Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography

Meng Zhang; César Díaz-Celis; Bibiana Onoa; Cristhian Cañari-Chumpitaz; Katherinne I Requejo; Jianfang Liu; Michael Vien; Eva Nogales; Gang Ren; Carlos Bustamante

doi:10.1016/j.molcel.2022.06.032

Molecular organization of the early stages of nucleosome phase separation visualized by cryo-electron tomography

Mol Cell. 2022 Aug 18;82(16):3000-3014.e9. doi: 10.1016/j.molcel.2022.06.032. Epub 2022 Jul 30.

Authors

Affiliations

¹ Applied Science and Technology Graduate Group, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
² California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
³ Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
⁴ Department of Chemistry, University of California, Berkeley, CA, USA.
⁵ The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁶ Department of Physics, University of California, Berkeley, CA, USA.
⁷ California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁸ The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. Electronic address: gren@lbl.gov.
⁹ California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA; Department of Physics, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, CA, USA. Electronic address: carlosjbustamante2@gmail.com.

Abstract

It has been proposed that the intrinsic property of nucleosome arrays to undergo liquid-liquid phase separation (LLPS) in vitro is responsible for chromatin domain organization in vivo. However, understanding nucleosomal LLPS has been hindered by the challenge to characterize the structure of the resulting heterogeneous condensates. We used cryo-electron tomography and deep-learning-based 3D reconstruction/segmentation to determine the molecular organization of condensates at various stages of LLPS. We show that nucleosomal LLPS involves a two-step process: a spinodal decomposition process yielding irregular condensates, followed by their unfavorable conversion into more compact, spherical nuclei that grow into larger spherical aggregates through accretion of spinodal materials or by fusion with other spherical condensates. Histone H1 catalyzes more than 10-fold the spinodal-to-spherical conversion. We propose that this transition involves exposure of nucleosome hydrophobic surfaces causing modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.

Keywords: chromatin; condensates; cryo-electron tomography; linker histone H1; liquid-liquid phase separation; nucleation and growth; nucleosome; nucleosome arrays; spinodal decomposition.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cell Nucleus
Chromatin
Electron Microscope Tomography*
Metaphase
Nucleosomes*

Substances

Chromatin
Nucleosomes

Abstract

Publication types

MeSH terms

Substances

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