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Structural basis of cyclobutane pyrimidine dimer recognition by UV-DDB in the nucleosome

Syota Matsumoto,Y. Takizawa,Mitsuo Ogasawara,Kana M. Hashimoto,Lumi Negishi,Wenjie Xu,Haruna Tachibana,Junpei Yamamoto,Shigenori Iwai,Kaoru Sugasawa,Hitoshi Kurumizaka

Published 2025 in Nature Communications

ABSTRACT

In mammalian global genomic nucleotide excision repair, UV-DDB plays a central role in recognizing DNA lesions, such as 6-4 photoproducts and cyclobutane pyrimidine dimers, within chromatin. In the present study, we perform cryo-electron microscopy analyses coupled with chromatin-immunoprecipitation to reveal that the cellular UV-DDB binds to UV-damaged DNA lesions in a chromatin unit, the nucleosome, at a position approximately 20 base-pairs from the nucleosomal dyad in human cells. An alternative analysis of the in vitro reconstituted UV-DDB-cyclobutane pyrimidine dimer nucleosome structure demonstrates that the DDB2 subunit of UV-DDB specifically recognizes the cyclobutane pyrimidine dimer lesion at this position on the nucleosome. We also determine the structures of UV-DDB bound to DNA lesions at other positions in purified cellular human nucleosomes. These cellular and reconstituted UV-DDB-nucleosome complex structures provide important evidence for understanding the mechanism by which UV lesions in chromatin are recognized and repaired in mammalian cells. UV-DDB is a protein that plays a key role in recognizing DNA lesions. Here, the authors determine the cryo-EM structure of UV-DDB bound to UV-damaged chromatin in human cells, identifying a nucleosome binding site.

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