GEO DataSets

(Submitter supplied) We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) in Escherichia coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3′-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL18956

18 Samples

Download data: WIG

(Submitter supplied) Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation. The three bacterial release factors (RFs) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release factors. Probing release factors mutations with reporter constructs containing programmed frameshifting sequences or premature stop codons had revealed a propensity for readthrough or frameshifting at these specific sites, but their effects on translation genome-wide have not been examined. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL14548

30 Samples

Download data: BEDGRAPH

(Submitter supplied) Translational regulation was investigated at the genome scale in Escherichia coli cells. Using the polysome profiling method, the ribosome occupancy (RO) and ribosome density (RD) of different mRNA copies were determined for several hundred mRNAs during the exponential and stationary phases, providing the most complete characterisation of such regulation in E. coli. Although for most genes, nearly all mRNAs (>90%) were undergoing translation, they were loaded with far fewer than the theoretical maximum number of ribosomes, suggesting translation limitation at the initiation step. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21726

42 Samples

Download data: CSV

(Submitter supplied) The recycling of ribosomal subunits after translation termination is critical for efficient gene expression. Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) function as 40S recycling factors in vitro, but it is unknown whether they perform this function in vivo or serve as alternative initiation factors. Ribosome profiling of strains missing these factors revealed 80S ribosomes queued behind the stop codon, consistent with a block in 40S recycling. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL13821 GPL17342

14 Samples

Download data: WIG

(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) We show that a single change in uL22 in the ribosomal exit tunnel can have a profound impact on gene expression, suggesting further investigation given that changes in the K90 have been clinically isolated and linked to antibiotic resistance in several species.

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26856

12 Samples

Download data: TXT

(Submitter supplied) Shine-Dalgarno (SD) motifs are thought to play an important role in translational initiation in bacteria. Paradoxically, ribosome profiling studies in E. coli show no correlation between the strength of the SD in an mRNA and how efficiently it is translated. Performing profiling on ribosomes with altered anti-Shine-Dalgarno sequences, we reveal a genome-wide correlation between SD strength and ribosome occupancy that was previously masked by other contributing factors. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18956

41 Samples

Download data

(Submitter supplied) The proline-rich antimicrobial peptide apidaecin (Api) inhibits bacterial protein synthesis in a distinctive way. In vitro biochemical and structural studies showed that Api binds in the nascent peptide exit tunnel of a ribosome that has completed translation of a gene and traps the release factors on the ribosome. By analyzing the distribution of ribosomes on mRNAs in Api-treated cells using Ribo-seq, we uncovered a range of effects that stem from the unique mechanism of Api action. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL21222

10 Samples

Download data: WIG

(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) In eukaryotes, ribosome profiling provides insight into the mechanism of protein synthesis at the codon level. In bacteria, however, the method has been more problematic and no consensus has emerged for how to best prepare profiling samples. Here, we identify the sources of these problems and describe new solutions for arresting translation and harvesting cells in order to overcome them. These improvements remove confounding artifacts and improve the resolution to allow analyses of ribosome behavior at the codon level. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL18956

10 Samples

Download data: WIG

(Submitter supplied) Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

20 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) Ribosome assembly occurs mainly in the nucleolus yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a novel sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. more...

Organism:

Xenopus laevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21248

2 Samples

Download data: TXT

(Submitter supplied) Local mRNA translation mediates the adaptive responses of axons to extrinsic signals but direct evidence that it occurs in mammalian CNS axons in vivo is scant. We developed an axon-TRAP-RiboTag approach in mouse that allows deep-sequencing analysis of ribosome-bound mRNAs in the retinal ganglion cell axons of the developing and adult retinotectal projection in vivo. The embryonic-to-postnatal axonal translatome comprises an evolving subset of enriched genes with axon-specific roles suggesting distinct steps in axon wiring, such as elongation, pruning and synaptogenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057

28 Samples

Download data: TXT, WIG

(Submitter supplied) RPL3L is a ribosomal protein expressed exclusively in adult straited muscle tissues, and a paralogue of the ubiquitously expressed RPL3. Here, we are looking into the effects of Rpl3l knockout on translation in adult mice hearts.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24973

12 Samples

Download data: TAB