Accepted_test

Nucleosomes are elementary building blocks of chromatin that wrap DNA around an octamer of histone proteins. They compact the genomic DNA in eukaryotes and also intricately participate in all genomic processes including gene expression regulation, epigenetic memory, and development. Understanding nucleosome structure and dynamics, as well as its functional implication, requires a complex integrative approach. To this end, we have employed a combination of experimental, molecular modeling, and bioinformatics approaches, including all-atom molecular dynamics simulations, DNA footprinting techniques, small angle X-ray scattering, solution NMR, fluorescence-based assays, en masse analysis of the available X-ray and cryo-EM structures. We have shown that all-atom molecular dynamics simulations at a multi-microsecond timescale may reveal new functional dynamics modes within nucleosomes. These are affected by different histone variants and mutations and through interactions with nucleosome-binding peptides and proteins. A comprehensive analysis of all available PDB structures of nucleosomes conducted by us suggests that certain modes of nucleosome dynamics can be characterized by such high-throughput comparison. Still, such processes as DNA unwrapping and histone tail dynamics remain poorly characterized. Our efforts in analyzing nucleosomes with small-angle X-ray scattering suggest that these methods can be used to understand the effects of DNA sequence on nucleosome compactness. The characterization of the flexible histone tails is possible through the application of solution NMR techniques. The measurement of the NMR relaxation parameters may be used to assess the histone tail dynamics and guide the choice of the most appropriate force fields for MD simulations.