Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

Abstract

The three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30 nm fiber.

Chromatin fiber breaks into clutches under tension and crowding

“…Interactions among the coarse-grained beads were parameterized by accounting for solvent effect implicitly with physically motivated potentials (see Methods for model details). Similar approaches have been extensively used to characterize single nucleosomes [57][58][59] and nucleosome oligomers 33,60 with great success.…”

“…The near-atomistic model has been used extensively in prior studies to investigate proteinprotein/protein-DNA interactions, 81,89 the energetics of single nucleosome unwinding, 58,63 nucleosome-nucleosome interactions, 57 and the folding pathways of a tetra-nucleosome. 33 More details on the model setup and force field parameters can be found in the Supporting Information.…”

“…Recently, we explored the folding landscape and pathways of a tetranucleosome, i.e., a minimal fibril unit. 33 Schalch et al captured the tetra-nucleosome in a two-helix zigzag conformation with X-ray crystallography. 34 Unfolded tetra-nucleosome configurations from the crystal structure indeed resemble those reported by in vivo studies, including the formation of trinucleosome motifs.…”

Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography

“…Here, we have used cryo-ET coupled to deep learning-based 3D reconstruction and segmentation processes to perform a systematic study of the earliest stages of nucleosomal phase separation in vitro , using reconstituted tetranucleosome arrays. Tetranucleosome arrays have been identified as the minimal unit capable of generating large-scale chromatin structures (Ding et al, 2021; Schalch et al, 2005; Song et al, 2014), and phase transition experiments with different nucleosome array numbers indicate that tetranucleosomes are at the boundary below which liquid droplets do not form (Gibson et al, 2019).…”

CENP-N promotes the compaction of centromeric chromatin

“…Molecular dynamics simulations suggest that the energy barriers between different nucleosome arrangements are relatively low (4). Variations of nucleosome composition, such as DNA sequence, length of linker DNA connecting individual nucleosomes, incorporation of histone variants, and post-translational modifications of histones all have the potential to affect 10 chromatin condensation and thus DNA accessibility, either directly or through the recruitment of a plethora of interacting factors (5).…”