Structural basis of pyrimidine-pyrimidone (6–4) photoproduct recognition by UV-DDB in the nucleosome

UV-DDB, an initiation factor for the nucleotide excision repair pathway, recognizes 6–4PP lesions through a base flipping mechanism. As genomic DNA is almost entirely accommodated within nucleosomes, the flipping of the 6–4PP bases is supposed to be extremely difficult if the lesion occurs in a nucleosome, especially on the strand directly contacting the histone surface. Here we report that UV-DDB binds efficiently to nucleosomal 6–4PPs that are rotationally positioned on the solvent accessible or occluded surface. We determined the crystal structures of nucleosomes containing 6–4PPs in these rotational positions, and found that the 6–4PP DNA regions were flexibly disordered, especially in the strand exposed to the solvent. This characteristic of 6–4PP may facilitate UV-DDB binding to the damaged nucleosome. We present the first atomic-resolution pictures of the detrimental DNA cross-links of neighboring pyrimidine bases within the nucleosome, and provide the mechanistic framework for lesion recognition by UV-DDB in chromatin.