GEO DataSets

(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) 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) 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) 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) 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) 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) 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 report the application of the Cross-Linking and cDNA (CRAC) technique to identify binding sites of DBP6, ribosome assembly factors, on RNAs in vivo. Once sequenced, RNAs associated have been aligned to the yeast genomes and enrichment of specific RNAs has been studied in more details. Specifically apparition of Mutation/deletion in the reads are of interesdt since they mostly corresponds to prceise site of cross-link between bait protein and target RNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17143

2 Samples

Download data: TXT

(Submitter supplied) RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate specificity and guide the helicase to a specific RNA. However, the in vivo RNA substrates of most helicase are currently not defined. more...

Organism:

Thermus thermophilus HB27

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27012

8 Samples

Download data: BED, BW

(Submitter supplied) The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here 
we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and 
genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies 
of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in 
membrane and secreted proteins. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19958

6 Samples

Download data: TXT

(Submitter supplied) The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

4 Samples

Download data: TXT

(Submitter supplied) We report widespread changes in ribosome biogenesis factor, aerobic respiration and hexose tranporter gene expression. We also identify antisense transcripts to hexose transporter genes in dbp2∆ cells.

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18742

2 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL16791

32 Samples

Download data: BW

(Submitter supplied) RNA expression profiles are not significantly altered by DDX3 WT or R534H expression as well as by 45 minute exposure of cells to sodium arsenite.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: BW

(Submitter supplied) By using ribosome profiling, we demonstrate that catalytic activity of the RNA helicase DDX3 is generally required for mediating translation repression under stress. Intriguingly, however, a cancer-related DDX3 variant DDX3 R534H selectively preserves translation of genes encoding core nucleosome components. Additionally, DDX3 variants also shift ORF usage on select genes, such as RPLP1 and stress-response factors as an added mechanism of translation regulation during stress. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

12 Samples

Download data: BW

(Submitter supplied) By iCLIP-seq, we demonstrated that DDX3 binds to specific sites on 18S ribosomal RNA and to messenger RNAs at 5’ leader and guanidine-rich sequences immediately upstream of ribosome-dense regions and that arsenite treatment redistributes DDX3 binding from 5'UTR to CDS, which is attenuated by DDX3 R534H.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

8 Samples

Download data: BW

(Submitter supplied) A major determinant of mRNA half-life is the codon-dependent rate of translational elongation. How the processes of translational elongation and mRNA decay communicate is unclear. In this study we establish that the DEAD-box helicase Dhh1p is the sensor of codon optimality (i.e. translational elongation rate) that targets an mRNA for decay. First, we find that mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a DHH1-dependent manner. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13821 GPL17342

18 Samples

Download data: TXT, WIG

(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