Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EiCLIP analysis of RBFOX2 in primary mouse hepatocytes

ABSTRACT: Rbfox2 is required for maintaining hepatic cholesterol levels under high fructose. Here we carry out an enhanced iCLIP (eiCLIP) protocol in order to determine the targets of Rbfox2 in primary mouse hepatocytes.

ORGANISM(S): Mus musculus

PROVIDER: GSE151747 | GEO | 2022/09/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNAseq of livers from WT mice or livers with Rbfox2 knockout fed CD

Project description:Rbfox2 is required for maintaining hepatic metabolic homeostasis, here we carry out RNAseq to of WT and aged matched littermate Rbfox2 knockout mice under high fructose in order to determine changes in alternative splicing and mRNA expression caused by knockout of this splicing factor in this metabolic environment.

2022-09-26 | GSE151748 | GEO

Rbfox2 controls autoregulation in RNA binding protein networks

Project description:We generated a global analysis of Rbfox2 splicing regulation combined with a highly specific, single nucleotide-resolution Rbfox2 RNA binding map. We found that Rbfox2 regulates the splicing and expression of many previously unknown targets, and particularly a number of RNA binding proteins (RBPs), by modulating alternative splicing coupled-NMD. Based on our observations of RBP-Rbfox2 co-regulation with a polarity predicted by Rbfox2 binding, we propose a model whereby Rbfox2 tunes autoregulatory splicing events to control RBP expression levels and in turn alter their respective splicing networks. iCLIP for epitope-tagged Rbfox2 and control untagged Rbfox2; RNAseq of control and Rbfox2 knockdown in mouse embryonic stem cells

2014-03-17 | E-GEOD-54794 | biostudies-arrayexpress

RNAseq of livers from WT mice or livers with Rbfox2 knockout fed CD with 30% (w/v) Fructose in the drinking water

Project description:Rbfox2 is required for maintaining hepatic metabolic homeostasis. Here we carry out RNAseq to of WT and aged matched litter mate Rbfox2 knockout mice under CD or HFD in order to determine changes in alternative splicing and mRNA expression caused by knockout of this splicing factor in the context of metabolic health and disease.

2022-09-26 | GSE151752 | GEO

Characterization of the role of RBFOX2 in the liver

Project description:Here we investigate the role of the splicing factor RBFOX2 in the liver. Our work describes a new regulatory mechanism where RBFOX2 controls cholesterol level, by coordinating the inclusion/exclusion of alternatively spliced exons in the liver. This SuperSeries is composed of the SubSeries listed below.

2022-09-26 | GSE151753 | GEO

Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice

Project description:RNA alternative splicing (AS) expands the regulatory potential of eukaryotic genomes. The mechanisms regulating liver-specific AS profiles and their contribution to liver function are poorly understood. Here, we identify a key role for the splicing factor RNA-binding Fox protein-2 (RBFOX2) in maintaining cholesterol homeostasis in an obesogenic environment in the liver. Using enhanced individual-nucleotide resolution UV-crosslinking and immunoprecipitation (eiCLIP), we identify physiologically relevant targets of RBFOX2 in mouse liver, including the scavenger receptor class B type I (Scarb1). RBFOX2 function is decreased in the liver in diet-induced obesity, causing a Scarb1 isoform switch and alteration of hepatocyte lipid homeostasis. Our findings demonstrate that specific AS programmes actively maintain liver physiology, and underlie the lipotoxic effects of obesogenic diets when dysregulated. Splice-switching oligonucleotides targeting this network alleviate obesityinduced inflammation in the liver and promote an anti-atherogenic lipoprotein profile in the blood, underscoring the potential of isoform-specific RNA therapeutics for treating metabolism-associated diseases.

2022-11-28 | PXD036976 | Pride

Transcriptomic analysis of primary hepatocytes and total livers from WT mice fed with CSAA or CDAA-HSHC diet during 2 weeks.

Project description:Mouse primary hepatocytes (PH) and total livers (TL) prepared from C57Bl6 male adult mice which were fed either a CDAA supplemented cholesterol with glucose and fructose or a CSAA diet during 2 weeks.

2024-04-01 | GSE212617 | GEO

Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [iCLIP-Seq]

Project description:iCLIP was performed in duplicates using RBFOX2 and CPSF2 antibodies. iCLIP was performed in duplicates using RBFOX2 and CPSF2 antibodies.

2015-07-15 | E-GEOD-60385 | biostudies-arrayexpress

Rbfox2 controls autoregulation in RNA binding protein networks

2014-03-17 | GSE54794 | GEO

RBFox2 regulates a broad RNA program and is required for genome-wide targeting of polycomb complex

Project description:Increasing evidence suggests that diverse RNA binding proteins interact with regulatory RNAs to regulate transcription. RBFox2 is a ubiquitous RNA binding protein with prevalent expression in stem cells, heart, and brain. Here, we report a systematic dissection of the RBFox2-regulated RNA program in the mouse heart, demonstrating its essential function for organizing the contractile apparatus and excitation-contraction (EC) coupling by modulating alternative splicing and microRNA activity. In this analysis, we unexpectedly encounter a major functional intersection between RBFox2 and Polycomb Complex 2 (PRC2), revealing a central requirement for RBFox2 to mediate genome-wide targeting of the PRC2 complex and transcriptional repression via chromatin-associated nascent RNAs. These findings unveil the mechanism underlying the enigmatic association of PRC2 with numerous active genes, highlight the importance of gene body sequences to gauge transcriptional output, and suggest nascent RNAs as critical signals for transcriptional feedback control to maintain homeostatic gene expression in mammalian cells. RASL-seq in cardiac myocytes (from WT and RBFox2 KO mouse hearts at ages of week 5, week 9 and week 18); RBFox2 whole cell and nucleus CLIP-seq in cardiac myocytes (from WT mouse hearts at age of week 9); Ago2 CLIP-seq in cardiac myocytes (from WT and RBFox2 KO mouse hearts at age of week 9); 3'-end RNA-seq in cardiac myocytes (from WT and RBFox2 KO mouse hearts at age of week 9); GRO-seq in mouse hearts (from WT and RBFox2 KO mice at age of week 9) and cultured MEF cells (negative control RNA, RBFox2 siRNA or SUZ12 siRNA treatment); RBFox2 and SUZ12 CHIP-seq in mouse hearts(from WT mice at age of week 9); RBFox2, SUZ12 and H3K27me3 CHIP-seq in cultured MEF cells (negative control RNA, RBFox2 siRNA or SUZ12 siRNA treatment, DRB treatment).

2015-10-22 | E-GEOD-57926 | biostudies-arrayexpress

Effect of hepatocyte-specific PPARgamma knock out in the regulation of hepatic gene expression in mice fed a low fat diet or and high fat, cholesterol and fructose diet that induces NASH

Project description:In this study we sought to determine how hepatocyte-specific PPARgamma expression regulates hepatic gene expression in normal (healthy) mice fed a LFCF diet, or mice that were fed a HFCF diet for 24 weeks to induce non-alcoholic steatohepatitis (NASH). Specifically, we used chow-fed adult (10 week-old) PPARgamma floxed male mice and injected them with AAV8-TBG-Cre to knockout PPARgamma in hepatocytes (KO). A subset of PPARgamma floxed mice were injected with AAV8-TBG-Null to generate controls (C). Two weeks after AAV injections, half of the mice in each group were fed a low fat, cholesterol and fructose (LFCF) diet, or a high fat, cholesterol and fructose (HFCF) diet for 24 weeks. Livers were collected at the end of the study to assess hepatic gene expression with RNA-seq (performed by Novogen, Inc.)

2021-01-15 | GSE162249 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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