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

Abstract

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.

Transcriptional suppression of ribosomal DNA with phase separation

“…To address these questions, we performed single-molecule tracking of the largest subunit of Pol I, POLR1A (RPA194), and rDNA chromatin bound protein, upstream binding factor (UBF), in living human cells (25)(26)(27)(28)(29). Active Pol I molecules were relatively stable and formed small clusters that constrained rDNA chromatin.…”

Heterogeneous fluid-like movements of chromatin and their implications to transcription

“…While active RNA polymerase II globally constrains chromatin movements, it is interesting to note that with cohesin KD, the slow chromatin becomes even slower and fast one becomes faster (Fig. 2) (Ashwin et al 2019). This is likely to be due to the following two factors: One is enhancement of compartments A and B, which represent "open" transcriptionally active chromatin and "closed" inactive chromatin, respectively, as found in the Hi-C contact pattern upon cohesin depletion (Schwarzer et al 2017;Rao et al 2017).…”

“…However, due to the low sample number of observed trajectories, the P(M, t) obtained by a direct sampling of M i (t) from single-nucleosome tracking was rather noisy. This problem was overcome (Ashwin et al 2019) by employing the method of iteration of integral equation introduced by Richardson (Richardson 1972) and Lucy (Lucy 1974) (RL). The RL method has been extensively used for reducing noise in the image "deconvolution" processing and recently applied to the data sampling problem in biophysics (Wang et al 2012) and condensed-matter physics (Bhowmik et al 2016;Bhowmik et al 2018).…”

“…Shown in Fig. 1d are MSDs averaged separately for fast and slow nucleosomes, which are fitted to the power law t β ; the different β are suggestive of the different local environments the fast and slow nucleosomes experience (Ashwin et al 2019).…”

“…Difference between fast and slow nucleosomes was highlighted by analyzing responses of chromatin to perturbations on cells (Ashwin et al 2019). For example, knockdown (KD) of the cohesin complex was shown to increase motion of chromatin (Ashwin et al 2019;Nozaki et al 2017;Dion et al 2013). The cohesin complex can bundle chromatin chains with its ring structure and constrain the chromatin movement.…”