RT Journal Article
SR Electronic
T1 Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.09.01.458650
DO 10.1101/2021.09.01.458650
A1 Meng Zhang
A1 César Díaz-Celis
A1 Bibiana Onoa
A1 Cristhian Cañari-Chumpitaz
A1 Katherinne I. Requejo
A1 Jianfang Liu
A1 Michael Vien
A1 Eva Nogales
A1 Gang Ren
A1 Carlos Bustamante
YR 2021
UL http://biorxiv.org/content/early/2021/09/02/2021.09.01.458650.abstract
AB 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 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 material 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 resulting in modified inter-nucleosome interactions. These results suggest a physical mechanism by which chromatin may transition from interphase to metaphase structures.Competing Interest StatementThe authors have declared no competing interest.LLPSLiquid-liquid phase separationHP1heterochromatin protein 1cryo-ETcryo-Electron TomographyOpNSoptimized negative stainingNCPsnucleosome core particlesIPETindividual-particle electron tomographycc-scorecross-correlation scoreDBSCANdensity-based clustering non-parametric algorithmPCAPrincipal Component Analysisrradial distribution functions gAFMAtomic Force MicroscopyPol IIRNA Polymerase II