Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (Ribosome profiling)

ABSTRACT: Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (Ribosome profiling)

PROVIDER: PRJNA545625 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9165310.fastq.gz	Fastqsanger.gz
	SRR9165320.fastq.gz	Fastqsanger.gz
	SRR9165311.fastq.gz	Fastqsanger.gz
	SRR9165312.fastq.gz	Fastqsanger.gz
	SRR9165313.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (CRISPR screen)

Project description:Sequences within 5' untranslated regions (UTRs) dictate the site and efficiency of translation initiation. In this study, an unbiased screen designed to interrogate the 5' UTR-mediated regulation of the growth-promoting gene MYC unexpectedly revealed the ribosomal pause-relief factor eIF5A as a regulator of translation initiation codon selection. Depletion of eIF5A enhanced upstream translation within 5' UTRs across yeast and human transcriptomes, including on the MYC transcript where this resulted in increased production of an N-terminally extended protein. Furthermore, ribosome profiling experiments established that the function of eIF5A as a suppressor of ribosomal pausing at sites of suboptimal peptide bond formation is conserved in human cells. We present evidence that proximal ribosomal pausing on a transcript triggers enhanced usage of upstream suboptimal or non-canonical initiation codons. Thus, we propose that eIF5A functions not only to maintain efficient translation elongation in eukaryotic cells, but also to maintain the fidelity of translation initiation.

2019-12-03 | GSE132009 | GEO

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (RNA-sequencing)

2019-12-03 | GSE132008 | GEO

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (Ribosome profiling)

2019-12-03 | GSE132007 | GEO

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection

Project description:Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection

| PRJNA545619 | ENA

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (CRISPR screen)

Project description:Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (CRISPR screen)

| PRJNA545621 | ENA

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (RNA-sequencing)

Project description:Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection (RNA-sequencing)

| PRJNA545624 | ENA

Suppression of Ribosomal Pausing by eIF5A Is Necessary to Maintain the Fidelity of Start Codon Selection.

Project description:Sequences within 5' UTRs dictate the site and efficiency of translation initiation. In this study, an unbiased screen designed to interrogate the 5' UTR-mediated regulation of the growth-promoting gene MYC unexpectedly revealed the ribosomal pause relief factor eIF5A as a regulator of translation initiation codon selection. Depletion of eIF5A enhances upstream translation within 5' UTRs across yeast and human transcriptomes, including on the MYC transcript, where this results in increased production of an N-terminally extended protein. Furthermore, ribosome profiling experiments established that the function of eIF5A as a suppressor of ribosomal pausing at sites of suboptimal peptide bond formation is conserved in human cells. We present evidence that proximal ribosomal pausing on a transcript triggers enhanced use of upstream suboptimal or non-canonical initiation codons. Thus, we propose that eIF5A functions not only to maintain efficient translation elongation in eukaryotic cells but also to maintain the fidelity of translation initiation.

| S-EPMC6917043 | biostudies-literature

Suppression of ribosomal pausing by eIF5A is necessary to maintain the fidelity of start codon selection

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

2019-12-03 | GSE132010 | GEO

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria

Project description: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 code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria using ribosome profiling-deep sequencing of ribosome-protected mRNA fragments. This approach enables high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare tRNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine-Dalgarno-(SD) like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we demonstrated that pausing is due to hybridization between mRNA and the 16S rRNA of the translating ribosome. In protein coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes. Identification of translation pause sites in vivo using ribosome profiling

2012-04-01 | E-GEOD-35641 | biostudies-arrayexpress

Translation initiation at a non-AUG start codon for mouse and human NELF-B

Project description:Negative elongation factor (NELF), a four-subunit protein complex in metazoan, plays an important role in regulating promoter-proximal pausing of RNA polymerase II (RNAPII). Genetic studies demonstrate that the B subunit of mouse NELF (NELF-B) is critical for embryonic development and homeostasis in adult tissue. We report here that both human and mouse NELF-B proteins are translated from a non-AUG codon upstream of the annotated AUG. This non-AUG codon sequence is conserved in mammalian NELF-B but not NELF-B orthologs of lower metazoan. The full-length and a truncated NELF-B that starts at the first AUG codon interact with the other three NELF subunits with comparable efficiency. Furthermore, these two forms of NELF-B have a similar impact on the transcriptomics and proliferation of mouse embryonic fibroblasts. These results strongly suggest that additional amino acid sequence upstream of the annotated AUG is dispensable for the essential function of NELF in supporting cell growth in vitro. While the majority of mouse adult tissues surveyed exclusively express the full-length NELF-B protein, mouse kidney only contains a truncated NELF-B protein with the same apparent size as the AUG-initiated version. This result raises the distinct possibility that translational initiation of mouse NELF-B is regulated in a tissue-dependent manner. triplicates for ATG-Nelf-B, triplicates for FL-Nelf-B

2014-10-11 | E-GEOD-62248 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data