DNA damage and epigenetic marks are well established to have profound influences on genome stability and cell phenotype, yet there are few technologies to obtain high-resolution genomic maps of the many types of chemical modifications of DNA. Here we present Nick-seq for quantitative, sensitive, and accurate mapping of DNA modifications at single-nucleotide resolution across genomes. Pre-existing breaks are first blocked and DNA modifications are then converted enzymatically or chemically to strand-breaks for both 3′-extension by nick-translation to produce nuclease-resistant oligonucleotides and 3′-terminal transferase tailing. Following library preparation and next generation sequencing, the complementary datasets are mined with a custom workflow to increase sensitivity, specificity and accuracy of the map. The utility of Nick-seq is demonstrated with genomic maps of site-specific endonuclease strand-breaks in purified DNA from Eschericia coli, phosphorothioate epigenetics in Salmonella enterica Cerro 87, and oxidation-induced abasic sites in DNA from E. coli treated with a sublethal dose of hydrogen peroxide. Nick-seq applicability is demonstrated with strategies for >25 types of DNA modification and damage.

中文翻译：

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Nick-seq用于DNA修饰和破坏的单核苷酸分辨率基因组图谱。

DNA损伤和表观遗传标记已经建立，可以对基因组稳定性和细胞表型产生深远影响，但很少有技术能够获得DNA多种化学修饰类型的高分辨率基因组图。在这里，我们介绍了Nick-seq，用于在整个基因组中以单核苷酸分辨率定量，敏感和准确地绘制DNA修饰。首先将预先存在的断裂阻断，然后通过缺口翻译将DNA修饰酶或化学转化为3'延伸的链断裂，以产生抗核酸酶的寡核苷酸和3'末端转移酶拖尾。在准备文库和进行下一代测序后，将使用自定义工作流程挖掘互补数据集，以提高图谱的敏感性，特异性和准确性。大肠埃希菌，小肠沙门氏菌Cerro 87中的硫代磷酸酯表观遗传学以及用亚致死剂量的过氧化氢处理的大肠杆菌DNA中的氧化诱导的无碱基位点。Nick-seq的适用性已通过> 25种类型的DNA修饰和破坏策略得到证明。