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Single-nucleotide resolution mapping of DNA abasic sites by snAP-seq

ABSTRACT: Single-nucleotide resolution mapping of DNA abasic sites by snAP-seq

PROVIDER: PRJEB28471 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2777650_1.fastq.gz	Fastqsanger.gz
	ERR2777650_2.fastq.gz	Fastqsanger.gz
	ERR2777660_1.fastq.gz	Fastqsanger.gz
	ERR2777660_2.fastq.gz	Fastqsanger.gz
	ERR2777670_1.fastq.gz	Fastqsanger.gz

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Single-nucleotide resolution mapping of DNA abasic sites by snAP-seq

Project description:Abasic (AP) sites are one of the most common forms of DNA damage which can lead to polymerase stalling, strand breaks and mutations. We developed snA-seq, a mapping method that reveals the location of abasic sites at base-resolution. Using synthetic DNA, we show that high selectivity for AP DNA is achieved. We use this method to explore the distribution of thymine modifications in the Leishmania major genome, by converting these into abasic sites using a glycosylase enzyme. We also apply snAP-seq to the human genome to study the distribution of endogenous AP sites, in both APE1 knockdown and control cells.

2019-06-12 | E-MTAB-7152 | biostudies-arrayexpress

Dual Chemical Labeling Enables Nucleotide-Resolution Mapping of DNA Abasic Sites and Common Alkylation Damage in Human Mitochondrial DNA

Project description:Understanding the genomic locations of DNA modifications is pivotal for deciphering their roles in gene regulation, mutagenesis, and pathology. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the specificity of labeling and enrichment of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mitochondrial DNA (mtDNA) from cultured human cells under different biological conditions. Also, we demonstrated the broader applicability of the method in sequencing additional DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.

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Dual Chemical Labeling Enables Nucleotide-Resolution Mapping of DNA Abasic Sites and Common Alkylation Damage in Human Mitochondrial DNA

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Sequencing abasic sites in DNA at single-nucleotide resolution.

Project description:In DNA, the loss of a nucleobase by hydrolysis generates an abasic site. Formed as a result of DNA damage, as well as a key intermediate during the base excision repair pathway, abasic sites are frequent DNA lesions that can lead to mutations and strand breaks. Here we present snAP-seq, a chemical approach that selectively exploits the reactive aldehyde moiety at abasic sites to reveal their location within DNA at single-nucleotide resolution. Importantly, the approach resolves abasic sites from other aldehyde functionalities known to exist in genomic DNA. snAP-seq was validated on synthetic DNA and then applied to two separate genomes. We studied the distribution of thymine modifications in the Leishmania major genome by enzymatically converting these modifications into abasic sites followed by abasic site mapping. We also applied snAP-seq directly to HeLa DNA to provide a map of endogenous abasic sites in the human genome.

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