GEO DataSets

(Submitter supplied) Cellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in response to glucose starvation and heat shock. Each stress induced rapid remodeling of the RNA-protein interactome, without corresponding changes in RBP abundance. Consistent with general translation shutdown, ribosomal proteins contacting the mRNA showed decreased RNA-association. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

74 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) We quantified the exact RNA binding sites of the Ssd1 protein in Saccharomyces cerevisiae, in exponential growth and heat shock conditions, using the CRAC protocol. We used a His-TEV-protein A tag (HTP) on the C-terminal of the genomic copy of Ssd1, with the 3'UTR replaced by the 3'UTR/terminator from the K. lactis Ssd1 homolog, followed by a KlURA3 selection marker.

Organism:

Saccharomyces cerevisiae BY4741

Type:

Other

Platform:

GPL29267

5 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) DEAD-box RNA helicases eIF4A and Ded1 promote translation by resolving mRNA secondary structures that impede preinitiation complex (PIC) attachment to mRNA or scanning. eIF4B is a cofactor for eIF4A but might also function independently of eIF4A. Ribosome profiling of mutants lacking eIF4B or with impaired eIF4A or Ded1 activity revealed that eliminating eIF4B reduces the relative translational efficiencies of many more genes than does inactivation of eIF4A, despite comparable reductions in bulk translation, and few genes display unusually strong requirements for both factors. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

16 Samples

Download data: CSV

(Submitter supplied) DEAD-box RNA helicases eIF4A and Ded1 are believed to promote translation initiation by resolving mRNA secondary structures that impede ribosome attachment at the mRNA 5’ end or subsequent scanning of the 5’UTR, but whether they perform distinct functions or act redundantly in vivo is poorly understood. We compared the effects of mutations in Ded1 or eIF4A on global translational efficiencies (TEs) in yeast by ribosome footprint profiling. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13821 GPL17342

32 Samples

Download data: CSV

(Submitter supplied) Rocaglamide A (RocA) typifies a class of protein synthesis inhibitors that selectively kill aneuploid tumor cells and repress translation of specific mRNAs. RocA targets eukaryotic initiation factor 4A (eIF4A), an ATP-dependent DEAD-box RNA helicase; its mRNA selectivity is proposed to reflect highly structured 5′ UTRs that depend strongly on eIF4A-mediated unwinding. However, rocaglate treatment may not phenocopy the loss of eIF4A activity, as these drugs actually increase the affinity between eIF4A and RNA. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL21616 GPL20301

8 Samples

Download data: FA

(Submitter supplied) Rocaglamide A (RocA) typifies a novel class of protein synthesis inhibitors that selectively kill aneuploid tumor cells and repress translation of specific mRNAs. RocA targets eukaryotic initiation factor 4A (eIF4A), the prototypical DEAD-box RNA helicase, and its mRNA selectivity is proposed to reflect highly structured 5′ UTRs that are very dependent on eIF4A-mediated unwinding. Here, we show that secondary structure in 5′ UTRs is only a minor determinant for RocA selectivity and RocA does not repress translation by reducing eIF4A activity. more...

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL15228

23 Samples

Download data: FA, TXT

(Submitter supplied) Each mutant was cultured in duplicate, and from each culture two fractions were sequenced: Total fragmented RNA, and small ribosomal subunit footprints.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

28 Samples

Download data: BED, TSV, TXT

(Submitter supplied) We analyzed the effect of deleting the gene encoding putative RNA helicase DBP1 in budding yeast on translational efficiencies (TEs) genome wide in wild-type or ded1-ts (temperature-sensitive allele of DED1) strains by combining ribosome footprint profiling with RNA-seq analysis of mRNA abundance. This study includes a total of 32 samples comprised of 16 RNA-Seq samples (mRNA) and 16 ribosome footprint profiling samples (ribo). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

32 Samples

Download data: CSV

(Submitter supplied) We use RNAseq to assess the gene expression as well as solubility of transcripts after 10 minutes of heat stress at either 40°C or 42°C compared to non-stressed yeast cells (30°C) for wildtype and Ded1-IDRm mutant cells.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26302

36 Samples

Download data: TXT

(Submitter supplied) We use ribosome footprinting to assess the gene expression changes occuring after 10 minutes of heat stress at either 40°C or 42°C compared to non-stressed yeast cells (30°C). We find that between 40°C and 42°C there is a shift in gene expression from the expression of genes harboring long and structured 5'UTRs to the expression of genes harboring thranscripts with short and unstructure 5'UTRs. We performed these experiments for WT yeast cells as well as for mutant yeast cells in which the RNA helicase Ded1 condensates at lower temperatures (Ded1-IDRm). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26302

12 Samples

Download data: TXT

(Submitter supplied) DEAD-box RNA helicases are ATP-dependent RNA binding proteins and RNA-dependent ATPases that possess weak, nonprocessive unwinding activity in vitro, but they can form long-lived complexes on RNAs when the ATPase activity is inhibited. Ded1 is a yeast DEAD-box protein, the functional ortholog of mammalian DDX3, that is considered important for the scanning efficiency of the 48S pre-initiation complex ribosomes to the AUG start codon. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

6 Samples

Download data: TXT

(Submitter supplied) Ribosome profiling of MDA-MB-231 cells treated with Silvestrol to monitor transcriptome wide, eIF4A-dependent changes in translation efficiency

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

13 Samples

Download data: TXT

(Submitter supplied) Cooperation between FGF and WNT signaling is well documented in normal development, stem cell biology and cancer progression. However, the molecular mechanisms underlying this cooperativity remain poorly understood. In this study, we employed an inducible FGFR1 to interrogate the dynamics of RNA, ribosome occupancy and protein expression as a function of FGFR signaling in the mouse mammary gland with constitutive WNT hyperactivation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: CSV

(Submitter supplied) We have developed a deep sequencing-based approach, Rec-Seq, that allows simultaneous monitoring of ribosomal 48S pre-initiation complex (PIC) formation on every mRNA in the translatome in an in vitro reconstituted system. Rec-Seq isolates key early steps in translation initiation in the absence of all other cellular components and processes. Using this approach we show that the DEAD-box ATPase Ded1 promotes 48S PIC formation on the start codons of >1000 native mRNAs, most of which have long, structured 5’-untranslated regions (5’UTRs). more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL27812

14 Samples

Download data: WIG

(Submitter supplied) We describe the subset of transcripts that require DDX3 for efficient translation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20301

16 Samples

Download data: BW, TSV

(Submitter supplied) We describe the subset of transcripts that require DDX3 for efficient translation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL16791 GPL18573 GPL20301

12 Samples

Download data: BW, CSV, TSV

(Submitter supplied) Yeast mRNA decapping-activators Pat1 and Dhh1 have been implicated in repressing translation and mRNA degardation in glucose-deprived cells, but the specific mRNAs targeted by each factor and their functions in nutrient replete cells are poorly understood. To test this, we performed ribosome profiling and RNA-Seq in WT, pat1D and pat1Ddhh1D. Further, CAGE-Seq and Rpb1-ChIP Seq were employed to determine their role in decapping mediated degradation of mRNAs

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL27812 GPL19756

26 Samples

Download data: CSV

(Submitter supplied) Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27812 GPL17342

14 Samples

Download data: CSV

(Submitter supplied) Degradation of most yeast mRNAs involves decapping by Dcp1/Dcp2. DEAD-box protein Dhh1 has been implicated as an activator of decapping, and as a translational repressor, but their functions in cells are incompletely understood. We have analyzed these questions by a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19756 GPL17342

24 Samples

Download data: CSV

(Submitter supplied) SSD1 is a polymorphic locus in budding yeast with many pleiotropic effects. Our lab had previously done transcript microarray of W303a in an ssd1-d background, and here we have carried out another transcript microarray across the cell cycle in an isogenic SSD1-V background. We find that a large fraction of budding yeast transcripts is differentially expressed in these cells. Ssd1 has recently been shown to bind mRNAs in vivo, but very few of these mRNAs show significant changes in levels in the SSD1-V versus ssd1-d comparison. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8782

13 Samples

Download data: GPR