GEO DataSets

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL18573

28 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) Snapshot of translation in mammalian cells that are depleted of polyamines or replete with polyamines. Hek293T cells treated with DFMO or Spermidine.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

4 Samples

Download data: CSV

(Submitter supplied) The eukaryotic translation factor eIF5A, originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. Using a combination of ribosome profiling and in vitro biochemistry, we report a much broader role for eIF5A in elongation and uncover a substantial function for eIF5A in termination. Ribosome profiling of an eIF5A-depleted strain reveals a global elongation defect, with abundant ribosomes stalling at many sequences, not limited to proline stretches. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

8 Samples

Download data: WIG

(Submitter supplied) eIF5A is an essential translation elongation factor present in all eukaryotes, and the only known protein to follow a post-translational modification called hypusination. Here, we performed a wide analysis of ribosome dynamics in S. cerevisiae eIF5A depleted cells using 5Pseq (Pelechano et al. 2015 PMID 26046441). This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

8 Samples

Download data: BEDGRAPH

(Submitter supplied) Members of the third domain of life, the Archaea, are ubiquitous in all environments on Earth but remain understudied in many aspects including regulatory processes of the central dogma. Archaea present unique biology because they utilize a mosaic of molecular features from both Bacteria and Eukarya, along with unique features. The advent of a high-throughput view of the translation landscape via ribosome profiling in the Bacteria and the Eukarya has illuminated the complexity and previously underappreciated regulation of translation (i.e. more...

Organism:

Haloferax volcanii DS2

Type:

Other

Platform:

GPL27628

8 Samples

Download data: GFF, WIG

(Submitter supplied) The fidelity of start codon recognition by ribosomes is paramount during protein synthesis. The textbook knowledge of eukaryotic translation initiation depicts 5’→3’ unidirectional migration of the pre-initiation complex (PIC) along the 5’UTR. In probing translation initiation from ultra-short 5’UTR, we report that an AUG triplet near the 5’ end can be selected via PIC backsliding. The bi-directional ribosome scanning is supported by competitive selection of closely spaced AUG codons and recognition of two initiation sites flanking an internal ribosome entry site. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL17021 GPL19057 GPL18573

22 Samples

Download data: TXT

(Submitter supplied) The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian ortholog DDX3 are critical for translation initiation. Mutations in DDX3 are linked to tumorigenesis and intellectual disability, and the enzyme is targeted by diverse viruses. How Ded1p and its orthologs engage RNAs to impact translation initiation has been a longstanding, unresolved question. Here we show that Ded1p associates with the pre-initiation complex at the mRNA entry channel of the small ribosomal subunit and that the helicase unwinds mRNA structure ahead of the scanning pre-initiation complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21656 GPL17342

38 Samples

Download data: TAB, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

10 Samples

Download data

(Submitter supplied) In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

4 Samples

Download data: TXT

(Submitter supplied) In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

2 Samples

Download data: TXT

(Submitter supplied) In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

4 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21741

4 Samples

Download data: TXT

(Submitter supplied) The journey of a newly synthesized polypeptide starts in the peptidyltransferase center of the ribosome, from where it traverses the exit tunnel. The interior of the ribosome exit tunnel is neither straight nor smooth. How the ribosome dynamics in vivo is influenced by the exit tunnel is poorly understood. Genome-wide ribosome profiling in mammalian cells reveals elevated ribosome density at the start codon and surprisingly the downstream 5th codon position as well. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that limitation for the amino acid arginine causes a selective loss of tRNA charging, which regulates translation through ribosome pausing at two of six arginine codons. Interestingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

34 Samples

Download data: TSV

(Submitter supplied) Translation initiation is considered overall rate-limiting for protein biosynthesis, whereas the impact of non-uniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ~10% of translating ribosomes in the disome state. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

6 Samples

Download data: TSV

(Submitter supplied) The goal of this study is to evaluate the competition between eIF5 and 5MP in utilizing non-AUG translation initiation sites

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

8 Samples

Download data: TAR

(Submitter supplied) Ribosome binding proteins function broadly in protein synthesis, gene regulation and cellular homeostasis but the complete complement of functional ribosome-bound proteins remains unknown. Using quantitative mass spectrometry we identified Late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog CCDC124 recovered 25S rRNA in a region near the A site that overlaps the GTPase activating center. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13821 GPL17342 GPL19756

25 Samples

Download data: BED, BEDGRAPH, FASTA, GFF, TXT, WIG