Visualizing cellular repair of UV-damaged genomic DNA enables insights into xeroderma pigmentosum treatments

A research group led by Assistant Professor Syota Matsumoto and Professor Hitoshi Kurumizaka from the Institute for Quantitative Biosciences at the University of Tokyo, in collaboration with Professor Kaoru Sugasawa from the Biosignal Research Center at Kobe University and Professor Emeritus Shigenori Iwai and Associate Professor Junpei Yamamoto from the Graduate School of Engineering Science at the University of Osaka, announced that they have successfully visualized the three-dimensional structure of the UV-DDB protein complex at the moment of repairing UV damage on genomic DNA inside cells. It was revealed that UV-DDB directly binds to damage on nucleosomes. The UV-DDB protein is involved in the repair of everyday UV damage and is also a causative factor of xeroderma pigmentosum (XP), a designated intractable disease. These findings are expected to lead to clarification of the mechanism of XP and development of therapeutic drugs. The results were published in Nature Communications on November 11.

In vitro experiments using fragmented DNA have confirmed that the UV-DDB protein has activity that specifically binds to UV damage occurring in DNA. On the other hand, it has been suggested that behavior may differ inside cells because genomic DNA wraps around histones to form nucleosomes, which are linked together in a chromatin structure. The UV-DDB protein is a complex of two subunits, DDB1 and DDB2, and DDB2 is known to be the gene product responsible for XP group E.

XP is a designated intractable disease characterized by sun sensitivity and a high frequency of skin cancer, which develops due to a congenital defect in nucleotide excision repair, one of the DNA repair mechanisms. Currently, there is no treatment, and the mechanism of onset is not understood.

In this study, to clarify the DNA repair mechanism inside cells, the research group induced damage by UV irradiation in human cell lines. After various separation and isolation procedures, the research group applied their original technique "ChIP-CryoEM," which combines chromatin immunoprecipitation and cryo-electron microscopy.

As a result, they succeeded in capturing the UV-DDB complex bound to UV damage on nucleosomes in their intracellular state. The three-dimensional structure was revealed, and it was clarified that the UV-DDB protein recognizes DNA damage on the nucleosome that has a complex structure and directly binds to it with almost no steric hindrance from histones.

Furthermore, in vitro, nucleosomes were reconstituted by incorporating DNA with cyclobutane pyrimidine dimer (CPD), a type of representative chemically synthesized UV damage. It was confirmed the UV-DDB protein directly binds to it.

Additionally, observations at high resolution revealed the detailed binding structure to CPD damage. Specifically, it was found that two amino acid residues of the UV-DDB protein specifically interact with CPD damage, directly recognizing and binding to CPD damage on nucleosomes.

CPD damage is the most common damage caused by UV light and may be involved in skin cancer, even amongst healthy individuals.

Matsumoto commented: "By understanding the binding to nucleosomes through this research, the first step of the DNA damage repair mechanism occurring inside cells has been clarified. We believe this is significant progress toward understanding xeroderma pigmentosum. We hope this will help establish treatments."

Kurumizaka commented: "This achievement is really just the gateway, and next we will proceed to the steps where the damage is repaired. We want to reveal the full picture of the DNA damage repair mechanism by directly visualizing the structure of these repair steps, rather than indirectly."

Journal Information
Publication: Nature Communications
Title: Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome
DOI: 10.1038/s41467-025-65486-5