Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of P-body (Dcp1) and Stress Granule (Pbp1) RNA content

ABSTRACT: Non-membrane-bound compartments such as mRNA processing bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. Here we perform RIP-seq to determine the RNA interactors of Dcp1 (PB marker) and Pbp1 (SG marker) before and after an appropriate glucose stress.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Michael Nelson

PROVIDER: E-MTAB-9096 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of RIP-seq of Ded1 and eIF4A(Tif1) with and without glucose depletion

Project description:The aim of this experiment was to look at RNAs which associate with DEAD-box RNA helicases with and without 10 minutes of glucose starvation.

2021-09-30 | E-MTAB-9095 | biostudies-arrayexpress

Integrated multi-omics reveals common properties underlying stress granule and P-body formation

Project description:Non-membrane-bound compartments such as mRNA processing bodies (PBs) and stress granules (SGs) play important roles in the regulation of gene expression following environmental stresses. We have systematically determined the protein and mRNA composition of PBs and SGs formed in response to a common stress condition imposed by glucose depletion. We find that high molecular weight (HMW) complexes exist prior to glucose depletion that may act as seeds for the further condensation of proteins forming mature PBs and SGs. Both before and after glucose depletion, these HMW complexes are enriched for proteins containing low complexity and RNA binding domains. The mRNA content of these HMW complexes is enriched for long, structured mRNAs that become more poorly translated following glucose depletion. Many proteins and mRNAs are shared between PBs and SGs, suggesting a complex pattern of functional protein and mRNA pools exist in different condensates. Even where the precise identity of mRNAs and proteins localizing to PBs and SGs is distinct, the mRNAs and proteins share common biophysical and chemical features that likely trigger their phase separation.

2021-11-03 | PXD018762 | Pride

RIP-seq of translation initiation factors eIF2γ, eIF3b and two RBPs involved in the process of mRNA degradation and storage, Pat1p and Lsm1p

Project description:The aim of this experiment is to determine the RNA binding partners of the translation initiation factors eIF2γ (GCD11), eIF3b (PRT1) and Pat1p and Lsm1p two RNA binding proteins (RBPs) involved in mRNA degradation and storage.

2023-09-06 | E-MTAB-13033 | biostudies-arrayexpress

RNA targets of FASTKD2 in Human HEK293 cells

Project description:A mutation within FASTKD2 causes a rare form of Mendelian mitochondrial encephalomyopathy. To investigate whether and how RNA binding of FASTKD2 contributes to the disease phenotype, we identified the RNA targets of FASTKD2 by iCLIP.

2015-11-09 | E-MTAB-4010 | biostudies-arrayexpress

Redox control of the cAMP/PKA pathway during protein misfolding stress

Project description:Protein aggregation is the abnormal association of misfolded proteins into larger, often insoluble structures that can be toxic during ageing and in protein aggregation-associated diseases. This RNA-seq study in Saccharomyces cerevisiae investigated the role of Tsa1, which is a member of the highly conserved 2-Cys peroxiredoxin (Prx) enzyme family, on protein aggregation.

2021-04-19 | E-MTAB-9355 | biostudies-arrayexpress

Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells (ChIP-seq)

Project description:Our study reports the first genome-wide atlas of functional nodes that mediate proviral silencing in ESCs. It provides evidences for the comprehensive, interconnected and multi-layered genetic/epigenetic machineries by which ESCs maintain the repressive state of provirus and ERVs. ChIP-seq analysis of Chaf1a, Trim28, Sumo2 and Zfp809 to demonstrate the mechanism of the silencing of Endogenous retroviruses

2015-09-14 | E-GEOD-70799 | biostudies-arrayexpress

MYC activation and BCL2L11 silencing by a tumor virus through the large-scale reconfiguration of enhancer-promoter hubs

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-08-04 | E-GEOD-82150 | biostudies-arrayexpress

MYC activation and BCL2L11 silencing by a tumor virus through the large-scale reconfiguration of enhancer-promoter hubs [EREB]

Project description:Lymphomagenesis in the presence of deregulated MYC expression requires suppression of MYC-driven apoptosis, often through downregulation of the pro-apoptotic BCL2L11 gene (Bim). Transcription factors (EBNAs) encoded by the lymphoma-associated Epstein-Barr virus (EBV) activate MYC and silence BCL2L11. We show that EBNA2 upregulates MYC by reconfiguring the 3 Mb MYC locus to increase upstream and decrease downstream enhancer-promoter interactions. EBNA2 recruits the SWI/SNF ATPase BRG1 to drive MYC enhancer-promoter interactions. MYC-Immunoglobulin translocation breakpoints in EBV-positive endemic Burkitt lymphoma localise to EBNA2-activated upstream MYC regions. This implicates EBV in the genesis and localisation of breakpoints, since active enhancers are targeted by activation-induced cytidine deaminase. We identify a novel haematopoietic BCL2L11 enhancer hub that is inactivated by EBNA3A and EBNA3C through recruitment of the H3K27 methyltransferase EZH2. Reversal of enhancer inactivation using an EZH2 inhibitor upregulates BCL2L11 and induces apoptosis. EBV therefore drives lymphomagenesis by hijacking long-range enhancer hubs and specific cellular co-factors. A study of MYC enhancer-promoter interactions using 4C on induction of MYC by the Epstein-Barr virus transcription factor EBNA2 in a lymphoblastoid cell line.

2016-08-04 | E-GEOD-82149 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae xylose metabolism mutants grown on glucose and xylose under aerobic and anaerobic conditions

Project description:Response of Saccharomyces cerevisiae engineered for xylose metabolism to changes in carbon source and aeration

2007-07-07 | E-GEOD-835 | biostudies-arrayexpress

The structure and target identification of the tandem RRM of yeast Npl3 bound to RNA reveal a cooperative sequence-specific recognition and an RNA chaperone role in splicing

Project description:The conserved SR-like protein Npl3 promotes the splicing of diverse pre-mRNAs. However, the RNA sequence(s) recognized by the RNA Recognition Motifs (RRM1 & RRM2) of Npl3 during the splicing reaction remain elusive. Here, we developed a split-iCRAC approach in vivo to determine the consensus sequence bound to each RRM in yeast. High-resolution NMR structures show that RRM2 recognizes a 5´-GNGG-3´ motif leading to an unusual mille-feuille topology. In addition, our data indicate a non-specific interaction of the RS domain with RNA. These structures reveal how RRM1 preferentially interacts with a CC-dinucleotide upstream of this motif, and how the inter-RRM linker and the region C-terminal to RRM2 contributes to cooperative RNA-binding. Structure-guided studies show that Npl3 genetically interacts with U2 snRNP specific factors and we provide evidence that Npl3 melts U2 snRNA stem-loop I, a prerequisite for U2/U6 duplex formation within the catalytic centre of the Bact spliceosomal complex. Our findings provide a mechanistic role for Npl3 during spliceosome active site formation.

2022-12-01 | E-MTAB-11736 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data