Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synonymous codon massive reporter library in zebrafish embryos

ABSTRACT: 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.

ORGANISM(S): Danio rerio

PROVIDER: GSE207584 | GEO | 2022/07/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Determination of decay rates across the transcriptome and identification of controlling features

Project description:In this work, we determine andenylated and total mRNA decay rates and correlate them with codon optimality. We conclude that optimality is a major contributor to mRNA stability in budding yeast.

2015-03-17 | GSE57385 | GEO

Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability

Project description:The half-life of mRNAs, as well as their translation, increases proportionally to the optimal codons, indicating a tight coupling of codon-dependent differential translation and degradation. Little is known about the regulation of this coupling. We found that the coupling in yeast displays a dichotomous behavior regarding the mRNA coding sequence length. Below a critical length, codon optimality fails to affect the stability of mRNAs even though they can be efficiently translated into short peptides and proteins. Above this threshold length, codon optimality-dependent differential mRNA stability emerges in a switch-like fashion, which coincides with a similar increase in the polysome propensity of the mRNAs. This threshold length can be tuned by the untranslated regions (UTR). Some of these UTRs can destabilize mRNAs without reducing translation, which plays a role in controlling the amplitude of the oscillatory expression of cell-cycle genes. Our findings help understand the translation of short peptides from noncoding RNAs and the translation by localized monosomes in neurons.

2023-09-28 | GSE235627 | GEO

The Ccr4-Not complex monitors the translating ribosome for codon optimality

Project description:Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo–electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae. This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.

2020-04-16 | GSE144250 | GEO

The Ccr4-Not complex monitors the translating ribosome for codon optimality

2020-04-16 | GSE131408 | GEO

Synonymous codon massive reporter library in zebrafish embryos

Project description:Synonymous codon massive reporter library in zebrafish embryos

| PRJNA856272 | ENA

Defining codon-mediated mRNA decay and No-go decay in zebrafish embryos

Project description:The control of mRNA stability plays a central role in regulating gene expression patterns. While much is known about the roles of 5´ and 3´ untranslated regions in the mRNA stability control, the impact of protein-coding sequences on mRNA stability had been obscure. Recently, several groups reported that codon composition in the ORF affects mRNA deadenylation and degradation rates in a translation-dependent manner. Hence, codons define not only the amino acid sequences to be synthesized but also the stability of mRNAs. However, how 61 codons differently affect mRNA stability remains unclear. Besides, aberrant stalling of the ribosome induces ribosome quality control (RQC) and No-go decay. The relationship between the two co-translational mRNA decay pathways is not systematically analyzed. To precisely characterize the effects of 61 codons on mRNA stability, we developed a simplified reporter system that allows detection of the effect of every single codon on mRNA stability in zebrafish embryos. Using this system, we show that the effect of codons on mRNA stability is partially but significantly correlated with the translation elongation rate and tRNA abundance. Interestingly, the codon effect is still maintained in zebrafish embryos lacking Znf598, an essential mediator of RQC and NGD. Znf598-dependent NGD targets a particular type of ribosome stalling but has limited impact on endogenous mRNA stability. Our study thus defines two related co-translational mRNA decay pathways during animal development.

2020-05-05 | GSE133392 | GEO

Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [ncRNA-seq]

Project description:In Caenorhabditis elegans germline, thousands of mRNAs are concomitantly expressed with antisense 22G-RNAs, which are loaded into the Argonaute CSR-1. Despite their essential functions for animal fertility and embryonic development, how CSR-1 22G-RNAs are produced remain unknown. Here, we show that CSR-1 slicer activity is primarily involved in triggering the synthesis of small RNAs on the coding sequences of germline mRNAs and post-transcriptionally regulates a fraction of targets. CSR-1-cleaved mRNAs prime the RNA-dependent RNA polymerase, EGO-1 to synthesize 22G-RNAs concurrently with ribosome translation in the cytoplasm, in contrast to other 22G-RNAs mostly synthesized in germ-granules. Moreover, differences in germline mRNA codon optimality and ribosome occupancy antagonistically affect the abundance of CSR-1 22G-RNAs and the stability of their mRNA targets. We propose that codon usage differences encoded into mRNA sequences might be a conserved strategy adopted in eukaryotes to regulate small RNA biogenesis and Argonaute targeting.

2021-04-22 | GSE155076 | GEO

Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [RIP-Seq]

2021-04-22 | GSE155075 | GEO

Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [RNA-Seq]

2021-04-22 | GSE155074 | GEO

Translation and codon usage regulate Argonaute slicer activity to trigger germline small RNA biogenesis [Ribo-Seq]

2021-04-22 | GSE155073 | GEO