Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide mapping of oxidative DNA damage via engineering of 8-oxoguanine DNA glycosylase

ABSTRACT: Genome-wide mapping of oxidative DNA damage via engineering of 8-oxoguanine DNA glycosylase

PROVIDER: PRJNA563884 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10067369_1.fastq.gz	Fastqsanger.gz
	SRR10067369_2.fastq.gz	Fastqsanger.gz
	SRR10067370_1.fastq.gz	Fastqsanger.gz
	SRR10067370_2.fastq.gz	Fastqsanger.gz
	SRR10067371_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Genome-wide mapping of oxidative DNA damage via engineering of 8-oxoguanine DNA glycosylase

Project description:7,8-dihydro-8-oxoguanine (OG) is one of the major DNA oxidative damages, which has been concerned by researchers for its potential of mutagenesis and epigenetic regulation. Genome-wide mapping of oxidative DNA damage is of great value for understanding the biological impact of these modifications. Here we present a novel appoach to profile guanine oxidation in the mouse genome. Through structure-guided mutagenesis, we've successufully engineered 8-oxoguanine DNA glycosylase into a useful tool for OG detection. By enrichment of glycosylase-DNA complex, thousands of OG peaks were identified in the mouse genome.

2019-10-18 | GSE136862 | GEO

Genome-wide analysis of 8-oxoguanine DNA glycosylase-1

Project description:We report the application of ChIP-Sequencing for profiling genome-wide distribution of 8-oxoguanine DNA glycosylase (OGG1) which is a DNA base excision repair protein, after TNF exposure of cells. By obtaining an average of over 18 million of total reads per sample and over 19.5 million of unique reads per sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HEK293 cells. We performed gene ontology and functional pathway analysis of genes associate with peaks, and identify regions of the genomes (e.g. promoter, introns, etc) where the peaks tend to occur. The results show that OGG1 is primarily associated with promoter regions in vicinity of transcription factor binding sites 5' of transcription start sites (TSS). This pattern of distribution occurs in spite of genome-wide oxidative modifications of guanine (primarily 8-oxoG). OGG1 increased highly significant (1e-09 to 1e-517) enrichment of 57 transcription factor binding sites including those for Sox(2, 3, 6, 10), RUNX, RUNX(1, 2), HOX(C, D), STAT(1, 3, 6), IRF(1 to 4), NF-κB. In controls, the DNA was chromatin immunoprecipitated using antibody to NF-κB/RelA. These and other data derived from further analysis, suggest that OGG1 modulates binding of transcription factors and gene expression.

2018-07-15 | GSE75562 | GEO

Genome-wide analysis of 8-oxoguanine DNA glycosylase-1 after oxidative stress exposure

Project description:We report the application of ChIP-Sequencing for profiling genome-wide distribution of 8-oxoguanine DNA glycosylase1 (OGG1, a DNA base excision repair protein), after oxidative stress exposure mediated by glucose oxidase (GOx) of cells. By obtaining an average of over 18 million of total reads per sample and over 19.5 million of unique reads per sample from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of HEK293 cells. We performed gene ontology and functional pathway analysis of genes associated with peaks to identify regions of the genomes (e.g. promoter, introns, etc) where the peaks tend to occur. The results show that OGG1 is primarily associated with promoter regions in vicinity of transcription factor binding sites 5' of transcription start sites (TSS). This pattern of distribution occurs in spite of genome-wide oxidative modifications of guanines (primarily 8-oxoG). OGG1 increased significantly at regulatory regions of CXC-, CC- chemokines, cytokines and growth factors. In controls, the DNA was chromatin immunoprecipitated using antibody to NF-κB/RelA. As expected NF-κB was enriched on gene regulatory regions including those of proinflammatory,cell proliferation ones. These and other data derived from further analysis, suggest that OGG1 modulates gene expression in coordination with NF-κB.

2018-07-06 | GSE89017 | GEO

8-Oxoguanine DNA glycosylase 1 conceals guanine oxidation in nucleoprotein-associated RNA of respiratory syncytial virus

Project description:Respiratory syncytial virus (RSV), along with other prominent respiratory RNA viruses such as influenza and SARS-CoV-2, significantly contributes to the global incidence of respiratory tract infections. These pathogens induce the production of reactive oxygen species (ROS), which play a crucial role in the onset and progression of respiratory diseases. However, the mechanisms by which viral RNA manages ROS-induced base oxidation remain poorly understood. Here we reveal that 8-oxo-7,8-dihydroguanine (8-oxoGua) is not merely an incidental byproduct of ROS activity but serves as a strategic adaptation of RSV RNA to maintain genetic fidelity within host cells. Through 8-oxoguanine DNA glycosylase 1 (OGG1) immunoprecipitation and LC_MS/MS, we discovered that RSV nucleoprotein is a principal partner of OGG1. Further investigation revealed that viral ribonucleoprotein complexes specifically hijack OGG1. Importantly, inhibiting OGG1's ability to recognize 8-oxoGua significantly reduces RSV progeny production. Our results underscore the viral replication machinery's adaptation to oxidative challenges, suggesting that inhibiting OGG1's reading function could be a novel strategy for antiviral intervention.

2024-10-09 | PXD053262 | Pride

Expression data from human fibroblasts 6 and 12 hours after 8-oxoguanine treatment

2011-01-27 | GSE26813 | GEO

Expression data from human fibroblasts 6 and 12 hours after 8-oxoguanine treatment

Project description:8-oxoguanine is excised from DNA by 8-oxoguanine DNA glycosylase-1 during DNA base excision repair. We used microarrays to gain insight into the potential biological function of the excised, free 8-oxoguanine base. MRC5, human diploid fibroblasts were exposed to 8-oxoguanine and changes in gene expression compared to mock control were analyzed 6 hours after exposure. MRC5, human diploid fibroblasts were exposed to 8-oxoguanine and changes in gene expression compared to mock control were analyzed 12 hours after exposure.

2011-01-27 | E-GEOD-26813 | biostudies-arrayexpress

8-Oxoguanine DNA glycosylase 1 hijacked by nucleoprotein conceals guanine oxidation in respiratory syncytial virus RNA

Project description:Respiratory Syncytial Virus (RSV), alongside other prominent respiratory RNA viruses such as influenza and SARS-CoV-2, significantly contributes to the global incidence of respiratory tract infections. These pathogens prompt the production of reactive oxygen species (ROS), which play a crucial role in the onset and progression of respiratory diseases. However, the strategies by which viral RNA manages ROS-induced base oxidation are not well understood. Here we uncover that 8-oxo-7,8-dihydroguanine (8-oxoGua) is not merely an incidental byproduct of ROS activity but serves as a strategic adaptation of RSV RNA during replication within host cells. Through RNA immunoprecipitation and next-generation sequencing, we discovered that 8-oxoguanine DNA glycosylase 1 (OGG1) binding sites are predominantly found in the RSV antigenome, especially within guanine-rich areas. Further investigation revealed that viral ribonucleoprotein complexes specifically hijack OGG1. Crucially, our findings show that inhibiting OGG1's ability to recognize 8-oxoGua leads to a substantial reduction in RSV progeny production. Our results underscore the viral replication machinery's adaptation to oxidative challenges, pointing to the inhibition of OGG1's reading function as a potential novel strategy for antiviral intervention.

2024-06-13 | GSE269769 | GEO

Effect of 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor on pro-inflammatory gene expression.

Project description:Effect of 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor on pro-inflammatory gene expression.

| PRJNA480274 | ENA

Effect of 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor on pro-inflammatory gene expression.

Project description:Effect of 8-oxoguanine DNA glycosylase 1 (OGG1) inhibitor on pro-inflammatory gene expression.

| PRJNA662307 | ENA

8-Oxoguanine DNA glycosylase 1 hijacked by nucleoprotein conceals guanine oxidation in respiratory syncytial virus RNA

Project description:8-Oxoguanine DNA glycosylase 1 hijacked by nucleoprotein conceals guanine oxidation in respiratory syncytial virus RNA

| PRJNA1123660 | ENA