GEO DataSets

(Submitter supplied) We report on how the absence of expansion segment 7S from the yeast ribosome alters A-site occupancy along transcripts. This has consequence for local translation rates and protein fidelity.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26302

11 Samples

Download data: TXT

(Submitter supplied) We report on how the association of mRNA to translating ribosomes changes due to the absence of the expansion segment 27L in S. cerevisiae. We observe specific enrichment and depletion of mRNA sets from rmutant ribosomes which reshapes the proteome.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23014

12 Samples

Download data: TXT

(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:

GPL17342 GPL13821 GPL19756

25 Samples

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

(Submitter supplied) We report on how the presence or absence of a 18 nt long ribosome-bound RNA affects the translation in S. cerevisiae. We observe that translation of all mRNAs is downregulated when the RNA is present.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23014

16 Samples

Download data: TXT

(Submitter supplied) Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. The anticodon modification mcm5s2U34 is required for normal growth and stress resistance in yeast; mutants lacking this modification have numerous phenotypes. Mutations in the homologous human genes are linked to neurological disease. The yeast phenotypes can be ameliorated by overexpression of specific tRNAs, suggesting that the modifications are necessary for efficient translation of specific codons. more...

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13272

24 Samples

Download data: TXT

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

Organism:

Caenorhabditis elegans; Saccharomyces cerevisiae; Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL18245 GPL17342

56 Samples

Download data: WIG

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens; Caenorhabditis elegans

Type:

Other

Platforms:

GPL16791 GPL18245 GPL17342

28 Samples

Download data: CSV, WIG

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

7 Samples

Download data: CSV

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

6 Samples

Download data: TSV

(Submitter supplied) Ribosomes undergo substantial conformational changes during translation elongation to accommodate incoming aminoacyl-tRNAs and translocate along the mRNA template. We used multiple elongation inhibitors and chemical probing to define ribosome conformational states corresponding to different sized ribosome-protected mRNA fragments (RPFs) generated by ribosome profiling. We show using various genetic and environmental perturbations that the previously identified 20-22 nucleotide (nt) RPFs correspond predominantly to ribosomes in a pre-accommodation state with an open 40S ribosomal A site while the classical 27-29 nt fragments correspond to ribosomes in a pre-translocation state with an occupied 40S ribosomal A site. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

15 Samples

Download data: TSV

(Submitter supplied) Ribosome queuing is a fundamental phenomenon suggested to be related to topics such as genome evolution, synthetic biology, gene expression regulation, intracellular biophysics, and more. However, this phenomenon hasn't been quantified yet at a genomic level. Nevertheless, methodologies for studying translation (e.g. ribosome footprints) are usually calibrated to capture only single ribosome protected footprints (mRPFs) and thus limited in their ability to detect ribosome queuing. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

3 Samples

Download data: TSV

(Submitter supplied) Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL13821

3 Samples

Download data: TXT

(Submitter supplied) Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. more...

Organism:

Caenorhabditis elegans; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19959 GPL19958

98 Samples

Download data: TXT

(Submitter supplied) Roles for ribosomal RNA (rRNA) in gene regulation remain largely unexplored. With hundreds of rDNA units positioned across multiple loci, it is not possible to genetically modify rRNA in mammalian cells, hindering understanding of ribosome function. It remains elusive whether expansion segments (ESs), tentacle-like rRNA extensions that vary in sequence and size across eukaryotic evolution, may have functional roles in translation control. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

7 Samples

Download data: TXT