DNA damage detection in nucleosomes involves DNA register shifting

Abstract

Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and repair. In humans, the UV-DDB complex detects ultraviolet light induced pyrimidine dimers throughout the genome, yet it remains unknown how these lesions are recognised in chromatin, where nucleosomes restrict DNA access. Here we report cryo-electron microscopy structures for UV-DDB bound to nucleosomes bearing a 6-4 pyrimidine-pyrimidone dimer, and a DNA damage mimic at a variety of positions. We find that UV-DDB binds UV damaged nucleosomes at lesions located in the solvent-facing minor groove without affecting the overall nucleosome architecture. For buried lesions facing the histone core, UV-DDB changes the predominant translational register of the nucleosome, and selectively binds the lesion in an accessible, exposed, position. These findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes. We identify s lide- a ssisted s ite- e xposure (SAsSE) as a mechanism for high-affinity DNA-binding proteins to access otherwise occluded sites in nucleosomal DNA.

Deciphering UV‐induced DNA Damage Responses to Prevent and Treat Skin Cancer

“…An important question related to slow DNA repair in heterochromatin is how UV‐DDB detects occluded DNA lesions in nucleosomes to initiate GGR. A recent study determined the mechanism by which UV‐induced DNA lesions are recognized in chromatin, in which nucleosomes restrict access to DNA (115) (Fig. 5B).…”

Structural Basis of Nucleosome Recognition and Modulation

“…[ 131 ] Cryo‐EM structures of UV‐DDB bound to nucleosome bearing cyclobutane‐pyrimidine dimers, 6‐4 pyrimidine‐pyrimidone photoproduct (6‐4PP) (forming an accessible lesion), or two tandem tetrahydrofuran (THF2) (forming a buried lesion) at different locations on the nucleosome, reveals that UV‐DDB uses distinct mechanisms to recognize the lesions present at distinct locations. [ 132 ] UV‐DDB reads 6‐4PP in the solvent‐exposed minor groove. DDB2 binds to 6‐4PP through its β‐hairpin that extrudes 6‐4PP and locally distorts the DNA.…”

“…UV‐DDB uses a mechanism called slide‐assisted site exposure, wherein the intrinsic DNA dynamics transiently expose the occluded lesions that get read by DDB2. [ 132 ] The mechanism of nucleosomal DNA access by UV‐DDB is known; however, it is not clear whether the DNA‐damage associated epigenetic modifications also assist the UV‐DDB.…”

Imaging the response to DNA damage in heterochromatin domains reveals core principles of heterochromatin maintenance

“…Noteworthy, H1 is also displaced from chromatin at sites of DNA breaks but the underlying mechanisms are still to be characterized 24,27 . Recent structural data indicate that the DDB2 complex can expose UV lesions occluded in nucleosomal DNA by promoting DNA shifting 75 . Such local activity at the nucleosome level is unlikely to sustain larger scale chromatin decompaction but it could stimulate displacement of H1, which bridges DNA at the entry and exit sites of the nucleosome core particle.…”