Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of glucose availability on microRNA expression and Ago2 occupancy.

ABSTRACT: For cells to grow and proliferate both a growth signal and available nutrients are required. Several lines of evidence suggest that there is recriprocal regulation of nutrients by growth signals and growth signals by nutrients. Since microRNAs are regulated by growth signals, we sought to determine if microRNAs could also be regulated by nutrient availability. We found that several microRNAs change expression following glucose starvation and that their Ago2 occupancy remains constant. Immortalized Bax/Bak double-knockout mouse embryonic fibroblasts were deprived of glucose for 5 days and then re-fed glucose for 2 days. Cells were collected at the beginning of the starvation period (d0), following five days of glucose deprivation (d5), and following two days of glucose re-feed (d7). Total RNA was isolated from half of the collected cells using Trizol and the remaining cells were used to perform Ago2 immunoprecipitation followed by isolation of bound RNA.

ORGANISM(S): Mus musculus

SUBMITTER: Bic MSKCC

PROVIDER: E-GEOD-41921 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effect of glucose availability on microRNA expression and Ago2 occupancy.

Project description:For cells to grow and proliferate both a growth signal and available nutrients are required. Several lines of evidence suggest that there is recriprocal regulation of nutrients by growth signals and growth signals by nutrients. Since microRNAs are regulated by growth signals, we sought to determine if microRNAs could also be regulated by nutrient availability. We found that several microRNAs change expression following glucose starvation and that their Ago2 occupancy remains constant.

2012-12-17 | GSE41921 | GEO

Islet-specific microRNA changes driven by nutrient shift trigger postnatal beta-cell maturation - dispersed islet cell mRNAs after miR-17-5p transfection

Project description:We found that in rodents, postnatal beta-cell maturation is associated with changes in the expression of several islet microRNAs and discovered that these modifications are driven by changes in the nutrient supply. Mimicking the microRNA changes observed during β-cell maturation in newborn rat islet cells was sufficient to promote glucose-induced insulin release and to achieve a mature β-cell secretory phenotype. Moreover, the modifications in the level of some of these microRNAs reduced the proliferation of newborn β-cells, suggesting that they contribute to the limited proliferative capacity of adult β-cells. These findings demonstrated that miRNAs contribute to postnatal beta-cell maturation and development. Their role is likely to promote beta-cell adaptation to fule supply and to maintain glucose homeostasis by regulating insulin release and proliferation. Islets from 10-day-old rats (P10) were taken, dispersed and transfected with control miRNA mimic or miR-17-5p. Total RNA was extracted and mRNA profiling via Illumina single-end sequencing of mRNA-seq libraries was performed. In parallel, Ago2 immunoprecipitation with RNA recovery and mRNA-seq was performed (RISC-seq).

2014-09-06 | E-GEOD-61181 | biostudies-arrayexpress

Analysis of RNA associated with the RISC complex (Ago2) in four day old mice carrying a mutation in miR-96

Project description:The diminuendo mouse carries a mutation in the seed region of miR-96. Homozygotes are deaf and exhibit vestibular dysfunction, heterozygotes display rapidly progressive hearing loss. Some targets of miR-96 are known, but it is likely that many still remain to be discovered. MicroRNAs function by recruiting the RISC complex to their mRNA targets, so one way to examine the mRNAs being controlled by microRNAs in a cell is to immunoprecipitate Ago2, one of the RISC proteins, and extract the RNA bound to it. This should detect all the mRNAs being targetted by microRNAs in the tissue. We extracted mRNA bound to Ago2 from the organs of Corti and olfactory bulbs of diminuendo homozygote and wildtype littermates at four days old, and carried out microarray analysis.

2016-02-26 | E-MTAB-3737 | biostudies-arrayexpress

miRNAs associated with the different human Argonaute proteins

Project description:microRNAs (miRNAs) are small non-coding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3’ untranslated region (UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer-independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected. Examination of miRNAs associated with endogenous human Ago1-4 in HeLa cells

2013-03-29 | E-GEOD-45506 | biostudies-arrayexpress

MicroRNA Directly Enhances Mitochondrial Translation during Muscle Differentiation.

Project description:MicroRNAs are well known to mediate translational repression and mRNA degradation in the cytoplasm. Various microRNAs have also been detected in membrane-compartmentalized organelles, but the functional significance has remained elusive. Here we report that miR-1, a microRNA specifically induced during myogenesis, efficiently enters the mitochondria where it unexpectedly stimulates, rather than represses, the translation of specific mitochondrial genome-encoded transcripts. We show that this positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW182, which is excluded from the mitochondria. We provide evidence for the direct action of Ago2 in mitochondrial translation by Ago2 CrossLinking ImmunoPrecipitation coupled with sequencing (CLIP-seq), functional rescue with mitochondria-targeted Ago2, and selective inhibition of the microRNA machinery in the cytoplasm. These findings unveil a positive function of microRNA in mitochondrial translation and suggest a highly coordinated myogenic program via miR-1 mediated translational stimulation in the mitochondria and repression in the cytoplasm. Examination of miRNA's regulation function in mitochondria in C2C12 myoblasts cells and myotubes cells with CLIP-seq (Ago2).

2014-08-01 | E-GEOD-57596 | biostudies-arrayexpress

Small-RNA asymmetry is directly driven by mammalian Argonautes

Project description:Asymmetric selection of single-stranded guide RNAs from double-stranded RNA (dsRNA) precursors is crucial for RNA silencing-mediated gene regulation. However, the precise mechanisms for small RNA asymmetry remain unclear, especially since asymmetric selection can still occur under depletion of putative asymmetry sensors, Drosophila R2D2 and mammalian Dicer. Here we report direct contribution of mammalian Argonaute 2 (Ago2) to microRNA (miRNA) asymmetry. Ago2 selects strands with 5´-uridine/adenosine and thermodynamically unstable 5´-ends in parallel through its two sensor regions, which contact 5´-nucleobase and 5´-phosphate(s) of the prospective guide strands, respectively. Consistently, miRNA asymmetry shows characteristic digital-analog superposed patterns reflecting 5'-end nucleotide identity and thermodynamic stability. Furthermore, we demonstrate that cancer-associated miRNA variations reprogram asymmetric selection. Finally, our study presents a model of this universal principle that will aid a comprehensive understanding of miRNA function and therapeutic reinvention of RNA silencing in precision medicine. Immunoprecipitation of WT or mutant Ago2 in mouse ES cells (Ago-null background) and small RNA sequencing

2015-06-15 | E-GEOD-66022 | biostudies-arrayexpress

PARN mediates 3'-end trimming of Argonaute-cleaved precursor microRNAs

Project description:microRNAs (miRNAs) are typically generated as ~22-nucleotide double-stranded RNAs via processing of precursor hairpins by the RNase III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, does not require Dicer processing. Instead, the short pre-miR-451 precursor hairpin is directly loaded into Ago, followed by cleavage of the 3' arm and trimming of the 3' end to the mature length by PARN. Here we show the in vivo activity of miR-430 Ago2-hairpin, a canonical microRNA engineered to fit the structure of miR-451 and hence become Ago2-dependent. Moreover, we test a modified miR-430 Ago2-haipin with 3x phoshorothioate bonds that impairs trimmng. Surprisingly, our data show that trimming of Ago-cleaved pre-miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than 22-nucleotides. Rescue of MZdicer zebrafish mutant with the injection of trimmable and nontrimmable miR-430 Ago2 hairpins: Transcriptome of wild type, MZdicer mutant, and MZdicer mutant micoinjected with miR-430 duplex, miR-430 (Ago2-haripin), miR-430 (Ago2-haripin 3xPhosphorothioate)

2013-11-13 | E-GEOD-51036 | biostudies-arrayexpress

A nuclear role for the Argonaute protein AGO2 in mammalian gametogenesis

Project description:The reduced sperm count observed in Ago2 cKO mice implies that AGO2 has non-redundant functions in the male germ line. Because AGO2 is a key protein in the RNA interference (RNAi) pathway, we first postulated that AGO2 loss disrupts normal transcriptional and translational dynamics of target mRNAs relevant to sperm maturation. To address this hypothesis, we took advantage of the apparently normal spermatogenesis in Ago2 cKO mice, which allowed us to purify matched meiotic and post-meiotic germ cells from Ago2 cKO and wild type controls. We examined changes in the transcriptome and proteome of these two spermatogenic stages in Ago2 cKO relative to control mice using RNA-seq and quantitative mass spectrometry (MS). To further examine if the changes in mRNA and protein levels detected in Ago2 cKO germ cells was due to a loss of regulation by the canonical AGO2-miRNA pathway, we characterized AGO2 protein interactors by AGO2 immunoprecipitation-mass spectrometry (IP-MS) in cytoplasmic and nuclear fractions of post-meiotic cells

2022-08-01 | PXD027935 | Pride

Argonaute-bound small RNAs from promoter-proximal RNA Polymerase II

Project description:Argonaute (Ago) proteins mediate post-transcriptional gene repression by binding guide microRNAs (miRNAs) to regulate targeted RNAs. To confidently assess Agobound small RNAs, we adapted a mouse embryonic stem cell system to express a single inducible epitope-tagged Ago protein. Here, we report the small RNA profile of Agodeficient cells and determine Ago-dependent stability is a common feature of mammalian miRNAs. Considering both in vivo Ago-dependence for stability and Ago2 binding as defined by immunopurification, we have identified a novel class of non-canonical miRNAs derived from protein-coding gene promoters, which we name transcriptional start site miRNAs (TSS-miRNAs). A subset of promoter-proximal RNA polymerase II complexes produce hairpin RNAs that are processed in a DGCR8/Drosha-independent, but Dicer-dependent manner. TSS-miRNA activity is detectable endogenously, upon transfection of a mimic or by mRNA overexpression. Finally, we present evidence of differential expression and conservation in humans, suggesting important roles in gene regulation. Examination of Ago immunoprecipitations and mESC without Ago proteins

2014-03-13 | E-GEOD-50595 | biostudies-arrayexpress

Identification of high-affinity microRNA targets

Project description:We report that microRNAs strongly regulate targets of exceptionally high affinity and that such targets can be identified upon microRNA silencing in Argonaute 2 ribonucleoprotein immunoprecipitation (Ago2-RIP) experiments

2017-08-03 | E-MTAB-5386 | 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