ИСТИНА

Nucleosomes are elementary building blocks of chromatin, which play crucial role in genome organization, DNA damage and repair. The core and linker histones are responsible for chromatin compaction and provide a means for genome dynamic regulation through specific histone variants. Translational and rotational positioning of DNA on nucleosomes as well as nucleosome dynamics modulate DNA accessibility and conformation, which in turn affect DNA damage and recognition by the DNA damage repair systems. Small variations in nucleosome positioning on DNA result in considerable changes in DNA rotation with respect to the histone octamer, which might profoundly affect interactions of nucleosomes with other proteins. Here we developed a method for detailed characterization of nucleosome conformation and DNA site accessibility in solution based on experimental DNA scission by hydroxyl-radicals combined with molecular modeling. We interpreted experimental data through careful quantification and comparison to the DNA strand scission profiles predicted from atomistic structures of nucleosomes enhanced by molecular dynamics simulations. We discuss the effects of nucleosome dynamics on the shape of experimental profiles and propose a computational method for precise determination of DNA positioning in nucleosomes with the single base pair resolution. We computationally analyze different histone variant nucleosomes and, as a proof of concept determine the DNA positioning and build a model for CEN3 centromeric nucleosome of yeast, for which structure is not available. This research was supported by the Intramural Research Programs of the National Library of Medicine and the National Cancer Institute and Russian Science Foundation (grant No. 14-24-00031).