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DNA-histone cross-link locks the nucleosome structure and disrupts its recognition and processing
Xiajing Shan1, Gaoyuan Ji2, Jiahui Li1
1State Key Laboratory of Elemento-Organic Chemistry, Frontiers Science Center for New Organic Matter, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
Protein & Cell
|November 8, 2025
Summary
DNA-histone cross-links (DHCs) lock nucleosome structure, enhancing stability and blocking DNA sliding and transcription. These findings reveal DHCs as toxic DNA damage that impedes cellular machinery.
Area of Science:
- Molecular Biology
- Epigenetics
- DNA Damage and Repair
Background:
- DNA-histone cross-links (DHCs) are DNA damage byproducts formed during DNA repair.
- The functional impact of DHCs within nucleosomes is not well understood.
Purpose of the Study:
- To investigate the structural and functional consequences of site-specific DHCs in nucleosomes.
- To evaluate the effect of DHCs on nucleosome stability, DNA accessibility, and transcription.
Main Methods:
- Preparation of structurally homogeneous nucleosomes with site-specific DHCs using click chemistry.
- Assessment of nucleosome thermal stability and DNA sliding.
- Analysis of RNA polymerase transcription elongation through DHC-containing nucleosomes.
- Evaluation of histone resistance to proteolytic digestion.
Main Results:
- DHCs significantly increase nucleosome thermal stability.
- DHCs completely inhibit both passive and active DNA sliding within nucleosomes.
- DHCs obstruct RNA polymerase transcription, causing premature termination.
- DHCs enhance histone resistance to proteolytic degradation.
Conclusions:
- A single DHC can rigidly lock nucleosome structure, impacting cellular machinery.
- DHCs represent a highly toxic and persistent form of DNA damage.
- This study provides in vitro insights into DHCs' effects on nucleosome architecture, prompting in vivo investigation.
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