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Journal Article
DNA damage detection in nucleosomes involves DNA register shifting
2019
Overview
Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA. Here we report cryo-electron microscopy structures of UV-DDB bound to nucleosomes bearing a 6–4 pyrimidine–pyrimidone dimer or a DNA-damage mimic in various 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. In the case of buried lesions that face the histone core, UV-DDB changes the predominant translational register of the nucleosome and selectively binds the lesion in an accessible, exposed position. Our findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes, and identify slide-assisted site exposure as a mechanism by which high-affinity DNA-binding proteins can access otherwise occluded sites in nucleosomal DNA.
Cryo-electron microscopy structures reveal that the DNA-repair factor UV-DDB exposes inaccessible nucleosome lesions for binding by inducing a translational shift in the nucleosome position.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ 13/106
/ 13/109
/ 82/29
/ 82/80
/ 82/83
/ 96/35
/ Dimers
/ DNA
/ DNA-Binding Proteins - chemistry
/ DNA-Binding Proteins - genetics
/ DNA-Binding Proteins - metabolism
/ DNA-Binding Proteins - ultrastructure
/ Genomes
/ Grooves
/ Humanities and Social Sciences
/ Humans
/ Lesions
/ Nucleosomes - radiation effects
/ Nucleosomes - ultrastructure
/ Proteins
/ Pyrimidine Dimers - analysis
/ Pyrimidine Dimers - chemistry
/ Pyrimidine Dimers - genetics
/ Science
/ Software
