Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression from C. elegans L1 animals

ABSTRACT: 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 transcriptional profiling of the O-GlcNAc cycling mutants confirmed dramatic deregulation of genes in these key pathways. As predicted, the O-GlcNAc cycling mutants show phenotypically altered lifespan and susceptibility to UV stress. L1 larvae were synchronized by starvation for two days after hatching in sterile buffer. Wild type and mutant animals were collected and total RNA isolated for gene expression analysis

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Michael Krause

PROVIDER: E-GEOD-18130 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Dynamic O-GlcNAc cycling at promoters of Caenorhabditis elegans genes regulating longevity, stress, and immunity.

Love Dona C DC Ghosh Salil S Mondoux Michelle A MA Fukushige Tetsunari T Wang Peng P Wilson Mark A MA Iser Wendy B WB Wolkow Catherine A CA Krause Michael W MW Hanover John A JA

Proceedings of the National Academy of Sciences of the United States of America 20100405 16

Nutrient-driven O-GlcNAcylation of key components of the transcription machinery may epigenetically modulate gene expression in metazoans. The global effects of GlcNAcylation on transcription can be addressed directly in C. elegans because knockouts of the O-GlcNAc cycling enzymes are viable and fertile. Using anti-O-GlcNAc ChIP-on-chip whole-genome tiling arrays on wild-type and mutant strains, we detected over 800 promoters where O-GlcNAc cycling occurs, including microRNA loci and multigene o ...[more]

PMID: 20368426

Similar Datasets

Expression from C. elegans L4 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 transcriptional profiling of the O-GlcNAc cycling mutants confirmed dramatic deregulation of genes in these key pathways. As predicted, the O-GlcNAc cycling mutants show phenotypically altered lifespan and susceptibility to UV stress. Similarly aged L4 animals (20) staged by degree of vulval development were hand picked. Wild type and mutant animals were collected and total RNA isolated for gene expression analysis

2010-01-01 | E-GEOD-18131 | biostudies-arrayexpress

THE INTRA-MITOCHONDRIAL O-GLCNACYLATION SYSTEM ACUTELY REGULATES OXPHOS CAPACITY AND ROS DYNAMICS IN THE HEART

Project description:O-linked N-acetylglucosamination (O-GlcNAcylation) of proteins is increasingly recognized as an important cellular regulatory mechanism. In the heart, nucleocytoplasmic O-GlcNAcylation is involved in the modulation of multiple pathophysiological processes. However, the mechanisms leading to O-GlcNAcylation in mitochondria and the consequences on their function remain poorly understood. In this study, we used an in vitro reconstitution assay to characterize the intra-mitochondrial O-GlcNAc cycling system without potential confounding effects of O-GlcNAcylation in other cellular compartments. We performed a comparative analysis of the O-GlcNAcylome of isolated cardiac mitochondria acutely (30 min) exposed to UDP-GlcNAc in presence/absence of NButGT, a specific O-GlcNAcylation inducer, and evaluated the impact on mitochondrial function. 412 O-GlcNAcylated mitochondrial proteins were identified by mass spectrometry analysis, with 189 (Q<0.05) displaying increased O-GlcNAcylation in response to NButGT. Among the O-GlcNAcylated pathways identified, oxidative phosphorylation was the main affected. These acute changes in protein O-GlcNAcylation were associated with enhanced Complex I (CI) activity, increased maximal respiration in presence of CI substrates, and a striking reduction of mitochondrial ROS release, which could be related to O-GlcNAcylation of subunits within the NADH dehydrogenase module of CI. In conclusion, our work underlines the existence of a dynamic mitochondrial O-GlcNAcylation system capable of rapidly modifying mitochondrial function.

2022-02-11 | PXD026495 | Pride

Expression from C. elegans L1 animals

2010-01-01 | GSE18130 | GEO

Expression from C. elegans L4 animals

2010-01-01 | GSE18131 | GEO

Expression 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. Here we compare gene expression in wild type and O-GlcNAc mutants (ogt-1 and oga-1) in synchronized, fed L1 animals. Whole genome transcriptional profiling of the O-GlcNAc cycling mutants confirmed dramatic deregulation of genes in these key pathways. As predicted, the O-GlcNAc cycling mutants show phenotypically altered lifespan and susceptibility to UV stress.

2018-06-04 | GSE40371 | GEO

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

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

Gene expression of SKOV3 cells after no treatment or treatment with 50 microM peracetylated GlcNAc or peracetylated 4-deoxy-GlcNAc for three days

Project description:Heparan sulfate (HS), a long linear polysaccharide, is implicated in various steps of tumorigenesis, including angiogenesis. We successfully interfered with HS biosynthesis using a peracetylated 4-deoxy analog of the HS constituent GlcNAc and studied the compoundM-bM-^@M-^Ys metabolic fate and its effect on angiogenesis. The 4-deoxy analog was activated intracellularly into UDP-4-deoxy-GlcNAc and HS expression was inhibited up to ~96% (IC50 = 16 M-BM-5M). HS chain size was reduced, without detectable incorporation of the 4-deoxy analog, likely due to reduced levels of UDP-GlcNAc and/or inhibition of glycosyltransferase activity. Comprehensive gene expression analysis revealed reduced expression of genes regulated by HS binding growth factors as FGF-2 and VEGF. Cellular binding and signaling of these angiogenic factors was inhibited. Micro-injection in zebrafish embryos strongly reduced HS biosynthesis, and angiogenesis was inhibited in both zebrafish and chicken model systems. All these data identify 4-deoxy-GlcNAc as a potent inhibitor of HS synthesis which hampers pro-angiogenic signaling and neo-vessel formation. 9 samples were analyzed: 3 biological replicates from untreated SKOV3 cells, 3 biological replicates from SKOV3 cells treated with peracetylated GlcNAc, 3 biological replicates from SKOV3 cells treated with peracetylated 4-deoxy-GlcNAc

2013-08-23 | E-GEOD-48284 | biostudies-arrayexpress

Fruit fly O-GlcNAc glycoproteomics

Project description:The reversible posttranslational O-GlcNAc modification of serine or threonine residues of intracellular proteins is involved in many cellular events from signaling cascades to epigenetic and transcriptional regulation. O-GlcNAcylation is a conserved nutrient-dependent process involving two enzymes, O-GlcNAc Transferase (OGT) adding O-GlcNAc while O-GlcNAcase (OGA) removing it in a manner that’s protein and context dependent. O-GlcNAcylation is essential for epigenetic regulation of gene expression through its action on Polycomb and Trithorax and Compass complexes. However, the important role of O-GlcNAc on adult life and healthspan have been largely unexplored, mainly due the lack of available model systems. Cataloging the O-GlcNAc proteome has proven useful in understanding the biology of this modification in vivo. In this study, we leveraged a recently developed oga knockout fly mutant to identify the O-GlcNAcylated proteins in adult Drosophila melanogaster. The adult O-GlcNAc proteome revealed many proteins related to cell and organismal growth, development, differentiation, and epigenetics. We identified many O-GlcNAcylated proteins that serve a role in increased growth and decreased longevity, including HCF, SIN3A, LOLA, KISMET, ATX2, SHOT, and FOXO.

2021-04-26 | PXD025344 | Pride

O-GlcNAc pattern of sOGT regulates its substrate selectivity and function

Project description:O-GlcNAcylation occurs on thousands of proteins involved in various cellular events. O-GlcNAc transferase (OGT), one of the enzymes responsible for protein O-GlcNAcylation, is known to be auto-O-GlcNAcylated at multiple sites. However, the role of O-GlcNAcylation on OGT is still unknown. Here, we report the role of O-GlcNAcylation on short form OGT (sOGT). By LC-ETD-MS analysis and western blot, we show that sOGT was mainly O-GlcNAcylated in the tetratricopeptide repeat (TPR) motifs with T12 and S56 being two “key” sites. T12 was a predominant O-GlcNAcylation site and the absence of S56 O-GlcNAcylation enhanced sOGT O-GlcNAcylation level. We found that O-GlcNAcylation of sOGT did not affect the enzyme activity but increased its binding to substrate proteins. S56A bound to and hence glycosylated more proteins, while T12A associated with fewer substrates. Proteomic studies combined with cell proliferation/cell cycle analyses indicated that S56A substantially enhanced cell proliferation, while T12A reduced it, and T12A led to a G2/M cell cycle arrest, due to O-GlcNAcylation of diverse proteins. These findings demonstrate that the O-GlcNAc pattern on sOGT modulates its function in cells by targeting different proteins.

2019-09-16 | PXD009731 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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