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Title: Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage.

Authors: Cao, Bo; Wu, Xiaolin; Zhou, Jieliang; Wu, Hang; Liu, Lili; Zhang, Qinghua; DeMott, Michael S; Gu, Chen; Wang, Lianrong; You, Delin; Dedon, Peter C

Published In Nucleic Acids Res, (2020 07 09)

Abstract: 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.

PubMed ID: 32484547 Exiting the NIEHS site

MeSH Terms: Chromosome Mapping; DNA Damage/drug effects*; DNA Damage/genetics; DNA/chemistry; DNA/drug effects; Epigenesis, Genetic/genetics*; Escherichia coli/genetics; Genome, Bacterial/drug effects; Genome, Bacterial/genetics*; Genomic Instability/drug effects*; High-Throughput Nucleotide Sequencing; Hydrogen Peroxide/toxicity; Nucleotides/chemistry; Salmonella enterica/genetics; Sequence Analysis, DNA

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