GEO DataSets

(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) 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) Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes. In a genetic screen in E. coli, we discovered a novel rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNA) to rescue upstream ribosomes. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18956

4 Samples

Download data: TXT, WIG

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

Organism:

Homo sapiens; Caenorhabditis elegans; Saccharomyces cerevisiae

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:

Caenorhabditis elegans; Saccharomyces cerevisiae; Homo sapiens

Type:

Other

Platforms:

GPL18245 GPL16791 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 stalling at problematic sequences in mRNAs leads to collisions that trigger a collection of quality control events including ribosome rescue, targeting the nascent polypeptide for decay (Ribosome-mediated Quality Control or RQC), and targeting of the mRNA for decay (No Go Decay or NGD). Using a reverse genetic screen in yeast, we identify Cue2 as the endonuclease that is recruited to stalled ribosomes to promote NGD. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

21 Samples

Download data: CSV

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

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

22 Samples

Download data: TXT

(Submitter supplied) Translation elongation stalling has the potential to produce toxic truncated protein fragments. Translation of either non-stop mRNA or transcripts coding for poly-basic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. During this process, the stalled ribosome is dissociated into subunits, and the polypeptide is ubiquitinated by the E3 ubiquitin ligase Listerin on the 60S large ribosomal subunit, leading to subsequent proteasomal degradation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

10 Samples

Download data: TXT

(Submitter supplied) Translation elongation rates are regulated to ensure proper conformation and biological function of proteins. Translation of either non-stop mRNA or transcripts coding for poly-basic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control system (RQC). During this process, the stalled ribosome is dissociated into subunits, and the polypeptide is ubiquitinated by the E3 ubiquitin ligase Listerin on the 60S large ribosomal subunit (LSU) leading to subsequent proteasomal degradation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

12 Samples

Download data: TXT

(Submitter supplied) Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, endogenous RQC-inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood. Here, we identified the SDD1 mRNA from S. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

4 Samples

Download data: TXT

(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:

GPL17342 GPL13821

14 Samples

Download data: TAR

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

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL14548 GPL21222

19 Samples

Download data

(Submitter supplied) The purpose of this experiment was to characterize MazF cleavage specificity with single-nucleotide resolution by enriching and sequencing 5’-OH ends (a 5’-OH end is generated by MazF cleavage).

Organism:

Escherichia coli

Type:

Other

Platform:

GPL14548

2 Samples

Download data: CSV

(Submitter supplied) The purpose of this experiment was to assess translation of mRNA after MazF expression to determine if cleavage events resulted in a loss in ribosome footprints.

Organism:

Escherichia coli

Type:

Other

Platform:

GPL21222

3 Samples

Download data: CSV

(Submitter supplied) The purpose of this experiment was to characterize MazF cleavage specificity and locations of cleavage genome-wide in E. coli and also identify any leaderless transcripts .To do this, MazF was expressed in a ΔmazF background and compared to an empty vector. rRNA-subtracted samples were used to assess cleavage in the mRNA, and total RNA samples were used to assess changes in the rRNA.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

14 Samples

Download data: CSV

(Submitter supplied) RNA-seq analyses of wild-type and DEDF1 cell lines show that the immediate-early JUN-dependent transcriptional response to collisions is dependent on EDF1.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: TSV