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Nick-seq for singlenucleotide resolution genomic maps of DNA modifications and damage:nickase mapping

ABSTRACT: Nick-seq for singlenucleotide resolution genomic maps of DNA modifications and damage:nickase mapping

PROVIDER: PRJNA574988 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10203779_1.fastq.gz	Fastqsanger.gz
	SRR10203779_2.fastq.gz	Fastqsanger.gz
	SRR10203780_1.fastq.gz	Fastqsanger.gz
	SRR10203780_2.fastq.gz	Fastqsanger.gz
	SRR10203781_1.fastq.gz	Fastqsanger.gz

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Nick-seq for singlenucleotide resolution genomic maps of DNA modifications and damage:nickase mapping

Project description:Endogenous and exogenous chemical modifications in DNA have profound influences on genome function. We have developed a novel technology, Nick-seq, for mapping variety of DNA chemical modifications across the genomes at single-nucleotide resolution, by which we achieved quantitative profiling of single-strand breaks, phosphorothioate modifications, and oxidative DNA damage sites. This method is applicable for mapping of any DNA metabolism events that are involved in or can be converted, enzymatically or chemically, to DNA strand breaks such as DNA modifications, damages, genome replication, and chromatin structures.

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Project description: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.

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