@article {70213, title = {Multiscale structure of chromatin condensates explains phase separation and material properties.}, journal = {Science}, volume = {390}, year = {2025}, month = {2025 Dec 04}, pages = {eadv6588}, 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 nonrandom 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.

}, keywords = {Animals, Biomolecular Condensates, Chromatin, Cryoelectron Microscopy, DNA, Electron Microscope Tomography, Histones, Humans, Molecular Dynamics Simulation, Nucleosomes, Phase Separation, Thermodynamics}, issn = {1095-9203}, doi = {10.1126/science.adv6588}, url = {https://doi.org/10.1126/science.adv6588}, author = {Zhou, Huabin and Huertas, Jan and Maristany, M Julia and Russell, Kieran and Hwang, June Ho and Yao, Run-Wen and Samanta, Nirnay and Hutchings, Joshua and Billur, Ramya and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K and Gibson, Bryan A and Soranno, Andrea and Riggi, Margot and Espinosa, Jorge R and Yu, Zhiheng and Villa, Elizabeth and Collepardo-Guevara, Rosana and Rosen, Michael K} } @article {69904, title = {Quantitative spatial analysis of chromatin biomolecular condensates using cryoelectron tomography.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 May 13}, pages = {e2426449122}, abstract = {

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here, we analyzed the structure of biochemically reconstituted chromatin condensates through cryoelectron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with context-aware template matching. Our approaches were developed on chromatin condensates and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 {\r A} resolution in reconstituted and native systems, respectively, found that nucleosomes form heterogeneous interaction networks in both cases, and gained insight into the molecular origins of surface tension in chromatin condensates. Our methods should be applicable to biomolecular condensates containing large and distinctive components in both biochemical reconstitutions and certain cellular systems.

Preprint:\ https://www.biorxiv.org/content/10.1101/2024.12.01.626131v2

}, keywords = {Animals, Biomolecular Condensates, Chromatin, Cryoelectron Microscopy, Electron Microscope Tomography, Nucleosomes}, issn = {1091-6490}, doi = {10.1073/pnas.2426449122}, url = {https://doi.org/10.1073/pnas.2426449122}, author = {Zhou, Huabin and Hutchings, Joshua and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K and Yang, Shixin and Yan, Rui and Jean, Nikki and Riggi, Margot and Yu, Zhiheng and Villa, Elizabeth and Rosen, Michael K} } @article {69688, title = {Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography}, journal = {bioRxiv}, year = {2024}, month = {2024 Dec 02}, abstract = {

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here we analyzed the structure of biochemically reconstituted chromatin condensates through cryo-electron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with novel context-aware template matching. Our approaches were developed on chromatin condensates, and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 {\r A} resolution in reconstituted and native systems, respectively, and found that nucleosomes have a nearly random orientation distribution in both cases. Our methods should be applicable to diverse biochemically reconstituted biomolecular condensates and to some condensates in cells.

}, doi = {10.1101/2024.12.01.626131}, url = {https://doi.org/10.1101/2024.12.01.626131}, author = {Zhou, Huabin and Hutchings, Joshua and Shiozaki, Momoko and Zhao, Xiaowei and Doolittle, Lynda K. and Yang, Shixin and Yan, Rui and Jean, Nikki and Riggi, Margot and Yu, Zhiheng and Villa, Elizabeth and Rosen, Michael K.} }