GEO DataSets

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

Organism:

Caenorhabditis elegans; Homo sapiens; Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL18245 GPL17342 GPL16791

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:

GPL18245 GPL17342 GPL16791

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

15 Samples

Download data: TSV

(Submitter supplied) We leverage a model statistical framework coupled with high resoluation ribosome profiling data to produce robust estimates of per-codon elongation rates in yeast.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

2 Samples

Download data: TSV

(Submitter supplied) Genome-wide detection of monosome and disome distributions in yeast cells

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25927 GPL17342

13 Samples

Download data: TXT

(Submitter supplied) Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this “nonstop/no-go” decay process is not understood. Here we performed ribosome profiling of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3’ ends of mRNA decay intermediates. We found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL13821 GPL17342

14 Samples

Download data: TAR

(Submitter supplied) Ribosome pauses are associated with diverse co-translational events and determine the fate of mRNAs and proteins. Thus the identification of the precise pause sites across transcriptome is a key, however, the landscape in bacterial has remained ambiguous. Here, we harnessed the multiple ribosome profiling strategies (standard, high-salt-wash, and disome) to survey the robust ribosome pause sites in E. more...

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platform:

GPL25368

2 Samples

Download data: TXT

(Submitter supplied) Ribosome pauses are associated with diverse co-translational events and determine the fate of mRNAs and proteins. Thus the identification of the precise pause sites across transcriptome is a key, however, the landscape in bacterial has remained ambiguous. Here, we harnessed the multiple ribosome profiling strategies (standard, high-salt-wash, and disome) to survey the robust ribosome pause sites in E. more...

Organism:

Escherichia coli

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21433

7 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

4 Samples

Download data: CSV

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

4 Samples

Download data: CSV

(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) Local translation in neurons is mediated in part by the reactivation of stalled polysomes. However, the mechanism for stalling of the polysomes is not understood. Stalled polysomes may be enriched in neuronal RNA granules defined by dense collections of compacted ribosomes found in the pellet of sucrose gradients used to separate polysomes from monosomes. We find that this fraction, isolated from P5 rat brains of both sexes, is enriched in proteins implicated in stalled polysome function, such as the fragile X mental retardation protein (FMRP) and Up-frameshift mutation 1 homolog (UPF1). more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

15 Samples

Download data: BEDGRAPH, BW, TXT

(Submitter supplied) In addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the A and E sites, its exact mechanism of action is unclear. Here we show that eEF3 acts at the mRNA–tRNA translocation step by promoting the dissociation of the tRNA from the E site, but independent of aminoacyl-tRNA recruitment to the A site. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

8 Samples

Download data: CSV

(Submitter supplied) Cells can respond to stalled ribosomes by sensing ribosome collisions and employing quality control pathways. How ribosome stalling is resolved without collisions, however, has remained elusive. Here, focusing on non-colliding stalling exhibited by decoding-defective ribosomes, we identified Fap1 as a stalling sensor triggering 18S non-functional rRNA decay via poly-ubiquitination of uS3. Ribosome profiling revealed an enrichment of Fap1 at the translation initiation site but also association with elongating individual ribosomes. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL21656 GPL26171

20 Samples

Download data: TXT

(Submitter supplied) Variation in translation-elongation kinetics along a transcript’s coding sequence plays an important role in the maintenance of cellular protein homeostasis by regulating co-translational protein folding, localization, and maturation. Translation-elongation speed is influenced by molecular factors within mRNA and protein sequences. For example, when proline is present in the ribosome’s P- or A-site translation slows down, but the effect of other pairs of amino acids, in the context of all 400 possible pairs, has not been characterized. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

20 Samples

Download data: WIG

(Submitter supplied) Techniques for systematically monitoring protein translation have lagged far behind methods for measuring mRNA levels. Here we present a ribosome profiling strategy, based on deep sequencing of ribosome protected mRNA fragments, that enables genome-wide investigation of translation with sub-codon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL9134

8 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:

Saccharomyces cerevisiae; Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19959 GPL19958

98 Samples

Download data: TXT

(Submitter supplied) During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9377 GPL13821

10 Samples

Download data: TXT