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Updated: Mar 7, 2026
Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair
Published on: May 24, 2017
The Human Ligase IIIα-XRCC1 Protein Complex Performs DNA Nick Repair after Transient Unwrapping of Nucleosomal DNA
Wendy J Cannan1, Ishtiaque Rashid2, Alan E Tomkinson2
1From the Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405 and.
Abstract:
Reactive oxygen species generate potentially cytotoxic and mutagenic lesions in DNA, both between and within the nucleosomes that package DNA in chromatin. The vast majority of these lesions are subject to base excision repair (BER). Enzymes that catalyze the first three steps in BER can act at many sites in nucleosomes without the aid of chromatin-remodeling agents and without irreversibly disrupting the host nucleosome. Here we show that the same is true for a protein complex comprising DNA ligase IIIα and the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1), which completes the fourth and final step in (short-patch) BER. Using in vitro assembled nucleosomes containing discretely positioned DNA nicks, our evidence indicates that the ligase IIIα-XRCC1 complex binds to DNA nicks in nucleosomes only when they are exposed by periodic, spontaneous partial unwrapping of DNA from the histone octamer; that the scaffolding protein XRCC1 enhances the ligation; that the ligation occurs within a complex that ligase IIIα-XRCC1 forms with the host nucleosome; and that the ligase IIIα-XRCC1-nucleosome complex decays when ligation is complete, allowing the host nucleosome to return to its native configuration. Taken together, our results illustrate ways in which dynamic properties intrinsic to nucleosomes may contribute to the discovery and efficient repair of base damage in chromatin.
Insights
The DNA ligase IIIα-XRCC1 complex repairs DNA nicks within nucleosomes by binding to transiently exposed DNA. This process facilitates efficient chromatin repair without disrupting the nucleosome structure.
Area of Science:
- Molecular Biology
- Chromatin Biology
- DNA Repair
Background:
- Reactive oxygen species cause DNA damage, forming lesions within chromatin nucleosomes.
- Base excision repair (BER) is the primary pathway for repairing most DNA lesions.
- Early BER enzymes access and repair lesions within nucleosomes without significant chromatin disruption.
Purpose of the Study:
- To investigate the ability of the DNA ligase IIIα-XRCC1 complex to complete the final step of short-patch BER within nucleosomes.
- To elucidate the mechanism by which this complex interacts with and repairs DNA nicks in chromatin.
Main Methods:
- Utilized *in vitro* assembled nucleosomes with precisely positioned DNA nicks.
- Characterized the interaction of the DNA ligase IIIα-XRCC1 complex with nucleosomal DNA.
- Assessed the enhancement of ligation by XRCC1 and the formation of a ligase-nucleosome complex.
Main Results:
- The ligase IIIα-XRCC1 complex binds to DNA nicks only when transiently exposed by spontaneous nucleosome DNA unwrapping.
- The scaffolding protein XRCC1 enhances the ligation efficiency.
- Ligation occurs within a stable complex formed between ligase IIIα-XRCC1 and the nucleosome.
- This complex dissociates upon completion of ligation, restoring the native nucleosome.
Conclusions:
- Dynamic nucleosome properties, specifically DNA unwrapping, facilitate access for the DNA ligase IIIα-XRCC1 complex.
- The ligase IIIα-XRCC1 complex efficiently repairs DNA nicks within chromatin through a nucleosome-associated mechanism.
- Intrinsic nucleosome dynamics play a crucial role in the discovery and repair of DNA base damage in chromatin.
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