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MetabolomicsVirus-induced codon-specific reprogramming to favor viral RNA translation
Recent evidence indicates that codon usage bias regulates gene expression. How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in rare codons remains a puzzling question. Using ribosome footprinting, here we analysed ...
2025-06-16 | MTBLS2443 | MetaboLights
TranscriptomicsCodon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe.
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 Schizosac...
ORGANISM(S): Schizosaccharomyces pombe 
2010-06-20 | E-GEOD-13554 | biostudies-arrayexpress
TranscriptomicsThe anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
Protein synthesis by ribosomes takes place on a linear substrate but at variable speeds. Transient pausing of ribosomes can impact a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the mRNA. Thus redundancy in the genetic...
ORGANISM(S): Escherichia coli 
2012-04-01 | E-GEOD-35641 | biostudies-arrayexpress
TranscriptomicsCodon usage and 3′ UTR length determine maternal mRNA stability in zebrafish
The control of mRNA stability plays a central role in regulating gene expression. In metazoans, the earliest stages of development are driven by maternally supplied mRNAs. The degradation of these maternal mRNAs is critical for promoting the maternal-to-zygotic transition of developmental programs, ...
ORGANISM(S): Danio rerio 
2016-03-17 | E-GEOD-71609 | biostudies-arrayexpress
GenomicsStress-adapted codon usage enables efficient virulence-gene expression in Salmonella
Synthetic codon-recoded fluorescent-protein sequences and plasmids used to study stress-adapted codon usage in Salmonella
PRJEB115179 | ENA
GenomicsCodon usage optimization in pluripotent embryonic stem cells [tRNA sequencing]
Codon usage optimization in pluripotent embryonic stem cells [tRNA sequencing]
PRJNA509375 | ENA
GenomicsCodon usage optimization in pluripotent embryonic stem cells [RNA-seq]
Codon usage optimization in pluripotent embryonic stem cells [RNA-seq]
PRJNA439265 | ENA
ProteomicsTranscriptomic, proteomic and functional consequences of codon usage bias in human cells
Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Integrative studies quantifying the phenotypic consequences of codon usage bias at different molecular and cellular l...
ORGANISM(S): Homo sapiens (Human) 
2024-05-24 | PXD038324 | Pride
Culture Mass spectrometry Hek-293 
ProteomicsThe temperature quickly modulates protein expression by Codon Usage in wheat filling grain
The protein content determines the cell state. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown. We quantified 47,535 mRNAs and 3,742 proteins in filling grain of wheat under two thermal e...
ORGANISM(S): Triticum aestivum (Wheat) 
2021-03-24 | PXD021460 | Pride
Heat stress  post-transcriptional regulation  codon usage  aag frequency  wheat 
Proteomics,MultiomicsAnalysis of peripheral neuron protein expression in the absence of Ikbkap/Elp1
Familial dysautonomia (FD) results from mutation in IKBKAP/ELP1, a gene encoding the scaffolding protein for the Elongator complex. This highly conserved complex is required for the methoxy-carbonyl-methyl (mcm5) modification of uridines located in the wobble position of tRNA molecules (U34). In F...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
MSV000081568 | MassIVE
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