Similar studies for GEO DataSets (Select 200157063) - GEO DataSets

(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

Series

Accession:: GSE66411

ID:: 200066411

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Select item 2000708044.

Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment

(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

Series

Accession:: GSE70804

ID:: 200070804

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Select item 2000708035.

Total RNA profiles associated with DDX3 wild-type (WT) or R534H variant expression with or without sodium arsenite treatment [RNA-seq]

(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

Series

Accession:: GSE70803

ID:: 200070803

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Select item 2000708026.

Profiles of ribosome-associated mRNAs regulated by expression of wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment [Ribo-Seq]

(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

Series

Accession:: GSE70802

ID:: 200070802

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Select item 2000708017.

Profile of RNAs bound by wild-type (WT) or R534H variant of DDX3 with or without Sodium Arsenite treatment [iCLIP-Seq]

(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

Series

Accession:: GSE70801

ID:: 200070801

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Select item 2002288288.

The DEAD-box RNA helicase Ded1 is a translation-elongation factor

(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

Series

Accession:: GSE228828

ID:: 200228828

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Select item 2000819669.

eIF4B preferentially stimulates translation of long mRNAs with structured 5’UTRs and low closed-loop potential but weak dependence on eIF4G

(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

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Series

Accession:: GSE81966

ID:: 200081966

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Select item 20012486310.

TCP-seq of yeast initiation factor mutants

(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

Series

Accession:: GSE124863

ID:: 200124863

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Select item 20011125511.

DBP1 in budding yeast

(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

Series

Accession:: GSE111255

ID:: 200111255

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Select item 20010508212.

RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs

(Submitter supplied) Translational control is a key determinant of protein abundance, which in turns defines the physiology and pathology of human cells. Initiation of translation is highly regulated in eukaryotes and is considered as the rate-limiting step of protein synthesis. mRNA secondary structures in 5’ untranslated region (UTR) and associated helicases have been characterised as key determinants of translation initiation. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL18573
24 Samples

Download data: BW, TXT

Series

Accession:: GSE105082

ID:: 200105082

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Select item 20009395913.

The RNA helicase Ded1p suppresses translation initiation from near-cognate start codons

(Submitter supplied) The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian ortholog DDX3 are critical for translation initiation. Mutations in DDX3 are linked to tumorigenesis and intellectual disability, and the enzyme is targeted by diverse viruses. How Ded1p and its orthologs engage RNAs to impact translation initiation has been a longstanding, unresolved question. Here we show that Ded1p associates with the pre-initiation complex at the mRNA entry channel of the small ribosomal subunit and that the helicase unwinds mRNA structure ahead of the scanning pre-initiation complex. more...

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL17342 GPL21656
38 Samples

Download data: TAB, TXT

Series

Accession:: GSE93959

ID:: 200093959

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Select item 20020150614.

A mRNA motif mediates TGF-β1 upregulation of NEU3 translation in human lung fibroblasts

(Submitter supplied) To elucidate how TGF-β1 regulates translation, we treated human lung fibroblasts (HLF) with TGF-β1 and used RNA-seq to determine the effect of TGF-β1 on total RNAs, and mRNA polysome/monosome ratios.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
24 Samples

Download data: XLSX

Series

Accession:: GSE201506

ID:: 200201506

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20024409315.

Transcriptome-wide analysis of the function of Ded1 in translation preinitiation complex assembly in a reconstituted in vitro system

(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

Series

Accession:: GSE244093

ID:: 200244093

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Select item 20023196416.

Human DDX6 regulates translation and decay of inefficiently translated mRNAs

(Submitter supplied) Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrate that the human ortholog of Dhh1p, DDX6, triggers deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21290
8 Samples

Download data: TXT

Series

Accession:: GSE231964

ID:: 200231964

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Select item 20014816617.

Stress-induced translation inhibition through release of 40S scanning initiation factors

(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

Series

Accession:: GSE148166

ID:: 200148166

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Select item 20013795618.

RNA helicase Belle (DDX3) non-autonomously suppresses germ cell tumorigenesis in the testes of Drosophila via regulation of multiple mRNAs

(Submitter supplied) DEAD-box RNA helicases DDX3 are important developmental regulators of multiple aspects of RNA metabolism of eukaryotes. belle, a single DDX3 ortholog in Drosophila, is essential for fly viability, fertility, and germline stem cell maintenance. Here we showed that RNAi belle knockdown in testis cyst cells caused a disruption of adhesion between germ cells and cyst cells and a generation of tumor-like clusters of stem-like germ cells. more...

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17275
2 Samples

Download data: XLSX

Series

Accession:: GSE137956

ID:: 200137956

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Select item 20015011119.

Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A [Bind-n-Seq]

(Submitter supplied) Small molecule compounds that sense the nucleic acid sequences, promise the attractive venue for drug development. Such an unusual effect has been observed in the natural product Rocaglamide A (RocA) from Aglaia plant, proving to exhibit anti-tumor effects by clamping eukaryotic initiation factor (eIF) 4A onto mRNA polypurine sequences. Although eIF4A has been speculated the unique target of RocA, the insensitization of eIF4A in human cells only partially rescued the translation repression from RocA, suggesting another alternative target of this compound. more...