Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HMGB1 ubiquitination related sites

ABSTRACT: HMGB1 ubiquitination related sites detected by IP-Mass

ORGANISM(S): Homo Sapiens

SUBMITTER: Yunxiao Shang

PROVIDER: PXD043938 | iProX | Wed Jul 19 00:00:00 BST 2023

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Hypermethylation of RNF125 promotes autophagy-induced oxidative stress in asthma by increasing HMGB1 stability.

Hu Jiapeng J Ding Ruiwei R Liu Shaozhuang S Wang Jia J Li Jianjun J Shang Yunxiao Y

iScience 20230727 8

Asthma is a global chronic airway disease. The expression and role of RNF125, an E3 ubiquitin ligase, in asthma remain uncertain. In this study, we revealed that RNF125 was downregulated in the bronchial epithelium of mice and patients with asthma. <i>Rnf125</i> hypermethylation was responsible for the low expression of RNF125 in primary airway epithelial cells of mice treated with OVA. Moreover, we demonstrated that RNF125 could attenuate autophagy, oxidative stress, and protect epithelial barr ...[more]

PMID: 37599832

Similar Datasets

Co-immunoprecipitation coupled with mass for RNR10 in rice&Identification of ubiquitination sites in rice DNR1

Project description:RNR10 is a key factor that regulates the response of rice roots to nitrogen.In an attempt to determine the target(s) of RNR10, we performed co-immunoprecipitation (Co-IP) coupled with mass spectrometry analysis to search for RNR10 interactors.DNR1 is a downstream target gene of RNR10.Previous studies have shown that rice DNR1 is subjected to ubiquitination modification. In order to identify the ubiquitination modification sites of DNR1,we performed mass spectrometry analyses.

2023-09-30 | PXD043400 | Pride

dBRWD3 manipulates chromatin signature by ubiquitination to regulate ORC

Project description:Ubiquitination and epigenetic modification both play essential roles in regulating cell fates and development, but little is known how two pathways crosstalk. A known chromatin-binding protein BRWD3, Bromodomain repeats and WD40 repeats domain contain protein 3, has been shown involved both in ubiquitination and histone modification regulation. BRWD3 has roles in multiple chromatin-related processes, including transcription, DNA replication, and chromatin modification. However, how ubiquitination is involved and what’s BRWD3’s ubiquitination targets are barely known. Here, we study the single Drosophila homolog dBRWD3 to uncover its mechanism. To find dBRWD3’s ubiquitination targets, we performed both dBRWD3 IP-MS and BRWD3 dependent ubiquitination IP-MS. Expectedly, the whole BRWD3-Cul4-DDB1 E3 ubiquitination complex and multiple histones are significantly enriched in dBRWD3-IP. Interestingly, multiple histone modification writers and the DNA replication initiation factor origin recognition complex (ORC) are among the intersection of two MS. ORC’s function is highly dependent on chromatin signature. dBRWD3 could provide a perspective on how chromatin signature is regulated by ubiquitination to regulate ORC function. In support of this, about 35% of ORC2 binding sites overlap with dBRWD3 binding sites among the genome. The H3K27ac occupancy rate of dBRWD3 related ORC sites is about 50% higher than that of dBRWD3 irrelevant ORC sites. Depletion of dBRWD3 significantly reduces DNA proliferation in the S phase. Further study will focus on determining which histone modification writer is targeted for ubiquitination and how does it contribute to the chromatin signature and ORC function.

2023-10-24 | PXD039708 | Pride

Arabidopsis DMC1 ubiquitination sites identification, LC-MS/MS

Project description:To characterize the mechanism of DMC1 ubiquitination as well as further explore the impact of DMC1’s ubiquitination on meiosis, we attempted to identify the potential DMC1 ubiquitination sites. The in vitro ubiquitination assay using recombinant DMC1 heterologously expressed and purified from E. coli as substrate was conducted. Then mass spectrometry assay was performed to identify the ubiquitination sites of DMC1. Five DMC1 lysine residues (K45, K70, K101, K162, and K290) were identified as potential ubiquitination sites.

2023-10-24 | PXD038116 | Pride

Identification of Merlin ubiquitination sites

Project description:To identify the ubiquitination sites on Merlin, Flag-tagged wild-type Merlin or the S518D mutant were stably transduced into LN229 cells. These cells were treated with thapsigargin for 15 minutes and subjected to immunoprecipitation and followed by Mass Spectrometry.

2020-12-07 | PXD021057 | Pride

Structural basis of PROTAC-induced target ubiquitination mechanism - identification of BRD4 ubiquitination sites

Project description:Proteolysis Targeting Chimeras (PROTACs) hijack the ubiquitin proteasome system to ubiquitinate target proteins, targeting them for degradation by the proteasome. An understudied process that is essential to the PROTAC mechanism of action is ubiquitination of the target protein and ubiquitin (Ub) chain elongation. To elucidate the mechanism of PROTAC-induced ubiquitination of BRD4(BD2) ubiquitination sites on Brd4BD2 were mapped by mass spectrometry following an in vitro ubiquitination assay containing neddylated-CRL2VHL, Brd4BD2, MZ1, Uba1 and either UBE2R1 or UBE2D2. Time points were taken at 0 minutes, 10 minutes, 0.5 hours, 1 hour and 3 hours. Proteins were separated by SDS-page analysis. To visualize proteins the gel was stained with Coomassie blue and gel slices containing ubiquitin modified Brd4BD2 across timepoints and increasing molecular weight were excised from the gel and were analyzed by mass spectrometry. To identify sites of ubiquitination a search for GG-K peptides was performed in MaxQuant. Based on existing structures the modified lysine residues were all situated on the same face of BD2.

2025-05-06 | PXD049043 | Pride

STUB1-mediated K63-linked ubiquitination of UHRF1 promotes the progression of cholangiocarcinoma by maintaining DNA hypermethylation of PLA2G2A

Project description:Cholangiocarcinoma (CCA) is a highly malignant tumor characterized by a lack of effective targeted therapeutic strategies. The protein UHRF1 plays a pivotal role in the preservation of DNA methylation and works synergistically with DNMT1. Posttranscriptional modifications (PTMs), such as ubiquitination, play indispensable roles in facilitating this process. Nevertheless, the specific PTMs that regulate UHRF1 in CCA remain unidentified. We confirmed the interaction between STUB1 and UHRF1 through mass spectrometry analysis. Furthermore, we investigated the underlying mechanisms of the STUB1-UHRF1/DNMT1 axis via co-IP experiments, denaturing IP ubiquitination experiments, nuclear‒cytoplasmic separation and immunofluorescence experiments. STUB1-UHRF1/DNMT1-mediated DNA methylation plays a crucial role in promoting the epigenetic silencing of tumor suppressor genes (TSGs) and facilitating tumor progression. To investigate the specific TSGs regulated by the STUB1-UHRF1/DNMT1 axis in CCA cells, RNA-seq analysis of overexpressed STUB1 and negative control TFK1 cells was performed.

2024-09-16 | GSE275480 | GEO

Project description:Increased small airway resistance and decreased lung elasticity contribute to the airflow limitation in chronic obstructive pulmonary disease (COPD). The lesion that corresponds to loss of lung elasticity is emphysema; the small airway obstruction is due to inflammatory narrowing and obliteration. Despite their convergence in altered physiology, different mechanisms contribute to these processes. The relationships between gene expression and these specific phenotypes may be more revealing than comparison with lung function. We measured the ratio of alveolar surface area to lung volume (SA/V) in lung tissue from 43 smokers. Two samples from 21 subjects, in which SA/V differed by > 49 cm2/mL were profiled to select genes whose expression correlated with SA/V. The level of expression of 181 transcripts was related to SA/V ( p< 0.05). The relationship between expression of these transcripts and SA/V was tested in the 22 remaining subjects as a replication. Thirty of the 181 genes remained significantly associated with SA/V (P<0.05) and the direction of association was the same in 164/181. Pathway and network analysis revealed enrichment of genes involved in protein ubiquitination, and western blotting showed altered expression of genes involved in protein ubiquitination in obstructed individuals. These data implicate modified protein ubiquitination and degradation as a potentially important pathway in the pathogenesis of emphysema. Raw data not available for this study

2014-11-07 | GSE63073 | GEO

Analysis of ubiquitination sites in Neh2Dual-sGFP substrate

Project description:Determination of ubiquitination sites on an artificial substrate consisting of an Neh2 domain from Nrf2 that has been modified to be able to be ubiquitinated with three different E3 ligase systems, Ubr1 (which forms K48 linkages), Rsp5 (which forms K63 linkages) and Cul3/Rbx1/Keap1 (which forms branched linkages).

2024-01-05 | MSV000093780 | MassIVE

Identification of sites of ubiquitination on protein TRIM52

Project description:Identification of ubiquitination sites on my protein of interest (TRIM52) through NiNTA pull-down of TRIM52 modified by his-ubiquitin.

2025-03-25 | PXD051295 | Pride

Inhibition of ABI2 Ubiquitination-Dependent Degradation Suppresses Breast Cancer Cell Growth via Down-regulating PI3K/Akt Signaling Pathway [RNAseq-20240420]

Project description:TNBC is a type of cancer that lacks receptor expression and has complex molecular mechanisms. Recent evidence shows that the ubiquitin-protease system is closely related to TNBC. In this study, we obtain a key ubiquitination regulatory substrate-abi2 protein by bioinformatics methods, which is also closely related to the survival and prognosis of TNBC. Further, through a series of experiments, we demonstrated that ABI2 expressed at a low level in TNBC tumors, and it has the ability to control cell cycle and inhibit TNBC cell migration, invasion and proliferation. Molecular mechanism studies proved E3 ligase CBLC could increase the ubiquitination degradation of ABI2 protein. Meanwhile, RNA-seq and IP experiments indicated that ABI2 can significantly inhibit PI3K/Akt signaling pathway via the interaction with Rho GTPase RAC1. Finally, we also found that the antibiotic Colistimethate could inhibit the growth of TNBC cells by inhibiting CBLC-induced ABI2 ubiquitination and down-regulating PI3K/Akt signaling pathway.

2024-06-04 | GSE268673 | 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