ArticleNucleic acids research2020
Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 65 citations in OpenAlex.
- DEPACE-seq enables high-fidelity, single-nucleotide-resolution mapping of abasic sites and characterization of dynamic and long-lived AP landscapes in mammalian genomes.Nucleic acids research · 2026Article
- Phosphorothioate DNA modification by BREX type 4 systems in the human gut microbiome.Nature communications · 2026Article
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- 3'-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors.Genome research · 2025Article
- Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.Nature communications · 2025Article
- Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability.Nature methods · 2025Article
- Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.Microbiome · 2025Article
- RRM1 promotes homologous recombination and radio/chemo-sensitivity via enhancing USP11 and E2F1-mediated RAD51AP1 transcription.Cell death discovery · 2024Article
- Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications.bioRxiv : the preprint server for biology · 2024Article
- PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities.bioRxiv : the preprint server for biology · 2024Article
- Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.bioRxiv : the preprint server for biology · 2024Article
- Long-run real-time PCR analysis of repetitive nuclear elements as a novel tool for DNA damage quantification in single cells: an approach validated on mouse oocytes and fibroblasts.Journal of applied genetics · 2024Article
- DNA Damage Atlas: an atlas of DNA damage and repair.Nucleic acids research · 2024Article
- Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA.Nucleic acids research · 2023Article
- Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0.Chemical communications (Cambridge, England) · 2023Article
- Locating, tracing and sequencing multiple expanded genetic letters in complex DNA context via a bridge-base approach.Nucleic acids research · 2023Article
- The Fission Yeast Mating-Type Switching Motto: "One-for-Two" and "Two-for-One".Microbiology and molecular biology reviews : MMBR · 2023Review
- OxiDIP-Seq for Genome-wide Mapping of Damaged DNA Containing 8-Oxo-2'-Deoxyguanosine.Bio-protocol · 2022Article
- High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution.PLoS genetics · 2022Article
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Corrections and comments
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Authors and funding
11 authors at 7 institutions in 3 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.