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PreprintCited by 10DNA and Nucleic Acid ChemistryDNA Repair MechanismsEpigenetics and DNA Methylation

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Click-chemistry-aided quantitation and sequencing of oxidized guanines and apurinic sites uncovers their transcription-linked strand bias in human cells

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Takhaveev, Vakil, Püllen, Nikolai J.L., Singh, Navnit K., Huber, Sabrina M., Schauer, Stefan, Gahlon, Hailey L., Poetsch, Anna R., Sturla, Shana J.·2024·Nature Chemical Biology
DOI 10.1101/2024.07.21.604463

Preprint — published as 10.1038/s41589-025-02052-6 · Paper page

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Abstract

DNA modifications drive aging, neurodegeneration, carcinogenesis, and chemotherapy drug action. To understand the functional genomic roles of DNA modifications, it is critical to accurately map their diverse chemical forms with single-nucleotide precision in complex genomes, but it remains challenging. Click-code-seq is a click-chemistry-aided single-nucleotide-resolution strategy for guanine-oxidation mapping, used in yeast DNA but having poor applicability to human genomes. Here, we upgraded click-code-seq to enable its first application for sequencing DNA oxidation and depurination in human genomes. For this, we developed a companion fluorescence assay, click-fluoro-quant, to rapidly quantify different common DNA modifications, and devised novel adapters to minimize false modification detection and assess modification frequency in cell populations. We uncovered that endogenous DNA oxidation in a human cell line has a highly similar pattern to cancer mutational signatures associated with reactive oxygen species. We established that the DNA-alkylating chemotherapy drug irofulven preferentially induces depurination in ApA dimers and promoter regions. Intriguingly, we revealed that oxidized guanines and apurinic sites, both irofulven-induced and endogenous, are depleted in gene transcribed strands, and the strand bias widens with increasing gene expression. This work substantially advances click-code-seq for deciphering the impacts of key modifications in human DNA on cellular physiology and toxicological responses.

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Metadata

Authors
Takhaveev, V., Püllen, N. J. L., Singh, N. K., Huber, S. M., Schauer, S., Gahlon, H. L., Poetsch, A. R., & Sturla, S. J.
Affiliations
  • ETH Zurich (CH)
  • University of Zurich (CH)
  • Nationales Centrum für Tumorerkrankungen Dresden (DE)
Corresponding author
Sturla, Shana J.
ORCID
Venue
Nature Chemical Biology
Publisher
openRxiv
Published
2024-07-23
Volume
22
Issue
5
Pages
716-727
ISSN
1552-4450 (ISSN-L)
DOI
10.1101/2024.07.21.604463
OpenAlex
W4415731709
Cited by
10
References
1
Citations by year
2026: 8 · 2025: 2
FWCI
3.01
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Chemical Biology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
Funders
  • National Science Foundation
  • Newcastle University
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (186332, 185020)
  • Eidgenössische Technische Hochschule Zürich
  • Functional Genomics Center Zurich
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
DNA oxidation, depurination, DNA modification, strand bias, oxidative stress, mutational signatures, irofulven, apurinic sites, oxidized guanine, promoter, gene expression, human genome
MeSH terms
DNA, Humans, Oxidation-Reduction, Genome, Human, Oxidative Stress, Click Chemistry

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