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Bio Protoc. 2022 Nov 5;12(21). doi: 10.21769/BioProtoc.4540.
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2
Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage.Nick-seq 用于单核苷酸分辨率的 DNA 修饰和损伤的基因组图谱。
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3
The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters.8-oxodG 的基因组景观揭示了在特定固有脆弱启动子处的富集。
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4
The genomics of oxidative DNA damage, repair, and resulting mutagenesis.氧化性DNA损伤、修复及由此产生的诱变的基因组学。
Comput Struct Biotechnol J. 2020 Jan 7;18:207-219. doi: 10.1016/j.csbj.2019.12.013. eCollection 2020.
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Genome-Wide Mapping of Oxidative DNA Damage via Engineering of 8-Oxoguanine DNA Glycosylase.通过 8-氧鸟嘌呤 DNA 糖基化酶的工程化实现全基因组范围的氧化 DNA 损伤绘图。
Biochemistry. 2020 Jan 14;59(1):85-89. doi: 10.1021/acs.biochem.9b00782. Epub 2019 Oct 25.
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Sequencing abasic sites in DNA at single-nucleotide resolution.单核苷酸分辨率下 DNA 中无碱基位点的测序。
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Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis.氧化 DNA 损伤与修复的基因组全景揭示了突变的区域选择性保护。
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Genome-wide mapping of 8-oxo-7,8-dihydro-2'-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells.全基因组范围内的 8-氧-7,8-二氢-2'-脱氧鸟苷的定位揭示了在哺乳动物细胞中转录的长基因的 DNA 复制起始点处氧化生成的损伤的积累。
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Sequencing the Mouse Genome for the Oxidatively Modified Base 8-Oxo-7,8-dihydroguanine by OG-Seq.通过 OG-Seq 对氧化修饰碱基 8-氧代-7,8-二氢鸟嘌呤进行小鼠全基因组测序。
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用于全基因组绘制含8-氧代-2'-脱氧鸟苷的受损DNA图谱的氧化DNA免疫沉淀测序法（OxiDIP-Seq）

OxiDIP-Seq for Genome-wide Mapping of Damaged DNA Containing 8-Oxo-2'-Deoxyguanosine.

作者信息

Gorini Francesca, Scala Giovanni, Ambrosio Susanna, Majello Barbara, Amente Stefano

机构信息

Department of Molecular Medicine and Medical Biotechnologies, University of Naples 'Federico II', Naples, Italy.

Department of Biology, University of Naples 'Federico II', Naples, Italy.

出版信息

Bio Protoc. 2022 Nov 5;12(21). doi: 10.21769/BioProtoc.4540.

DOI:10.21769/BioProtoc.4540
PMID:36505028
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9711933/
Abstract

8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) is considered to be a premutagenic DNA lesion generated by 2'-deoxyguanosine (dG) oxidation due to reactive oxygen species (ROS). In recent years, the 8-oxodG distribution in human, mouse, and yeast genomes has been underlined using various next-generation sequencing (NGS)-based strategies. The present study reports the OxiDIP-Seq protocol, which combines specific 8-oxodG immuno-precipitation of single-stranded DNA with NGS, and the pipeline analysis that allows the genome-wide 8-oxodG distribution in mammalian cells. The development of this OxiDIP-Seq method increases knowledge on the oxidative DNA damage/repair field, providing a high-resolution map of 8-oxodG in human cells.

摘要

8-氧代-7,8-二氢-2'-脱氧鸟苷（8-oxodG）被认为是由活性氧（ROS）导致的2'-脱氧鸟苷（dG）氧化产生的一种前诱变DNA损伤。近年来，利用各种基于新一代测序（NGS）的策略已经突显了人类、小鼠和酵母基因组中8-oxodG的分布情况。本研究报告了OxiDIP-Seq方案，该方案将单链DNA的特异性8-oxodG免疫沉淀与NGS相结合，以及允许在哺乳动物细胞中进行全基因组8-oxodG分布分析的流程。这种OxiDIP-Seq方法的开发增加了对氧化性DNA损伤/修复领域的认识，提供了人类细胞中8-oxodG的高分辨率图谱。