Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RIP-seq of livers in C57BL/6J mice with antibodies against Cnot3, Ago2, and BRF1

ABSTRACT: Shortening of polyadenosine (poly(A)) tails (deadenylation) is the initial step in the decay of most mRNAs. The CCR4-NOT complex is the major deadenylase in mammals. Interaction of Cnot1 with RNA binding proteins, including the miRNA-induced silencing complex (miRISC), which includes Argonaute (Ago) and GW182 as core proteins, and the TTP family of AU-rich element (ARE)-binding proteins (TTP and BRF1/2), recruits the CCR4-NOT complex to the 3’-untranslated regions (3’-UTR) of mRNAs, leading to their degradation. This experiment aimed to determine the binding affinity of the CCR4-NOT complex, Ago2, and BRF1 with their target mRNAs in liver. Liver isolated from C57BL/6J wild-type mice at 8 weeks of age was solubilized in TNE buffer for 30 min at 4ºC. Lysate was incubated with antibodies against Cnot3, Ago2, and BRF1 for 1 hr at 4ºC, and then incubated with Dynabeads (Invitrogen) for 2 hr at 4ºC. mRNAs in immune complexes were isolated using Isogen II. 100 ng of total RNA was used for RNA-seq library preparation with TruSeq Stranded mRNA Library Prep Kit for NeoPrep. 150 base-pair pair-end read RNA-seq was performed with Hiseq 3000/4000 PE Cluster Kit and Hiseq 3000/4000 SBS Kit on Hiseq4000.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Toru Suzuki

PROVIDER: E-MTAB-6941 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Examination of mRNA decay rate in mouse embryonic fibroblasts

Project description:The CCR4-NOT dedadenylase complex is essential for mRNA decay and various biological events.To understand roles of the complex in mouse embryonic fibroblasts, we compared mRNA half-lives between control and Cnot complex-deficient mouse embryonic fibroblasts

2020-01-29 | E-MTAB-8287 | biostudies-arrayexpress

RNA-seq of mouse islets from Ins1-cre driven Cnot3 KO and control islets

Project description:The CCR4-NOT dedadenylase complex is essential for mRNA decay and various biological events.To understand roles of the complex in pancreatic beta cells, we compared global gene expression in Ins1-cre driven Cnot3 KO and control islets. Cnot3 is an important subunit of the complex and its knockout affects the complex activity.

2020-08-29 | E-MTAB-8729 | biostudies-arrayexpress

Genome-wide mapping of decay factor-mRNA interactions in yeast identifies nutrient responsive transcripts as targets of the deadenylase Ccr4

Project description:The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. All three proteins were preferentially bound to lowly abundant mRNAs, most often at the 3’ end of the transcript. Furthermore, Ccr4, Dhh1 and Puf5 are recruited to mRNAs that are targeted by other RNA-binding proteins that promote decay, mRNA transport and inhibit translation. Although Ccr4-Not regulates mRNA transcription and decay, Ccr4 recruitment to mRNAs correlates better with decay rates, suggesting it imparts greater control over transcript abundance through decay. Ccr4-enriched mRNAs are refractory to control by the other deadenylase complex in yeast, Pan2/3, suggesting a division of labor between these deadenylation complexes. Finally, Ccr4 and Dhh1 associate with mRNAs whose abundance increases during nutrient starvation and those that fluctuate during metabolic and oxygen consumption cycles, which explains the known genetic connections between these factors and nutrient utilization and stress pathways.

2017-12-04 | GSE72366 | GEO

Expression data from fetal hepatocytes from control or Cnot3KO E16.5 embryos treated with Actinomycin D for 0, 6 or 12h

Project description:mRNA degradation critically contributes to liver development and function. The CCR4-NOT complex serves as a major deadenylase that initiates mRNA degradation. We used microarrays to identify abnormally stabilized mRNAs in the fetal hepatocytes lacking Cnot3, a core subunit of the CCR4-NOT complex.

2019-02-21 | GSE120911 | GEO

Expression data from mouse embryonic fibroblasts

Project description:In addition to transcriptional regulation, mRNA degradation critically contributes to gene expression as shown by various biological analysis. The CCR4-NOT complex serves as a major deadenylase that initiates mRNA degradation. We used microarrays to identify CCR4-NOT targets by searching for genes specifically stablized in the absence of CNOT3, a core subunit of the CCR4-NOT complex. Primary mouse embryonic fibroblasts (MEFs) were used for RNA extraction and hybridization on Affymetrix microarrays. CNOT3-knockdown MEFs were generated by Cre-mediated somatic recombination. We treated both control and CNOT-knockdown (CNOT3KD) MEFs with a transcriptional inhibitor, actinomycin D to focus on a stability of mRNAs.

2015-09-01 | E-GEOD-67418 | biostudies-arrayexpress

Identification of miRNA targets in breast cancer cells (Ago2-IP)

Project description:miRNAs regulate mRNA stability and translation through the action of the RNAi-induced silencing complex. In this study, we systematically identified endogenous miRNA target genes by using AGO2 immunoprecipitation (AGO2-IP) and microarray analyses in two breast cancer cell lines, MCF7 and MDA-MB-231, representing luminal and basal-like breast cancer, respectively. The expression levels of ~70% of the AGO2-IP mRNAs were increased by DROSHA or DICER1 knockdown. In addition, integrated analysis of miRNA expression profiles, mRNA-AGO2 interaction, and the 3'-UTR of mRNAs revealed that >60% of the AGO2-IP mRNAs were putative targets of the fifty most abundantly expressed miRNAs. To identify mRNAs associated with AGO2, cell lysate was precleaned with control IgG and immunoprecipitated with anti-human Ago2 (Clone 2E12-1C9, Abnova). Total RNA from cell lysate or coimmunoprecipitated with AGO2 was extracted with Trizol and subjected to microarray analysis, with three biological repeats for each experimental condition.

2013-10-21 | E-GEOD-48158 | biostudies-arrayexpress

TTP mRNA targets identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts

Project description:Tristetraprolin (TTP) is a tandem CCCH zinc finger protein that was identified through its rapid induction by mitogens in fibroblasts. Studies of TTP-deficient mice, and cells derived from them, showed that TTP could bind to certain AU-rich elements in mRNAs, leading to increases in the rates of mRNA deadenylation and destruction. Known physiological target mRNAs for TTP include tumor necrosis factor alpha (TNF), granulocyte macrophage colony stimulating factor (GM-CSF) and interleukin 2 beta (IL2 beta). Here we used microarray analysis of RNA from wild-type and TTP-deficient fibroblast cell lines to identify transcripts with different decay rates, after serum stimulation and actinomycin D treatment. Of 250 mRNAs apparently stabilized in the absence of TTP, 23 contained conserved TTP binding sites; 10 of these were shown by secondary analyses to be stabilized. The most dramatically affected transcript encoded the protein Ier3, recently implicated in the physiological control of blood pressure. The Ier3 transcript contained several conserved TTP binding sites that could bind TTP directly, and conferred TTP sensitivity to the mRNA in cell transfection studies. These studies have identified several new, physiologically relevant TTP target transcripts in fibroblasts; these target mRNAs encode proteins from a variety of functional classes. Keywords: mRNA degradation, time course, knockout experiment

2006-10-17 | GSE5324 | GEO

Gene expression data from mice Ago2-amygdala

Project description:In this study we aimed to uncover which mRNAs are changed in the Ago2-amygdala complex following chronic social defeat in mice We used microarrays to determine which mRNAs are changed in the Ago2-amygdala complexof mice following chronic social defeat compared to control

2016-09-30 | GSE87489 | GEO

Comparative analyses of vertebrate CPEB-family of proteins define two sub-families with distinct, but coordinated, functions in post-transcriptional regulation of gene expression

Project description:Background: The vertebrate CPEB-family of RNA-binding proteins promote translational repression or activation of their target mRNAs, which harbor cytoplasmic polyadenylation elements (CPEs) in their 3’ UTRs, through cytoplasmic changes in their poly(A) tail lengths. However, their regulation(s) and mechanism(s) of action have not been systematically addressed as a family. Results: Here we perform a comparative analysis of the four vertebrate CPEBs in their regulation by phosphorylation, supramolecular assemblies’ composition and properties and in their mRNA targets. Conclusions: We show that although all four CPEBs are able to recruit CCR4-NOT deadenylation complex when not phosphorylated, their mechanisms of action determine two subfamilies with distinct, but coordinated, regulation by phosphorylation and target specificity. Thus, CPEB1 forms ribonucleoprotein complexes that are remodeled upon a single phosphorylation event, by AurkA, and are associated with mRNAs containing canonical CPEs. On the other hand, CPEB2-4 are regulated by multiple proline-directed phosphorylations that control their liquid-liquid phase-separation. CPEB2-4 mRNA-targets include CPEB1-bound transcripts, with canonical CPEs, but also a specific subset of mRNAs with non-canonical CPEs. In turn, CPEB2-4 coacervates display compositional, morphological and dynamic differences. Altogether, these results show how, globally, the CPEB family of proteins is able to integrate cellular cues to generate a finetuned adaptive response in gene expression regulation.

2022-10-05 | PXD033349 | Pride

Identification of miRNA targets in breast cancer cells (DICER1 and DROSHA knockdown)

Project description:miRNAs regulate mRNA stability and translation through the action of the RNAi-induced silencing complex. In this study, we systematically identified endogenous miRNA target genes by using AGO2 immunoprecipitation (AGO2-IP) and microarray analyses in two breast cancer cell lines, MCF7 and MDA-MB-231, representing luminal and basal-like breast cancer, respectively. The expression levels of ~70% of the AGO2-IP mRNAs were increased by DROSHA or DICER1 knockdown. In addition, integrated analysis of miRNA expression profiles, mRNA-AGO2 interaction, and the 3'-UTR of mRNAs revealed that >60% of the AGO2-IP mRNAs were putative targets of the fifty most abundantly expressed miRNAs. To identify mRNAs responsive to miRNA synthesis inhibition, total RNA was prepared from control cells and cells that stably express small hairpin RNA against DICER1 or DROSHA. Expression array analysis was performed with duplicates for each cell type.

2013-10-21 | E-GEOD-48160 | 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