Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ubiquitination analysis of OTUD5

ABSTRACT: TMT quantification of UBR5 knockdown HT1080 cells. Label-free quantification of OTUD5-interacting proteins.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Fumiaki Ohtake

LAB HEAD: Fumiaki Ohtake

PROVIDER: PXD054556 | Pride | 2025-02-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20190531_TMT_UBR5kd.pep.xml	Pepxml
	20190531_TMT_UBR5kd_01.raw	Raw
	20190531_TMT_UBR5kd_02.raw	Raw
	20190531_TMT_UBR5kd_03.raw	Raw
	20190531_TMT_UBR5kd_04.raw	Raw

Items per page:

1 - 5 of 14

Similar Datasets

Proteome analysis in hepatocyte-specific Atg7-knockout mice with different p62 mutations

Project description:To investigate global proteome changes dependent on KEAP1-p62 binding in vivo, we performed cytoplasmic proteome profiling.

2025-04-23 | PXD061879 | Pride

ubiquitin chain linkage of uS10

Project description:Quantification of ubiquitin chain linkage of uS10. Quantification of ubiquitin chain linkage of uS10in UbiR54A mutant strain.

2025-09-18 | PXD052346 | Pride

Orphan quality control shapes network dynamics and gene expression

Project description:All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-MYC oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over orphan transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression, while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers unique opportunities to modulate gene expression in disease. Crosslinking mass spec experiment with UBR5 HECT domain STREP-SUMO-MCRS1 and DSSO.

2023-05-30 | PXD041519 | Pride

Proteome changes upon knockdown of ubiquitin E3 ligases

Project description:Proteome analysis upon knockdown of UBR1, UBR2, UBR4, UBR5, KCMF1, UBE4B, TRIP12

2025-08-18 | PXD066132 | Pride

UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors

Project description:RIG-I like receptors (RLRs) are the major viral RNA sensors essential for the initiation of antiviral immune responses to numerous RNA viruses. RLRs are subjected to stringent transcriptional and posttranslational regulations, of which ubiquitination is one of the most important. However, the role of ubiquitination in RLR transcription is unknown. Here, we generated, screened 375 definite ubiquitin ligase knockout cell lines and identified UBR5 as a positive regulator of RLR transcription. UBR5 deficiency (UBR5-/-) reduced antiviral immune responses to RNA viruses, while increased viral replication in primary cells and mice. Ubr5-/- mice were more susceptible to lethal RNA virus infection than Ubr5+/+ littermates. Mechanistically, UBR5 mediated the Lysine 63-linked ubiquitination of TRIM28, an epigenetic repressor of RLRs. This modification prevented intramolecular SUMOylation of TRIM28, thus disengaged the TRIM28-imposed brake on RLR transcription. In sum, UBR5 enables rapid upregulation of RLR expression to boost antiviral immune responses by ubiquitinating and de-SUMOylating TRIM28.

2023-12-13 | GSE245604 | GEO

UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors (RNA-Seq)

2023-12-13 | GSE245603 | GEO

UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors (ChIP-Seq)

2023-12-13 | GSE245602 | GEO

Evaluation and Optimization of High-Field Asymmetric Waveform Ion Mobility Spectrometry for Multiplexed Quantitative Site-specific N-glycoproteomics

Project description:The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has shown to improve the scope of bottom-up proteomics. The benefits of FAIMS for quantitative N-glycoproteomics have not been investigated yet. In this work, we optimized FAIMS settings for N-glycopeptide identification, with or without the tandem mass tag (TMT) label. The optimized FAIMS approach significantly increased the identification of site-specific N-glycopeptides derived from the purified IgM protein or human lymphoma cells. We explored in detail the changes in FAIMS mobility caused by N-glycopeptides with different characteristics, including TMT labeling, charge state, glycan type, peptide sequence, glycan size and precursor m/z. Importantly, FAIMS also improved multiplexed N-glycopeptide quantification, both with the standard MS2 acquisition method and with our recently developed Glyco-SPS-MS3 method. The combination of FAIMS and Glyco-SPS-MS3 provided the highest quantitative accuracy and precision. Our results demonstrate the advantages of FAIMS for improved mass-spectrometry-based qualitative and quantitative N-glycoproteomics.

2021-05-05 | PXD023951 | Pride

Gene expression profiling of human whole-blood samples before and after the administration of recombinant human erythropoietin

Project description:As part of cross-platform comparisons of microarray and RNA-seq, this current experiment using the Affymetrix Human Transcriptome Array 2.0 aimed to quantify gene-level expression in subjects administered recombinant human erythropoietin over a 10-week protocol for the identification of gene signatures of blood doping. These results were compared to results obtained from other gene expression quantification platforms using the same experimental cohort, including the Illumina HumanHT-12v4 Expression BeadChips (archived in ArrayExpression; E-MTAB-2874), Illumina NextSeq 500 and MGI DNBSEQ-G400RS.

2021-11-04 | E-MTAB-11080 | biostudies-arrayexpress

UBR5 mediates chemoresistance in colorectal cancer by attenuating ferroptosis via Lys11 ubiquitin-dependent stabilization of Smad3-SLC7A11 signaling

Project description:To elucidate the mechanisms underlying UBR5 deficiency-enhanced cytotoxic effects of Oxaliplatin, we performed transcriptome profiling by RNA-seq to explore the signaling pathways affected by UBR5.

2024-01-22 | GSE236003 | 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