Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomewide measurements of neural-specific mRNA decay in Drosophila embryos

ABSTRACT: Neural-specific mRNA decay measurements by TU-Decay technique in control and Pumilio knockdown embryos

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE67512 | GEO | 2015/04/02

SECONDARY ACCESSION(S): PRJNA280113

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genomewide measurements of neural-specific mRNA decay in Drosophila embryos

Project description:Neural-specific mRNA decay measurements by TU-Decay technique in control and Pumilio knockdown embryos These TU-Decay microarrays analyze mRNA levels at three timepoints: a one hour pulse, one hour chase, and three hour chase. Neural-specific RNA purification was achieved using prospero-GAL4 driving UAS-T.g.UPRT. Pumilio knockdown in the nervous system was acheived using UAS-Pum(RNAi) driven by prospero-Gal4.

2015-04-02 | E-GEOD-67512 | biostudies-arrayexpress

Genomewide measurements of whole embryo mRNA decay in Drosophila

Project description:whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase These TU-Decay microarrays analyze mRNA levels at three timepoints: a one hour pulse, one hour chase, and three hour chase. Measurements with or without transcription inhibition by actinomycin D (ActD) were compared.

2015-03-31 | E-GEOD-67435 | biostudies-arrayexpress

Genomewide measurements of whole embryo mRNA decay in Drosophila

Project description:whole embryo (all tissues) measurement of mRNA decay by 4-thiouridine pulse-chase

2015-03-31 | GSE67435 | GEO

Measurements of mRNA abundance and decay for two strains 211 (wt) and 212 (mutant)

Project description:For each strain two time courses for mRNA abundance: Oxidative and MMS and two time courses for decay: reference decay and following oxidative stress We used Affymetrix microarrays to quantify changes in mRNA abundance following oxidative stress and DNA damage stress and also decay following transcription inhibition with and without oxidative stress. Each of the experiments were done for both strains 211 (wt) and 212 (mutant)

2011-07-29 | E-GEOD-26829 | biostudies-arrayexpress

Measurements of mRNA abundance and decay for two strains 211 (wt) and 212 (mutant)

Project description:For each strain two time courses for mRNA abundance: Oxidative and MMS and two time courses for decay: reference decay and following oxidative stress

2011-07-30 | GSE26829 | GEO

Defining codon-mediated mRNA decay and No-go decay in zebrafish embryos

Project description:Defining codon-mediated mRNA decay and No-go decay in zebrafish embryos

| PRJNA551383 | ENA

Defining codon-mediated mRNA decay and No-go decay in zebrafish embryos

Project description: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. Hence, codons define not only the amino acid sequences to be synthesized but also the stability of mRNAs. However, how 61 codons differently affect mRNA stability remains unclear. Besides, aberrant stalling of the ribosome induces ribosome quality control (RQC) and No-go decay. The relationship between the two co-translational mRNA decay pathways is not systematically analyzed. To precisely characterize the effects of 61 codons on mRNA stability, we developed a simplified reporter system that allows detection of the effect of every single codon on mRNA stability in zebrafish embryos. Using this system, we show that the effect of codons on mRNA stability is partially but significantly correlated with the translation elongation rate and tRNA abundance. Interestingly, the codon effect is still maintained in zebrafish embryos lacking Znf598, an essential mediator of RQC and NGD. Znf598-dependent NGD targets a particular type of ribosome stalling but has limited impact on endogenous mRNA stability. Our study thus defines two related co-translational mRNA decay pathways during animal development.

2020-05-05 | GSE133392 | GEO

Pumilio regulates mRNA decay during the late maternal-to-zygotic transition in Drosophila melanogaster

Project description:Pumilio (PUM) is a Drosophila member of a conserved family of sequence-specific RNA-binding proteins that have been shown to regulate mRNA stability and/or translation in a variety of organisms. PUM has been shown to repress the translation of several mRNAs in the Drosophila early embryo; failure to repress these targets leads to lethal developmental defects. Here we use a combination of microarray-based gene expression profiling and next-generation sequencing to identify more than 200 mRNAs that are associated with full-length PUM protein in early embryos and to define a global role for PUM in mRNA decay. Surprisingly, despite the fact that PUM is maternally supplied and thus is present from the beginning of embryogenesis, the vast majority of PUM-directed decay occurs only after zygotic genome activation. We show that the smaug mRNA, which itself encodes an RNA-binding protein that directs transcript decay, is a direct target of PUM via binding sites in the smg 3'UTR. Whereas the endogenous smaug mRNA and the transgenic reporter mRNA that carries the smaug 3'UTR undergo decay after zygotic genome activation, a reporter with an array of PUM-binding sites decays before zygotic genome activation. These data support a model in which additional cis-elements in the smg 3'UTR delay decay until after zygotic genome activation.

2017-07-01 | GSE48645 | GEO

Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells

Project description:We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity. Cells were pulsed with 4-thiouridine for 2 hours and then RNA was extracted at 0, 2, 4, and 7 hr time-points in quadruplicate from each cell line. 4sU labeling followed by RNA-seq was then used to measure the abundance of transcripts in each population. A decay rate was estimated based on the rate at which transcript abundance was reduced at these time-points.

2014-07-24 | E-GEOD-49608 | biostudies-arrayexpress

Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

Project description:Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

| PRJNA414048 | ENA