Data from: Multi-scale structure of chromatin condensates explains phase separation and material properties
Data files
Oct 23, 2025 version files 18.10 GB
Abstract
The structure and interaction networks of molecules within biomolecular condensates are poorly understood. Using cryo-electron tomography and molecular dynamics simulations, we elucidated the structure of phase separated chromatin condensates across scales, from individual amino acids to network architecture. We found that internucleosomal DNA linker length controls nucleosome arrangement and histone tail interactions, shaping the structure of individual chromatin molecules within and outside condensates. This structural modulation determines the balance between intra- and intermolecular interactions, which governs the molecular network, thermodynamic stability, and material properties of chromatin condensates. Mammalian nuclei contain dense clusters of nucleosomes whose non-random organization is mirrored by the reconstituted condensates. Our work explains how the structure of individual chromatin molecules determines physical properties of chromatin condensates and cellular chromatin organization.
Dataset DOI: 10.5061/dryad.p2ngf1w45
Description of the data and file structure
This repo is for the data and its associated analysis that used in the multi-scale chromatin structure paper! The data includes:
tomograms_fiber_tracing_25bp_condensates.tar.gz, which contains tomograms and star files for the traced nucleosome arrays that can be open using ChimeraX
tomograms_fiber_tracing_25bp_dilute.tar.gz, similar to previous one, but in 25bp chromatin in low salt dilute phase
tomograms_fiber_tracing_30bp_condensates.tar.gz, similar to previous one, but in 30bp condensate
tomograms_fiber_tracing_30bp_dilute.tar.gz, similar to previous one, but in 30bp chromatin in low salt dilute phase
Description: tomograms from 30bp chromatin and star files for the traced nucleosome arrays that can be open using ChimeraX
Parameters
ChimeraX automatically reads the pixel size from the MRC file. However, when working with the star file, the PixelSize Factor should be set to 8.
Naming Convention
The star file names consist of two main parts: the first part, “sxx”, corresponds to the associated tomogram, and the second part, “fiberx”, represents the ID of the fiber extracted from that tomogram.
Code/software
ChimeraX (v>1.3) with Artaix plugin, pixel size of the starfile is 8 Å/pixel