Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic profiling of FBXO11 protein complexes

ABSTRACT: FBXO11, a member of the F-box protein family, plays a critical role in cellular processes such as protein degradation, cell cycle regulation, and signaling pathways by serving as a substrate recognition component of the SKP1-Cullin-F-box (SCF) ubiquitin ligase complex. Dysregulation of FBXO11 has been implicated in various diseases, including cancer and developmental disorders, yet its full spectrum of interactions and functional roles remains poorly understood. This project aims to perform a comprehensive proteomic profiling of FBXO11-associated protein complexes to uncover its interaction network and better understand its biological functions. Using advanced mass spectrometry-based proteomics, we will identify and characterize the proteins that interact with FBXO11 under different cellular conditions. Additionally, bioinformatics tools will be employed to analyze the identified interactome and explore their functional enrichment in specific pathways and biological processes.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood

SUBMITTER: Zuo-Fei Yuan

LAB HEAD: Anthony A High

PROVIDER: PXD059844 | Pride | 2025-11-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Crispigrp_011023_ip_b1.1.pepXML	Pepxml
	Crispigrp_011023_ip_b1.raw	Raw
	Crispigrp_011023_ip_b2.1.pepXML	Pepxml
	Crispigrp_011023_ip_b2.raw	Raw
	Crispigrp_011023_ip_b3.1.pepXML	Pepxml

Items per page:

1 - 5 of 12

Similar Datasets

Identification of RNA Pol II polymerase interactome in ALL cells

Project description:RNA polymerase II is a protein encoded by the POLR2A gene in humans. In coordination with a wide array of interacting partners, RNA polymerase II has been shown to participate in the regulation of the cell cycle, transcription, and splicing, all of which are important for ALL growth. Here, we investigated the RNA Pol II polymerase interactome, focusing on the splicing-related apparatus to identify the splicing factors involved in co-transcriptional splicing, which is important for ALL cell growth.

2025-05-06 | PXD048846 | Pride

A putative network of actin-associated cytoskeletal proteins in glomerular podocytes defined by co-purified mRNAs

Project description:Identification of a putative network of actin-associated cytoskeletal proteins in glomerular podocytes defined by co-purified mRNAs. An experimental purification in which a presumed RNA binding protein was used for an RNA immunoprecipitation and microarray analysis (RIP-CHIP). Total cell extracts were harvested from the conditionally immortalized mouse MPC-5 podocyte cell line 14 days after transfer from 33 to 37 degrees Celsius. The MPC-5 cell lines were stably expressing the Wilm's Tumor protein (+KTS) isoform carrying a modified TAP tag. A fraction of each extract (Input samples) was saved and the remaining extract was applied to a sepharose IgG column, washed, and eluates were harvested after addition of TEV protease and elution in microbiospin columns. Four input and four eluate samples were then used to harvest RNA using Trizol. Total RNA was harvested from 4 input samples and 4 eluate samples. RNAs that were enriched in the eluate samples relative to input samples were further investigated and characterized. These RNAs were shown to be enriched in the eluates independent of the TAP-tagged protein. Complete data matrices reporting all 46,657 unique probe IDs (i.e., including the 14 control IDs not reported in the Sample data tables) are linked below as supplementary files.

2009-08-01 | E-GEOD-16942 | biostudies-arrayexpress

Timed use of digoxin prevents heart ischemia-reperfusion injury through a REV-ERBα-UPS signaling pathway

Project description:Myocardial ischemia-reperfusion injury (MIRI) is a major threat to heart functional integrity and pharmacological means to achieve cardioprotection are sorely needed. The sequential hypoxic/normoxic status of the cardiac tissue triggers life-threatening damages through the activation of multiple intra-cellular pathways. Heart tolerance to MIRI varies according to a day-night cycle and is regulated by components of the molecular clock such as the transcriptional repressor and nuclear receptor REV-ERBα. Timed REV-ERBα antagonism alleviates sensitivity to myocardial infarction in mice. Here we show that timed administration of digoxin is cardioprotective by triggering REV-ERBα protein degradation. Kinomics and transcriptomic assays revealed that in several cardiomyocyte cellular models, digoxin and other cardiotonic steroids induced multiple signaling pathways. Pharmacological inhibition and knockdown approaches revealed that inhibition of the Src tyrosine-kinase partially alleviated digoxin-induced REV-ERBα degradation, which was fully prevented upon proteasome inhibition. REV-ERBα is increasingly ubiquitinylated in digoxin-treated cells, and its degradation depends on its ability to bind its natural ligand, heme. In unchallenged conditions, the proteasomal degradation of REV-ERBα is controlled by several known (HUWE1, FXW7, SIAH2) or novel (CBL, UBE4B)E3 ubiquitin ligases. Only SIAH2 together with the proteasome subunit PSMB5 were found tocontribute to the digoxin-induced degradation of REV-ERBα. Taken together, these results show that controlling REV-ERBα proteostasis is an appealing cardioprotective strategy, and bring further support to the rationale, timed use of CTS in prophylactic cardiac preconditioning to MIRI.

2022-09-13 | PXD036607 | Pride

EZHIP / CXorf67 mimics K27M mutated oncohistones and functions as an intrinsic inhibitor of PRC2 function in aggressive posterior fossa ependymoma

Project description:Posterior fossa A (PFA) ependymomas comprise one out of nine molecular groups of ependymoma. PFA tumors are mainly diagnosed in infants and young children, show a poor prognosis and are characterized by a lack of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark. Recently, we reported CXorf67 overexpression as hallmark of PFA ependymoma and showed that CXorf67 can interact with EZH2 thereby inhibiting polycomb repressive complex 2 (PRC2). Here, we report that the inhibitory mechanism of this interaction is similar as in diffuse midline gliomas harboring H3K27M mutations. A small, highly conserved peptide sequence located in the C-terminal region of CXorf67 mimics the H3K27M peptide and binds to the SET domain of EZH2. This interaction blocks EZH2 methyltransferase activity and causes H3K27 hypomethylation, an oncogenic mechanism that may be exploited for targeted therapy in PFA ependymoma. Based on its function, we have renamed CXorf67 into EZH2 Inhibitory Protein (EZHIP).

2019-07-08 | PXD012318 | Pride

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis

Project description:Cell fate plasticity enables development, yet unlocked plasticity is a cancer hallmark. Regulating cell identity requires gene activation and repression. While master regulators induce lineage-specific genes to restrict plasticity, it remains unclear whether unwanted plasticity is actively suppressed by lineage-specific repressors. Here, we computationally predict so-called safeguard repressors for 18 cell types that block phenotypic plasticity lifelong. We validated hepatocyte-specific candidates using reprogramming, revealing that Prospero homeobox protein 1 (PROX1) enhanced hepatocyte identity by direct repression of alternate fate master regulators. In line with patient data, PROX1 overexpression in mice blocked initiation and progression of hepatocellular carcinoma and extended survival. Remarkably, Prox1 depletion caused hepatocyte fate loss in vitro, and promoted transdifferentiation of hepatocellular- to cholangio-carcinoma in vivo. Our findings provide mechanistic evidence for PROX1 as a hepatocyte-specific safeguard and support a model where individual cell type-specific repressors actively suppress plasticity throughout life to safeguard lineage choice and prevent disease.

2024-11-11 | PXD053043 | Pride

Control of cell identity and early neural fate commitment by the enhancer module of Integrator

Project description:Lineage-specific transcription factors (TFs) operate as master orchestrators of developmental processes by activating select cis-regulatory enhancers and proximal promoters. Direct DNA binding of TFs ultimately drives context-specific recruitment of the basal transcriptional machinery that comprises RNA Polymerase II (RNAPII) and a host of polymerase-associated multiprotein complexes, including the metazoan-specific Integrator complex. Integrator is primarily known to modulate RNAPII processivity and to surveil RNA integrity across coding genes. Here we show an enhancer module of Integrator that directs cell fate specification by promoting epigenetic changes and TF binding at neural enhancers. Depletion of Integrator’s INTS10 upends neural traits and derails cells towards mesenchymal identity. Commissioning of neural enhancers relies on Integrator’s enhancer module, which stabilizes SOX2 binding at chromatin upon exit from pluripotency. We propose Integrator as a functional bridge between enhancers and promoters and a main driver of early development, providing new insight into a growing family of neurodevelopmental syndromes.

2024-08-15 | PXD054928 | Pride

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

Project description:Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about the distribution and function of 5hmC. Here we present a genome-wide profile of 5hmC in mouse embryonic stem (ES) cells. A combined analysis of global 5hmC distribution and gene expression profile in wild-type and Tet1-depleted ES cells revealed suggests that 5hmC is enriched at both gene bodies of actively transcribed genes and extended promoter regions of Polycomb-repressed developmental regulators. Thus, our study reveals the first genome-wide 5hmC distribution in pluripotent stem cells and supports its dual function in regulating gene expression. Genomic DNA extracted from control (Con) or Tet1 knockdown (KD) mouse ES cells was immunoprecipitated with 5-hydroxymethylcytosine (5hmC) antibodies and analyzed by NimbleGen 2.1M mouse whole genome tiling microarrays (a 4-array set covering the entired non-repetitive portion of mouse genome). Whole cell extract (WCE) was used as input controls in IP/input experiments.

2011-03-30 | E-GEOD-27613 | biostudies-arrayexpress

Expression data from Th2 cell of ECM1 KO mice vs WT mice

Project description:CD4+ helper T cells are critical for immunological response. Th2 cells, a subset of CD4+ helper T cells, are responsible for asthma and other immune diseases. We found a Th2 secreted protein, ExtraCellular Matrix protein 1 (ECM1), which is highly induced by classic IL-4 signaling pathway during helper T cells differentiation. We used microarrays to clarify the global programme of gene expression difference underlying fully developed Th2 cells from WT and ECM1 KO mice and identified distinct classes of up and down regulated genes by ECM1. Naïve CD4+ T cells are seperated from WT and ECM1 mice, cultured and harveseted for RNA extraction and hybridization on Affymetrix microarrays.

2010-12-31 | E-GEOD-19707 | biostudies-arrayexpress

Ago2-bound short RNAs in HeLaS3 cell line

Project description:Characterization of AGO2 bound short RNAs from nuclear extracts of HeLaS3 cell line. Nuclei were isolated from HeLaS3 cells; a fraction of Nuclear lysates was harvsted and sequenced as the 'input' samples. The rest of nuclear lysates were Immunoprecipitated using AGO2 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO2 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.

2015-05-17 | E-MTAB-2084 | biostudies-arrayexpress

AGO2 bound short RNAs in Jurkat cell line

Project description:Characterization of AGO2 bound short RNAs from nuclear extracts of Jurkat cell line. Nuclei were isolated from cells; a fraction of Nuclear lysates was harvested and sequenced as the input samples. The rest of nuclear lysates were Immunoprecipitated using AGO2 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO2 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.

2015-05-17 | E-MTAB-2104 | biostudies-arrayexpress

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