Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA551383 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13046868.fastq.gz	Fastqsanger.gz
	SRR13046869.fastq.gz	Fastqsanger.gz
	SRR9604615.fastq.gz	Fastqsanger.gz
	SRR9604617.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

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

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

Codon usage and 3â² UTR length determine maternal mRNA stability in zebrafish

Project description: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, although the underlying mechanisms are poorly understood in vertebrates. Here, we characterized maternal mRNA degradation pathways in zebrafish using a transcriptome analysis and systematic reporter assays. Our data demonstrate that ORFs enriched with uncommon codons promote deadenylation by the CCR4-NOT complex in a translation-dependent manner. This codon-mediated mRNA decay is conditional on the context of the 3â² UTR, with long 3â² UTRs conferring resistance to deadenylation. These results indicate that the combined effect of codon usage and 3â² UTR length determines the stability of maternal mRNAs in zebrafish embryos. Our study thus highlights the codon-mediated mRNA decay as a conserved regulatory mechanism in eukaryotes. zebrafish embryonic mRNA profile at 2 different stages (2 hpf and 6 hpf) in wildtype and 3 additional conditions (miR-430 inhibition, RNApol II inhibition and CNOT7 inhibition) at 6 hpf. All experiments are performed as triplicates

2016-03-17 | E-GEOD-71609 | biostudies-arrayexpress

Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay

Project description:New1 is a homolog of fungal translation elongation factor 3 (eEF3) inSaccharomyces cerevisiae. Its absence has previously been described to lead to cold sensitivity, ribosome biogenesis defects, and ribosomal queues upstream of Stop codons on selected mRNAs. Here, we find that, especially in cold conditions, lack of New1 induces no-go decay (NGD) on specificmRNAs, leading, as a consequence, to decreased mRNA and protein levels of such genes.The effect correlates with the presence of specific Lysine and Arginine codons just upstream of the Stop codon. In total, more than 10% of yeast coding sequences end with the affected codons. We have confirmed NGD and subsequent downregulation at the protein level for the metabolic enzymes Pgk1, Gpm1, and Adh1, translation elongation factors EF-1 alpha and EF-1 beta (gamma-subunit), ribosomal protein Rps5, as well as ribosome biogenesis factor Nop1 and adenosine kinase Ado1.

2024-11-26 | GSE275093 | GEO

Codon usage and 3′ UTR length determine maternal mRNA stability in zebrafish

Project description: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, although the underlying mechanisms are poorly understood in vertebrates. Here, we characterized maternal mRNA degradation pathways in zebrafish using a transcriptome analysis and systematic reporter assays. Our data demonstrate that ORFs enriched with uncommon codons promote deadenylation by the CCR4-NOT complex in a translation-dependent manner. This codon-mediated mRNA decay is conditional on the context of the 3′ UTR, with long 3′ UTRs conferring resistance to deadenylation. These results indicate that the combined effect of codon usage and 3′ UTR length determines the stability of maternal mRNAs in zebrafish embryos. Our study thus highlights the codon-mediated mRNA decay as a conserved regulatory mechanism in eukaryotes.

2016-03-17 | GSE71609 | GEO

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay

Project description:Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay

| PRJNA757956 | ENA

Synonymous codon massive reporter library in zebrafish embryos

Project description:Synonymous codon massive reporter library in zebrafish embryos

| PRJNA856272 | ENA

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [QuantMseq]

Project description:Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [QuantMseq]

| PRJNA757960 | ENA

Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [DecaySeq]

Project description:Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [DecaySeq]