Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Nanomolar-Affinity Antibody Enabling Sensitive Labeling and High-Resolution Genomic Mapping of O-GlcNAc

ABSTRACT: High-affinity O-GlcNAc-specific antibodies are crucial for the sensitive detection and functional study of O‑GlcNAcylation. Here, we report the development of a pan-specific, nanomolar-affinity O-GlcNAc antibody named EPR19847 by using a degenerate O‑GlcNAcylated peptide as the immunogen. The EPR19847 antibody can be used for O‑GlcNAc detection, imaging, isolation, and chromatin immunoprecipitation. Using this novel antibody, O-GlcNAcylated proteins were enriched and identified in mouse embryonic stem cells (mESCs). Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) demonstrates that O-GlcNAc is enriched around the promoters of highly expressed genes, and that its genomic distribution is positively correlated with transcription-activating marks including H3K4me3, H3K9ac, and RNA Pol II in mESCs. Further analysis suggests a high occupancy of O-GlcNAcylation within super-enhancers. We anticipate that EPR19847 will serve as a powerful tool for the highly-sensitive detection and systematic functional dissection of O-GlcNAc.

ORGANISM(S): Mus musculus

PROVIDER: GSE342353 | GEO | 2026/08/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

O-GlcNAcylation in mitochondrial protein in rat astrocytes

Project description:To further investigate this idea that O-GlcNAcylation in mitochondria can improve the efficacy and benefit of mitochondrial transfer, we asked what mitochondrial proteins were modified with O-GlcNAc. To identify O-GlcNAcylated proteins and the potential target sites of O-GlcNAcylation, rat astrocytes were stimulated with NAD to induce O-GlcNAcylation in mitochondria, then we isolated mitochondria and extracted O-GlcNAcylated proteins by immunoprecipitation using O-GlcNAc antibody followed by silver staining.

2023-10-20 | PXD045316 | Pride

Gene expression analysis of pluripotent and differentiated genes during EB formation treated with streptozotocin, o-glacnacylation inhibitor

Project description:O-linked-N-acetylglucosamine (O-GlcNAc) has emerged as a critical regulator of diverse cellular processes, but its role in embryonic stem cells (ESCs) and pluripotency has not been investigated. Here we show that O-GlcNAcylation directly regulates core components of the pluripotency network. Blocking O-GlcNAcylation disrupts ESC self-renewal and reprogramming of somatic cells to induced pluripotent stem cells. The core reprogramming factors Oct4 and Sox2 are O-GlcNAcylated in ESCs, but the O-GlcNAc modification is rapidly removed upon differentiation. O-GlcNAc modification of Threonine 228 in Oct4 regulates Oct4 transcriptional activity and is important for inducing many pluripotency related genes, including Klf2, Klf5, Nr5a2, Tbx3 and Tcl1. A T228A point mutation that eliminates this O-GlcNAc modification reduces the capacity of Oct4 to maintain ESC self-renewal and reprogram somatic cells. Overall, our study makes a direct connection between O-GlcNAcylation of key regulatory transcription factors and the activity of the pluripotency network. 2 of E14 stem cell, 2 of embryonic body at day 2, 2 of embryonic body at day 2 treated with streptozotocin, 1 of ZHBTc4 stem cell treated with doxicyclin, and 1 of ZHBTc4 stem cell treated with doxicyclin and streptozotocin were analysed

2012-07-05 | E-GEOD-36322 | biostudies-arrayexpress

Gene expression analysis of R1 mESCs stably expressing WT ESRRB and Ser 25A (the O-GlcNAc residue mutant) ESRRB

Project description:Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per O-acetylated, which, however, can induce a long-overlooked side reaction, non enzymatic S-glycosylation. Herein, we develop 1,3-di-esterified N azidoacetylgalactosamine (GalNAz) as the next generation chemical reporters for metabolic glycan labeling. Both 1,3-di-O-acetylated GalNAz (1,3-Ac2GalNAz) and 1,3-di-O propionylated GalNAz (1,3-Pr2GalNAz) exhibited high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying 1,3-Pr2GalNAz in mouse embryonic stem cells (mESCs), we identified ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We showed that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase (OGT) at serine 25 (Ser 25), which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.

2019-07-27 | GSE131246 | GEO

Gene expression analysis of pluripotent and differentiated genes during EB formation treated with streptozotocin, o-glacnacylation inhibitor

2012-07-06 | GSE36322 | GEO

Genome-wide distribution of H2AS40Gc in mouse embryonic stem cells.

Project description:We report genome-wide distribution of O-GlcNAcylated H2A at serine 40 (H2AS40Gc) in mouse embryonic stem cells (mESCs, J1 line) cultured in 25 mM glucose (HG-mESCs) or 1 mM glucose (LG-mESCs) condition. We found that H2AS40Gc was mainly located at genic area, positively correlated with the gene expression both in HG- and LG-mESCs. Interestingly, H2AS40Gc localization was overlapped with H2AX, γH2AX and O-GlcNAc transferase (Ogt), and varied by extracellular glucose concentration. This study using ChIP-seq and RNA-seq analysis provides genomic distribution of newly O-GlcNAc histone modification in mESCs.

2020-02-02 | GSE77999 | GEO

O-GlcNAc Chromatin Marks from C. elegans L1 animals

Project description:Nutrient-driven O-GlcNAcylation of key components of the transcription machinery may epigenetically modulate gene expression in metazoans. Knockouts of the O-GlcNAc cycling enzymes in C. elegans are viable and fertile, allowing a global analysis of the impact of GlcNAcylation. Whole genome ChIP profiling of the O-GlcNAc cycling mutants identified over 800 genes associated with GlcNAcylated chromatin. This novel chromatin mark is preferentially found with genes involved in stress, longevity, and innate immunity, the same set of processes affected by global changes in gene expression analysis. This experiment collected data on fed animals (3 hours) for comparisons to previoulsy collected starved data to see what acute effects nutritional flux would have on either O-GlcNAc chromatin marks or RNA Pol II distributions.

2010-01-01 | GSE18611 | GEO

Chemoproteomic profiling of O-GlcNAcylated proteins and identification of O-GlcNAc transferases in rice

Project description:O-linked β-N-acetylglucosaminylation (O-GlcNAcylation) is a ubiquitous posttranslational modiﬁcation occurring in both animals and plants. Thousands of proteins along with their O-GlcNAcylation sites have been identified in various animal systems, yet the O-GlcNAcylated proteomes in plants remain poorly understood. Here, we report a large-scale profiling of protein O-GlcNAcylation in a site-specific manner in rice. We first established the metabolic glycan labeling strategy (MGL) with N-azidoacetylgalactosamine (GalNAz) in rice seedlings, which enabled incorporation of azides as a bioorthogonal handle into O-GlcNAc. By conjugation of the azide-incorporated O-GlcNAc with alkyne-biotin containing a cleavable linker via click chemistry, O-GlcNAcylated proteins were selectively enriched for mass spectrometry (MS) analysis. A total of 1,591 unambiguous O-GlcNAcylation sites distributed on 709 O-GlcNAcylated proteins were identified. Additionally, 102 O-GlcNAcylated proteins were identified with their O-GlcNAcylation sites located within a serine/threonine-enriched peptide, causing ambiguous site assignment. The identified O-GlcNAcylated proteins are involved in multiple biological processes such as transcription, translation and plant hormone signaling. Furthermore, we discovered two O-GlcNAc transferases (OsOGTs) in rice. By expressing OsOGTs in Escherichia coli and Nicotiana benthamiana leaves, we confirmed their OGT enzymatic activities and used them to validate the identified rice O-GlcNAcylated proteins. Our dataset provides a valuable resource for studying O-GlcNAc biology in rice, and the MGL method should facilitate the identification of O-GlcNAcylated proteins in various plants.

2023-05-10 | PXD036527 | Pride

GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data]

Project description:We have found that histone H2B is GlcNAcylated at residue S112 by O-GlcNAc transferase and that H2B S112 GlcNAcylation fluctuates in response to extracellular glucose level. We have also found that H2B S112 GlcAcylation promotes H2B K120 ubiquitination. To investigate whether these histone modification correlate to transcriptional activation, we performed comprehensive gene expression analysis using Affymetrix GeneChip in HeLa cell cultured with different conditions, i.e. without glucose, with glucose and with FBS.

2011-10-27 | GSE33050 | GEO

Next generation unnatural monosaccharides reveal that ESRRBO GlcNAcylation enhances pluripotency of mouse embryonic stem cells

Project description:Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per O acetylated, which, however, can induce a long-overlooked side reaction, non enzymatic S-glycosylation. Herein, we develop1,3 di esterified N azidoacetylgalactosamine (GalNAz) as the next generation chemical reporters for metabolic glycan labeling. Both 1,3 di O-acetylated GalNAz (1,3-Ac2GalNAz) and1,3 di O propionylated GalNAz (1,3-Pr2GalNAz)exhibited high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying1,3 Pr2GalNAz in mouse embryonic stem cells (mESCs), we identified ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We showed that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase (OGT) at serine 25 (Ser 25), which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.

2019-09-09 | PXD015035 | Pride

Next generation unnatural monosaccharides reveal that ESRRBO GlcNAcylation enhances pluripotency of mouse embryonic stem cells

Project description:Unnatural monosaccharides such as azidosugars that can be metabolically incorporated into cellular glycans are currently used as a major tool for glycan imaging and glycoproteomic profiling. As a common practice to enhance membrane permeability and cellular uptake, the unnatural sugars are per O acetylated, which, however, can induce a long-overlooked side reaction, non enzymatic S-glycosylation. Herein, we develop1,3 di esterified N azidoacetylgalactosamine (GalNAz) as the next generation chemical reporters for metabolic glycan labeling. Both 1,3 di O-acetylated GalNAz (1,3-Ac2GalNAz) and1,3 di O propionylated GalNAz (1,3-Pr2GalNAz)exhibited high efficiency for labeling protein O-GlcNAcylation with no artificial S-glycosylation. Applying1,3 Pr2GalNAz in mouse embryonic stem cells (mESCs), we identified ESRRB, a critical transcription factor for pluripotency, as an O-GlcNAcylated protein. We showed that ESRRB O-GlcNAcylation is important for mESC self-renewal and pluripotency. Mechanistically, ESRRB is O-GlcNAcylated by O-GlcNAc transferase (OGT) at serine 25 (Ser 25), which stabilizes ESRRB, promotes its transcription activity and facilitates its interactions with two master pluripotency regulators, OCT4 and NANOG.

2019-09-12 | PXD014785 | Pride

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