Structural and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome

DNA glycosylase engaging with damaged base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic genome obstructs DNA accessibility, and how DNA glycosylases locate the substrate site on nucleosomes is currently unclear. Here, we report cryo-electron microscopy structures of nucleosomes bearing a deoxyinosine (DI) in various geometric positions and structures of them in complex with DNA glycosylase AAG. The apo nucleosome structures show that the presence of a deoxyinosine alone perturbs nucleosomal DNA globally, leading to a general weakening of the interface between DNA and the histone core and a greater flexibility to the exit/entry of the nucleosomal DNA. AAG makes use of this nucleosomal plasticity and imposes further local deformation of the DNA through the formation of the stable enzyme-substrate complex. Mechanistically, local distortion augment, translation/rotational register shift and partial opening of the nucleosome are employed by AAG to cope with substrate sites in fully exposed, occluded and complete buried positions, respectively. Our findings reveal the molecular basis for the DI-induced modification on the structural dynamics of the nucleosome and elucidate how DNA glycosylase AAG accesses damaged sites on the nucleosome with different solution accessibility.