[Paper Review] Organization of fast and slow chromatin revealed by single-nucleosome dynamics

Sarah Ashwin, Tadasu Nozaki+2 more|arXiv (Cornell University)|Aug 16, 2019

Genomics and Chromatin Dynamics65 references108 citations

TL;DR

This study reveals that chromatin in living human cells organizes into dynamically correlated fast and slow nucleosome domains through single-nucleosome tracking and statistical analysis. By analyzing mean squared displacement (MSD) distributions, the authors identify bimodal dynamics, and a minimal polymer model confirms that nucleosome-nucleosome interactions and chromatin tethering jointly drive the formation of fluid-like dynamic domains, offering a mechanistic basis for chromatin organization in living cells.

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. Bi-modal nature of the mean squared 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.

Motivation & Objective

• To understand the dynamic organization of chromatin in living human cells, particularly how chromatin domains fluctuate and influence gene regulation.
• To resolve the paradox of structurally fluctuating chromatin domains despite functional importance by analyzing real-time nucleosome dynamics.
• To identify whether heterogeneous nucleosome movement reflects distinct dynamic states (fast/slow) and their underlying organizational principles.
• To test whether nucleosome-nucleosome interactions and chromatin tethering are key drivers of dynamic domain formation using perturbation experiments and modeling.
• To develop a minimal polymer model that reproduces observed single-nucleosome dynamics and validates the dynamic domain hypothesis.

Proposed method

• Single-nucleosome trajectories were extracted from live-cell imaging data (HeLa cells, ~200–250 nm nuclear thickness) using CRISPR/dCas9-based labeling.
• Mean squared displacement (MSD) distributions, P(M,t), were reconstructed from noisy experimental data using the Richardson-Lucy (RL) deconvolution algorithm to recover smooth distributions.
• The self-part of the van Hove correlation function, Gs(r,t), was calculated and expanded in Gaussian basis functions to model P(M,t) via Gs(r,t) = ∫P(M,t)q(r,M)dM.
• Nucleosomes were classified as fast or slow based on bimodal peaks in the MSD distribution at t = 0.5 s, with M* as the minimum between peaks.
• Auto- and pair-correlation functions of nucleosome displacements were computed within fast and slow categories to identify dynamically correlated regions.
• A minimal bead-spring polymer model with two loop domains (I and II) was used to simulate chromatin dynamics under varying interaction strengths (εI, εII) and tethering conditions, with Langevin dynamics and Lennard-Jones potentials.

Experimental results

Research questions

• RQ1 Do single-nucleosome movements in living human cells exhibit bimodal dynamics that can be classified as fast or slow?
• RQ2 Are fast and slow nucleosomes organized into dynamically correlated domains, and what is the spatial and temporal nature of these correlations?
• RQ3 How do nucleosome-nucleosome interactions and chromatin tethering contribute to the formation of fast and slow dynamic domains?
• RQ4 Can a minimal polymer model reproduce the observed bimodal MSD distribution and dynamic domain behavior under varying interaction and tethering conditions?
• RQ5 What is the role of chromatin geometry (e.g., compact vs. open, core vs. surface) in determining nucleosome mobility and domain identity?

Key findings

• The MSD distribution of single nucleosomes exhibits a clear bimodal peak at t = 0.5 s, enabling natural classification into fast (high MSD) and slow (low MSD) nucleosomes.
• Fast and slow nucleosomes form dynamically correlated fluid-like domains, with significant spatial and temporal correlations in their movements.
• Perturbations such as global histone acetylation or cohesin inactivation disrupt nucleosome dynamics, indicating that histone modifications and structural proteins are key regulators of domain organization.
• The minimal polymer model successfully reproduces the bimodal MSD distribution and shows that domain mobility depends on both local interaction strength (εI, εII) and tethering position: compact domains can be fast if tethered externally, while open domains are consistently fast.
• When two compact loop domains merge, their motions become correlated, forming a single large slow domain with increased radius of gyration.
• The model demonstrates that multiple mechanisms—local interactions, chromatin geometry, and tethering—act in concert to produce the observed dynamic domain organization, with no single mechanism sufficient alone.