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Related Experiment Video

Updated: May 23, 2025

Quantification of three DNA Lesions by Mass Spectrometry and Assessment of Their Levels in Tissues of Mice Exposed to Ambient Fine Particulate Matter

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Published on: May 29, 2019

Genome-wide mapping and quantification of DNA damage induced by catechol estrogens using Click-Probe-Seq and LC-MS².

Quynh-Trang Do¹, Shun-Fen Tzeng², Chih-Yen Wang³

¹Department of Chemistry, National Cheng Kung University, Tainan, Taiwan.

Communications Biology

|March 12, 2025

Summary

Genotoxic estrogen metabolites cause DNA damage, primarily targeting guanine in accessible chromatin. This novel finding reveals new cancer research mechanisms beyond estrogen receptor signaling.

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Area of Science:

Molecular Biology
Genetics
Cancer Research

Background:

Genotoxic estrogen metabolites can cause DNA damage, but their specific targets and roles in cancer are not fully understood.
Estrogen receptor (ER) signaling is linked to cancer, but the direct DNA damaging effects of its metabolites present a distinct carcinogenic pathway.

Purpose of the Study:

To develop and apply a novel method for genome-wide identification of DNA damage induced by the genotoxic estrogen metabolite 4-hydroxy-17β-estradiol (4OHE2).
To characterize the specific DNA adducts and target genes affected by 4OHE2 in cellular chromatin.
To elucidate the impact of 4OHE2-induced DNA damage on gene transcription, DNA repair, and cell viability.

Main Methods:

Development of Click-Probe-Seq/LC-MS² (click probe enrichment coupled with liquid chromatography-tandem mass spectrometry) for genome-wide DNA damage mapping.
Application of Click-Probe-Seq/LC-MS² to identify 4OHE2-induced DNA lesions in MCF-7 cell chromatin.
Correlation analysis of damage sites with genomic features like GC-rich regions and DNase hypersensitive sites.

Main Results:

Guanine nucleobases within GC-rich, transcription-relevant domains were identified as primary targets of 4OHE2.
DNA damage abundance correlated positively with DNase hypersensitive sites, indicating preferential attack on accessible chromatin.
Accumulated 4OHE2-induced damage led to suppressed gene transcription, impaired DNA repair, and reduced cell viability, distinct from ER-driven proliferation.

Conclusions:

The Click-Probe-Seq/LC-MS² method provides the first chromatin damage map for an endogenous genotoxic metabolite.
4OHE2 induces DNA damage in accessible chromatin regions, impacting gene expression and cell health independently of canonical ER signaling.
This research opens new avenues in cancer research by highlighting the genotoxic potential of estrogen metabolites and offering a versatile method for studying other genotoxic agents.