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8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [8oxoG-seq]

ABSTRACT: We observed that transcriptional activity and the number of active genes were significantly correlated with the distribution of 8-oxoG in gene promoter regions, as determined by liquid chromatography/mass spectrometry (LC/MS), and 8-oxoG and RNA sequencing

ORGANISM(S): Mus musculus

PROVIDER: GSE124712 | GEO | 2019/06/30

REPOSITORIES: GEO

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8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [RNA-Seq]

Project description:We observed that transcriptional activity and the number of active genes were significantly correlated with the distribution of 8-oxoG in gene promoter regions, as determined by liquid chromatography/mass spectrometry (LC/MS), and 8-oxoG and RNA sequencing

2019-06-30 | GSE124359 | GEO

8-OxoG in GC-rich Sp1 binding sites enhances gene transcription in adipose tissue of juvenile mice.

Project description: Not available

| S-EPMC6821754 | biostudies-literature

Dysregulation of acrosome formation network by 8-oxoguanine (8-oxoG) in infertile sperm

Project description:Various environmental factors contribute to dysregulated spermatogenic gene network, abnormal spermatogenesis, and eventually impaired sperm fertility. 8-hydroxyguanine (8-oxoG) is the most common and well-studied oxidative DNA lesion of the four DNA bases and unrepaired 8-oxoG modifications are associated with DNA fragmentation in sperms. However, the molecular effects of 8-oxoG generated in sperm DNA by oxidative stress on spermatogenesis are not entirely understood. Here, we identified one infertile Korean native striped cattle at 6-year old (C14) due to asthenozoospermia and teratozoospermia. We compared global concentration of 8-oxoG by reverse-phase liquid chromatography/mass spectrometry (RP-LC/MS), the genomic distribution of 8-oxoG by next-generation sequencing (OG-seq), and expression of sperm proteins by 2-dimensional electrophoresis followed by mass spectrometry (2D/MS) in sperms of C14 with those of normal counterpart (C13). We found that averaged levels of 8-oxoG in C13 and C14 sperms were 0.027% and 0.044% of total dG and 8-oxoG was significantly greater in infertile sperm DNA (p = 0.0028). More than 81% of the 8-oxoG loci were distributed around the transcription start site (TSS) and 8-oxoG harboring 165 genes, including phospholipases, were annotated exclusively into infertile sperm DNA. Gene set enrichment analysis (GSEA) and the protein-protein interaction networking revealed that the Golgi apparatus was significantly enriched with the 8-oxoG genes of infertile sperm (q = 2.20E-07). Proteomic analysis verified that acrosome-related proteins including Acrosin-binding protein (ACRBP) and Sperm equatorial segment protein 1 (SPESP1) were 1.6-fold and 2.6-fold down-regulated in infertile sperm, respectively. These results suggest that 8-oxoG formation during spermatogenesis would dysregulate the acrosome-related gene network, causing structural and functional defects of sperm, leading to infertility.

2021-06-30 | GSE165538 | GEO

8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-06-30 | GSE124713 | GEO

8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice

Project description:8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice

| PRJNA513196 | ENA

8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [RNA-Seq]

Project description:8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [RNA-Seq]

| PRJNA511834 | ENA

8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [8oxoG-seq]

Project description:8-OxoG in GC-rich Sp1 binding sites enhances gene transcription during adipose tissue development in juvenile mice [8oxoG-seq]

| PRJNA513197 | ENA

Identification of 8-oxoG binding proteins in Deinococcus radiodurans

Project description:8-oxo-7,8-dihydroguanine (8-oxoG) is a common RNA oxidation that has been implicated in carcinogenesis, neurodegeneration, and aging. Some? Many? RNA-binding proteins have shown binding preference for 8-oxoG modified RNA; such binding? can protect cells from oxidative stress. To date, the presence of specific 8-oxoG-recognizing proteins is only known in model organisms, but, how these proteins cooperate is still unclear. Here, we use RNA affinity chromatography and mass spectrometry to search for proteins that specifically bind 8-oxoG-modified RNA in Deinococcus radiodurans, an extremophilic bacterium with extraordinary resistance to oxidative stresses. We identified four proteins that selectively bind to oxidized RNA: polynucleotide phosphorylase (DR_2063/PNPase), ATP-dependent DEAD-box RNA helicase (DR_0335/RhlB), ribosomal protein S1 (DR_1983/RpsA), and transcriptional termination factor (DR_1338/Rho). The knockout of PNPase and RhlB in D. radiodurans caused increased sensitivity to hydrogen peroxide and a significant accumulation of 8-oxoG modified RNA. Importantly, PNPase directly interacts with RhlB in D. radiodurans; however, no additional phenotypic effect was observed for the double deletion of pnp and rhlB compared to the individual single deletions. Overall, our findings suggest a role of the PNPase-RhlB complex in targeting 8-oxoG-modified RNAs for rapid degradation and thereby constitutes an important component of D. radiodurans resistance to oxidative stress.

2022-07-10 | PXD028861 | Pride

Identification of targets of the protein disulfide reductase thioredoxin

Project description:Identification of targets of the protein disulfide reductase thioredoxin using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and thiol specific differential labeling with isotope-coded affinity tags (ICAT). Reduction of specific target disulfides is quantified by measuring ratios of cysteine residues labeled with the heavy (13C) and light (12C) ICAT reagents in peptides derived from tryptic digests of Trx-treated and non-treated samples. Keywords: protein, LC-MS/MS, ICAT

2008-11-20 | GSE11650 | GEO

Nuclear receptors modulate the interaction of Sp1 and GC-rich DNA via ternary complex formation.

Project description: Not available

| S-EPMC1221515 | biostudies-other