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Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

ABSTRACT: Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

PROVIDER: PRJNA751557 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15324461_1.fastq.gz	Fastqsanger.gz
	SRR15324461_2.fastq.gz	Fastqsanger.gz
	SRR15324462_1.fastq.gz	Fastqsanger.gz
	SRR15324462_2.fastq.gz	Fastqsanger.gz
	SRR15324463_1.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

Project description:8-Oxo-7,8-dihydro-2’-deoxyguanosine (OG), one of the most common oxidative DNA damages, causes genome instability and is associated with cancer, neurological diseases and aging. In addition, OG and its repair intermediates can regulate gene transcription, and thus play a role in sensing cellular oxidative stress. However, the lack of methods to precisely map OG has hindered the study of its biological roles. Here we developed a single-nucleotide resolution OG-sequencing method, named CLAPS-seq (Chemical Labeling And Polymerase Stalling Sequencing), to measure the genome-wide distribution of both exogenous and endogenous OGs with high specificity. Our data identified decreased OG occurrence at G-quadruplexes (G4s), in association with underrepresentation of OGs in promoters which have high GC content. Furthermore, we discovered that potential quadruplex sequences (PQSs) were hotspots of OGs which may in turn stimulate the formation of G4s at PQSs, implying a role of non-G4-PQSs in OG-mediated oxidative stress response.

2021-10-09 | GSE181312 | GEO

Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites.

Project description:8-Oxo-7,8-dihydro-2'-deoxyguanosine (OG), one of the most common oxidative DNA damages, causes genome instability and is associated with cancer, neurological diseases and aging. In addition, OG and its repair intermediates can regulate gene transcription, and thus play a role in sensing cellular oxidative stress. However, the lack of methods to precisely map OG has hindered the study of its biological roles. Here, we developed a single-nucleotide resolution OG-sequencing method, named CLAPS-seq (Chemical Labeling And Polymerase Stalling Sequencing), to measure the genome-wide distribution of both exogenous and endogenous OGs with high specificity. Our data identified decreased OG occurrence at G-quadruplexes (G4s), in association with underrepresentation of OGs in promoters which have high GC content. Furthermore, we discovered that potential quadruplex sequences (PQSs) were hotspots of OGs, implying a role of non-G4-PQSs in OG-mediated oxidative stress response.

| S-EPMC8643665 | biostudies-literature

G-Quadruplex structures are stable and detectable in human genomic DNA.

Project description:The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. Our high sensitivity structure-based pull-down strategy enables the isolation of genomic DNA fragments bearing a single as well as multiple G-quadruplex structures. Stable G-quadruplex structures are found in sub-telomeres, gene bodies and gene regulatory regions. For a sample of identified target genes, we show that G-quadruplex stabilizing ligands can modulate transcription. These results confirm the existence of G-quadruplex structures and their persistence in human genomic DNA. Four independent libraries have been enriched in DNA G-quadruplex structures using a G-quadruplex-specific probe. One genomic input library was sequenced as control. Deep-sequencing of these libraries allowed the mapping of G-quadruplexes on the genome.

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Analysis of RA vs 4-oxo-RA gene expression regulation in Xenopus laevis

Project description:We analyzed anterior halves of NF stage 15 embryos that were treated with 10uM DMSO (control), or 1uM RA and 10uM 4-oxo-RA (experimental) for changes in gene expression induced by the two mophogens. RNA-sequencing revealed significant overlap in genes upregulated by both RA and 4-oxo-RA, and to a lesser extent, those downregulated by them. We report all Zic-1 targets described in accompanying manuscript to be regulated by both RA and 4-oxo-RA.

2022-03-09 | GSE180269 | GEO

Genome-wide mapping of 8-oxodG in G0-arrested MCF10A cells

Project description:8-oxo-7,8-dihydro-2’-deoxyguanine (8-oxodG) is one of the major DNA modifications and a potent pre-mutagenic lesion prone to mispair with deoxyadenine (dA). Here, by using OxyDIP-Seq, we report the genome-wide distribution of 8-oxodG in human MCF10A cells arrested in G0.

2020-04-02 | GSE137929 | GEO

G4 Quadruplex Binding Proteins

Project description:In this study we discover proteins that bind to G4 quadruplex DNA structure. We use modified c-myc quadruplex as a bait, and compare it to the control bait - T15 oligo. We use spectral counts and G-test to determine significant binders. T15 and G4 datafiles are uploaded

2016-07-07 | PXD003501 | Pride

RNA-seq of hESCs and hiPSCs treated with 5-OXO-ETE and Calcitriol, respectively

Project description:To know gene expression patterns affected by 5-OXO-ETE and Calcitriol

2024-03-13 | GSE213410 | GEO

G-Quadruplex structures are stable and detectable in human genomic DNA.

2013-05-08 | GSE45241 | GEO

AUF1 recognizes 8-oxo-guanosine embedded in DNA and stimulates APE1 endoribonuclease activity

Project description:The presence of rNMPs embedded in DNA represents a frequent genomic event able to destabilize the DNA backbone and to alter DNA replication and transcription. Usually, rNMPs are excised by RNase H2 and fully repaired by other enzymes belonging to the ribonucleotide excision repair pathway. The existence of modified rNMPs embedded in DNA, including 8-oxo-guanosine (8-oxo-G) and ribose monophosphate abasic site (rAP), have been recently highlighted by several works including ours. While eukaryotic RNase H2 is unable to process rAP and 8-oxo-G embedded in DNA, we demonstrated a role of APE1, a key enzyme of the base excision repair pathway, on these lesions. Notably, though APE1 activity on the repair of rAP sites results as efficient as the canonical dAP site, its incision repair activity on 8-oxo-G is very weak. Therefore, in order to guarantee an efficient repair activity of 8-oxo-G, additional processing mechanisms should be active in cells. In this work, by using an unbiased proteomic approach to isolate proteins able to recognize 8-oxo-G embedded in DNA, we discovered that AUF1 actively and specifically recognize 8-oxo-G and, interestingly, stimulates the APE1 enzymatic activity on this substrate. Although further structural analysis should be performed, it is reasonable that AUF1 facilitates the endoribonuclease activity of APE1 on 8-oxo-G by stabilizing the lesion substrate. Furthermore, by two orthogonal approaches including GST-pulldown and proximity ligation assay, we uncovered a novel protein-protein interaction between AUF1 and APE1. Remarkable, this interaction is modulated by H2O2-treatment, playing a putative biological role during cell response to oxidative stress.

2024-10-17 | PXD027252 | Pride

Microarray analysis of effect of N-(3-oxo-dodecanoyl) homoserine lactone on S. cerevesiae

Project description:We examined whether the budding yeast Saccharomyces cerevisiae can sense chemical signals from prokaryotes, specifically a variety of quorum sensing molecules from different bacteria species and from Candida albicans. We found that only N-acyl-3-oxo-dodecanoyl homoserine lactone (C12) from the opportunistic human pathogen Pseudomonas aeruginosa induces a stress response in yeast. Microarray experiments were performed in order to continue investigating the stress response. We treated S. cerevesiae (WT strain W303) with N-(3-oxo-dodecanoyl) homoserine lactone (C12), a quorum sensing molecule of Pseudomonas aeruginosa, which we found causes a stress response using a GFP reporter for HSP-12. Treatment conditions: 100 uM C12, 100 uM C12-lactam (control: synthetic analogue of C12 that is inactive in P. aeruginosa), DMSO (control: solvent), and 0.3 mM H2O2 (for comparison to oxidative stress).

2020-03-02 | E-MTAB-4802 | biostudies-arrayexpress

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