Histone dynamics mediate DNA unwrapping and sliding in nucleosomes

Nucleosomes tightly wrap similar to 147 DNA base pairs around an octamer of histone proteins, but how nucleosome structural dynamics affect genome functioning is not completely clear. Here authors employ all-atom molecular dynamics simulations of nucleosome core particles and observe that octamer dynamics and plasticity enable DNA unwrapping and sliding. Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly wrap similar to 147 DNA base pairs around an octamer of histone proteins. How nucleosome structural dynamics affect genome functioning is not completely clear. Here we report all-atom molecular dynamics simulations of nucleosome core particles at a timescale of 15 microseconds. At this timescale, functional modes of nucleosome dynamics such as spontaneous nucleosomal DNA breathing, unwrapping, twisting, and sliding were observed. We identified atomistic mechanisms of these processes by analyzing the accompanying structural rearrangements of the histone octamer and histone-DNA contacts. Octamer dynamics and plasticity were found to enable DNA unwrapping and sliding. Through multi-scale modeling, we showed that nucleosomal DNA dynamics contribute to significant conformational variability of the chromatin fiber at the supranucleosomal level. Our study further supports mechanistic coupling between fine details of histone dynamics and chromatin functioning, provides a framework for understanding the effects of various chromatin modifications.

Automated summary

Nucleosomes tightly wrap around 147 DNA base pairs with an octamer of histone proteins, and their dynamics enable DNA unwrapping and sliding. Molecular dynamics simulations revealed functional modes of nucleosome dynamics such as DNA breathing, unwrapping, twisting, and sliding. This study highlights the importance of nucleosomal DNA dynamics in chromatin conformational variability and the effects of chromatin modifications.