIDER: PRJNA509373 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6869740_1.fastq.gz	Fastqsanger.gz
	SRR6869740_2.fastq.gz	Fastqsanger.gz
	SRR6869750_1.fastq.gz	Fastqsanger.gz
	SRR6869750_2.fastq.gz	Fastqsanger.gz
	SRR6869741_1.fastq.gz	Fastqsanger.gz

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Codon usage optimization in pluripotent embryonic stem cells [RNA-seq]

Project description:Codon usage optimization in pluripotent embryonic stem cells [RNA-seq]

| PRJNA439265 | ENA

Codon usage optimization in pluripotent embryonic stem cells [tRNA sequencing]

Project description:Codon usage optimization in pluripotent embryonic stem cells [tRNA sequencing]

| PRJNA509375 | ENA

Codon usage optimization in pluripotent embryonic stem cells [RNA-seq]

Project description:The uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the importance of this codon bias on regulating cell state-specific expression programs is currently debated. Here, we asked whether the gene expression program in the well-defined cell states of self-renewal and differentiation in embryonic stem cells is driven by optimized codon usage. Using ribosome and transcriptome profiling, we identified distinct codon signatures for human self-renewing and differentiating embryonic stem cells. One driver for the cell state-specific codon bias was the genomic GC-content of the differentially expressed genes and thus, determined by transcription rather than translation. However, by measuring the codon frequencies at the ribosome’s active sites interacting with transfer RNAs (tRNA), we discovered that the wobble position tRNA modification inosine strongly influenced the codon optimization in self-renewing embryonic stem cells. This effect was conserved in mice and independent of the differentiation stimulus. In summary, we newly reveal how translational mechanisms based on RNA modifications can shape optimized codon usage in embryonic stem cells.

2019-05-17 | GSE112085 | GEO

Codon usage optimization in pluripotent embryonic stem cells [tRNA sequencing]

2019-05-17 | GSE123608 | GEO

Codon usage optimization in pluripotent embryonic stem cells.

Project description:BackgroundThe uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the importance of this codon bias in regulating cell state-specific expression programmes is currently debated. Here, we ask whether different codon usage controls gene expression programmes in self-renewing and differentiating embryonic stem cells.ResultsUsing ribosome and transcriptome profiling, we identify distinct codon signatures during human embryonic stem cell differentiation. We find that cell state-specific codon bias is determined by the guanine-cytosine (GC) content of differentially expressed genes. By measuring the codon frequencies at the ribosome active sites interacting with transfer RNAs (tRNA), we further discover that self-renewing cells optimize translation of codons that depend on the inosine tRNA modification in the anticodon wobble position. Accordingly, inosine levels are highest in human pluripotent embryonic stem cells. This effect is conserved in mice and is independent of the differentiation stimulus.ConclusionsWe show that GC content influences cell state-specific mRNA levels, and we reveal how translational mechanisms based on tRNA modifications change codon usage in embryonic stem cells.

| S-EPMC6555954 | biostudies-literature

Codon usage optimization in pluripotent embryonic stem cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-05-17 | GSE123611 | GEO

Maximizing Heterologous Expression of Engineered Type I Polyketide Synthases: Investigating Codon Optimization Strategies

Project description:Type I polyketide synthases (T1PKSs) hold an enormous potential as a rational production platform for the biosynthesis of speciality chemicals. However, despite the great progress in this field, the heterologous expression of PKSs remains a major challenge. One of the first measures to improve heterologous gene expression can be codon optimization. Although controversial, choosing the wrong codon optimization strategy can have detrimental effects on protein and product levels. In this study, we analyzed 11 different codon variants of an engineered T1PKS and investigated in a systematic approach their influence on heterologous expression in Corynebacterium glutamicum, Escherichia coli, and Pseudomonas putida. Our best performing codon variants exhibited a minimum 50-fold increase in PKS protein levels, which also enables the production of an unnatural polyketide in each of the hosts. Furthermore, we developed a free online tool (https://basebuddy.lbl.gov) that offers transparent and highly customizable codon optimization with up-to-date codon usage tables. Here, we not only highlight the significance of codon optimization but also establish the groundwork for high-throughput assembly and characterization of PKS pathways in alternative hosts.

2023-09-01 | PXD042749 | Pride

Synonymous codon usage regulates translation initiation

Project description:Synonymous codon usage regulates translation initiation

| PRJNA837608 | ENA

Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

2018-08-02 | MSV000082680 | GNPS

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

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