Expression analysis of edc3 cell
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE6647 | GEO | 2007/01/06
SECONDARY ACCESSION(S): PRJNA98627
REPOSITORIES: GEO
Similar Datasets
Project description:The goal of this experiment is to identify transcripts regulated by Edc3p, an activator of mRNA decapping. Experiment Overall Design: Five independent expression profiling experiments were carried out for isogenic wild-type (HFY114) and edc3Δ (CFY25) strains using Affymetrix Yeast Genome S98 Arrays.
2007-10-23 | E-GEOD-6647 | biostudies-arrayexpress
Project description:The goal of this experiment is to identify transcripts regulated by Cbc2, the small subunit of nuclear cap binding complex (CBC) in Saccharomyces cerevisiae. Keywords: Genetic modification
2007-01-17 | GSE6705 | GEO
Project description:The object of this study was to explore whether the loss of mRNA decapping in the Arabidopsis mutant tdt-1 resulted in global dfferences of RNA profiles, as compared to wild type. Keywords: Genetic modification affect on gene expression
2007-07-31 | GSE7359 | GEO
Project description:To assess the role of the decapping activator Scd6 in mRNA decay, we used RNA-Seq to analyze the expression profile of yeast cells harboring a deletion of the SCD6 gene. Consistent with our recent model for decapping regulation, we found that Scd6 targets a small number of specific mRNAs in yeast cells. Interestingly, degradation of Scd6-targeted transcripts also requires the functions of the decapping activators Pat1, Lsm1, and Dhh1, suggesting that Scd6 functions together with Pat1, Lsm1, and Dhh1 in promoting mRNA decapping.
2018-05-15 | GSE114428 | GEO
Project description:The composition of the transcriptome is regulated by both mRNA synthesis and degradation. One route for mRNA decay is through 5’ decapping, which can be initiated by decapping enzymes and small RNAs. Although decapped RNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale. Here we present an experimental method for transcriptome-wide profiling of decapped mRNAs. We applied the method to study the prevalence of decapped transcripts during the early stages of Arabidopsis thaliana flower development. Decapped transcripts were identified for the majority of expressed genes, although at different levels. By comparing decapped RNA levels with steady-state overall transcript levels, our study provides evidence for widespread decapping-mediated mRNA degradation control in numerous biological processes and for genes of varied molecular functions, implying that mRNA decapping is a dynamically regulated process. Sequence analyses identified structural features of transcripts and cis-elements that were associated with levels of decapping.
2008-10-10 | GSE12043 | GEO
Project description:The composition of the transcriptome is regulated by both mRNA synthesis and degradation. One route for mRNA decay is through 5’ decapping, which can be initiated by decapping enzymes and small RNAs. Although decapped RNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale. Here we present an experimental method for transcriptome-wide profiling of decapped mRNAs. We applied the method to study the prevalence of decapped transcripts during the early stages of Arabidopsis thaliana flower development. Decapped transcripts were identified for the majority of expressed genes, although at different levels. By comparing decapped RNA levels with steady-state overall transcript levels, our study provides evidence for widespread decapping-mediated mRNA degradation control in numerous biological processes and for genes of varied molecular functions, implying that mRNA decapping is a dynamically regulated process. Sequence analyses identified structural features of transcripts and cis-elements that were associated with levels of decapping. Four sets of biologically independent tissue samples were collect 0,1,2,3,4, and 5 days after activation of the AP1-GR fusion protein. Decapped mRNA and total mRNA of each time point from each set were co-hybridized to micoarrays. Dyes used for labeling the RNA populations derived from the individual samples were switched in the replicate experiments to reduce dye-related artefacts.
2008-10-10 | E-GEOD-12043 | biostudies-arrayexpress
Project description:The goal of this set of experiments was to identify transcripts that are differentially expressed upon reactivation of NMD in an nmd2::HIS3 strain by galactose-induced expression of the NMD2 gene. Keywords: Genetic modification and time course
2007-11-01 | GSE9482 | GEO
Project description:The goal of this study is to identify, in the head of adult flies, mRNA species whose expresson level are altered by overexpression of the Drosophila RNA-binding protein LARK in CNS neurons. Keywords: genetic modification, gene experssion profile
2006-12-30 | GSE6420 | GEO
Project description:The decapping complex is crucial in regulating gene expression by removing the mRNA cap structure. While DCP2 serves as the catalytic subunit in this complex, DCP1 is recognized as its major activator. In humans, there exist two distinct paralogs of DCP1, DCP1a and DCP1b, which each form separate decapping complexes. However, the endogenous mRNA targets of these DCP1 paralogs are largely unknown. To address the role of human DCP1 paralogs, we generated multiple DCP1-knockout cell lines and evaluated the importance of human DCP1 in mRNA decapping. Surprisingly, our results revealed that human DCP1 is essential for decapping process. We also discovered that the EVH1 domain of DCP1 is indispensable for the decapping activity of DCP2, as it enhances the mRNA-binding affinity of DCP2. Additionally, the knock-out of DCP1 paralogs led to the significant activation of several pathways associated with cancer and mRNA processing, as well as the downregulation of DCP1a in various cancer types. Moreover, the knock-out cell lines of the two paralogs also exhibited distinct metabolome profiles. Overall, our findings highlight the crucial role of human DCP1 in mRNA decapping and shed light on the distinct functions of its two paralogs.
2024-10-26 | GSE230847 | GEO
Project description:The IkB kinase (IKK) is considered to control gene expression primarily through activation of the transcription factor NF-kB. However, we show here that IKK additionally regulates gene expression on post-transcriptional level. IKK interacted with several mRNA binding proteins, including a (P)-body scaffold protein, termed Enhancer of Decapping 4 (EDC4). IKK bound to and phosphorylated EDC4 in a stimulus-sensitive manner, leading to co-recruitment of P-body components, mRNA Decapping Proteins 1a and 2 (DCP1a and DCP2) and to an increase in P-body numbers. Using RNA sequencing, we identified scores of transcripts whose stability was regulated via the IKK-EDC4 axis. Strikingly, in the absence of stimulus IKK-EDC4 promoted destabilization of pro-inflammatory cytokines and regulators of apoptosis. Our findings expand the reach of IKK beyond its canonical role as a regulator of transcription.
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