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Nucleotide resolution genome-wide mapping of 8-oxoG damage

ABSTRACT: Single nucleotide resolution sequencing of DNA damage is required to decipher the complex causal link between the identity and location of DNA adduct and mutation patterns in the genome. We coupled the specificity of the repair enzyme with the efficiency of a one-pot click-DNA ligation reaction to insert a readable oligonucleotide code sequence. The biocompatible code enabled high-throughput, base resolution sequencing of the 8-oxoguanine site and thus have named the method click-code-seq. By applying click-code-seq to a eukaryotic (yeast) genome, we uncovered thousands of 8-oxoguanine sites with features and patterns suggesting a potential relationship to chromatin formation and transcription.

ORGANISM(S): Saccharomyces cerevisiae BY4741

PROVIDER: GSE112212 | GEO | 2018/06/28

REPOSITORIES: GEO

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Click-chemistry-aided quantitation and sequencing of oxidized guanines and apurinic sites uncovers their transcription-linked strand bias in human cells

Project description:DNA alterations are drivers of aging, neurodegeneration, carcinogenesis, and chemotherapy drug action. To understand the functional genomic roles of DNA modifications, it is critical to accurately map their diverse chemical forms with single-nucleotide precision in complex genomes, which however remains challenging. Click-code-seq is the click-chemistry-aided single-nucleotide-resolution method introduced to map oxidation in yeast DNA. Here, we upgraded click-code-seq to enable its first application for sequencing DNA oxidation and depurination in the human genome. For this, we developed a companion fluorescence tagging assay, click-fluoro-quant, to rapidly quantify common modifications. Moreover, we devised novel adapters to minimize false modification detection and assess modification frequency in cell populations. We uncovered that endogenous DNA oxidation in a human cell line has a highly similar pattern to the cancer mutational signatures associated with the effects of reactive oxygen species. We established that the chemotherapy drug irofulven preferentially depurinates ApA dimers and promoter regions. Intriguingly, we revealed that oxidized guanines and apurinic sites, both irofulven-induced and endogenous, are depleted in the transcribed strand of genes, and the strand bias widens with increasing gene expressions. This work advances click-code-seq for deciphering the impacts of key DNA modifications in the human genome on cellular physiology and toxicological responses.

2024-07-21 | GSE272366 | 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

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

2011-01-27 | GSE26813 | GEO

Real-time quantitative PCR analysis of mouse lungs

2014-08-26 | GSE60711 | GEO

Real-time quantitative PCR analysis of mouse lungs

Project description:Balb/cJ mouse received control RNAi or RNAi to 8-oxoguanine DNA glycosylase (Ogg1) intranasally prior to the exposure for 1 h to a) glucose oxidase (1 mU) to induce OGG1-BER or b) OGG1-BER product 8-oxoguanine (1 M-NM-<M). We used SABiosciences Mouse Inflammatory Cytokines & Receptors PCR Array (PAMM-011A) to quantitate inflammatory gene expression dependent on OGG1 and its product 8-oxoguanine. After intranasal challenge with glucose oxidase or 8-oxoguanine, mice were sacrificed and lungs were collected and processed to obtain RNA. Total pooled (n=5) RNA (1 M-NM-<g) was reverse transcribed into cDNA using SuperscriptM-BM-. III First Strand Synthesis System (Invitrogen), mixed with equal amounts of 2X SYBR Green Supermix (Qiagen) and 20 M-NM-<l of reaction mixture was added to each well of the PAM-011A array. The reaction was evaluated using an ABI PRISMM-BM-. 7000 Sequence Detection System using recommended settings by SABiosciences.

2014-08-26 | E-GEOD-60711 | biostudies-arrayexpress

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

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Genome-wide single nucleotide resolution of oxaliplatin-DNA adduct repair in drug sensitive and resistant colorectal cancer cell lines

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