Organization of fast and slow chromatin revealed by single-nucleosome dynamics

Abstract

Significance Recent live cell imaging has revealed that chromatin is not a static, rigid structure but is dynamically fluctuating in cells. We study chromatin motion by using single-nucleosome tracking data in living human cells. The distribution of single-nucleosome movement shows a distinct 2-peak feature: fast and slow fractions. Nucleosome movement is investigated using statistical analyses and a polymer model to elucidate the mechanism of dynamic organization of fast and slow chromatin. Understanding chromatin organization and dynamics is important, since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bimodal nature of the mean square displacement distribution of nucleosomes allows for a natural categorization of the nucleosomes as fast and slow. Analyses of the nucleosome–nucleosome correlation functions within these categories along with the density of vibrational modes show that the nucleosomes form dynamically correlated fluid regions (i.e., dynamic domains of fast and slow nucleosomes). Perturbed nucleosome dynamics by global histone acetylation or cohesin inactivation indicate that nucleosome–nucleosome interactions along with tethering of chromatin chains organize nucleosomes into fast and slow dynamic domains. A simple polymer model is introduced, which shows the consistency of this dynamic domain picture. Statistical analyses of single-nucleosome movement provide rich information on how chromatin is dynamically organized in a fluid manner in living cells.