Organization of Chromatin by Intrinsic and Regulated Phase Separation

Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and organized into subdomains. We demonstrate that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dens...

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Bibliographic Details
Published in:	Cell Vol. 179; no. 2; pp. 470 - 484.e21
Main Authors:	Gibson, Bryan A., Doolittle, Lynda K., Schneider, Maximillian W.G., Jensen, Liv E., Gamarra, Nathan, Henry, Lisa, Gerlich, Daniel W., Redding, Sy, Rosen, Michael K.
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 03-10-2019
Subjects:	Acetylation Animals BRD4 Cell Cycle Proteins - metabolism Cell Nucleus - metabolism Chromatin - metabolism chromatin organization E1A-Associated p300 Protein - metabolism epigenetics Escherichia coli - genetics genome HeLa Cells histone histone H1 Histones - metabolism Humans Nuclear Proteins - metabolism nucleosome nucleosome spacing phase separation Sf9 Cells Transcription Factors - metabolism chromatin organization acetylation genome phase separation histone H1 nucleosome histone nucleosome spacing epigenetics BRD4
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Summary:	Eukaryotic chromatin is highly condensed but dynamically accessible to regulation and organized into subdomains. We demonstrate that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets. Linker histone H1 and internucleosome linker lengths shared across eukaryotes promote phase separation of chromatin, tune droplet properties, and coordinate to form condensates of consistent density in manners that parallel chromatin behavior in cells. Histone acetylation by p300 antagonizes chromatin phase separation, dissolving droplets in vitro and decreasing droplet formation in nuclei. In the presence of multi-bromodomain proteins, such as BRD4, highly acetylated chromatin forms a new phase-separated state with droplets of distinct physical properties, which can be immiscible with unmodified chromatin droplets, mimicking nuclear chromatin subdomains. Our data suggest a framework, based on intrinsic phase separation of the chromatin polymer, for understanding the organization and regulation of eukaryotic genomes. [Display omitted] •Chromatin undergoes liquid-liquid phase separation (LLPS) under physiologic conditions•Linker DNA length and patterning, histone H1, and acetylation modulate chromatin LLPS•Acetylated chromatin only phase separates upon binding multi-bromodomain proteins•LLPS could enable establishment and maintenance of distinct chromatin compartments Properties inherent to chromatin, including nucleosomal spacing, allow it to phase separate within the nucleoplasm, and this ability can be further modulated by regulatory factors.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 AUTHOR CONTRIBUTIONS M.K.R. and B.A.G. conceived the study, and M.K.R., B.A.G., D. G. and S.R. designed the research program. L.H. performed insect cell protein expression, and N.G, L.E.H. and S.R. prepared recombinant X. laevis histone octamers. All other biochemical materials preparation was performed by B.A.G. and L.K.D. M.W.G.S. performed all nuclear microinjections and their subsequent image analyses. B.A.G. performed in vitro biochemical experiments, fluorescence microscopy, and computational analyses. M.K.R., S.R., and D.G. secured funding and supervised the work. M.K.R. and B.A.G. wrote the manuscript with D.G., M.W.G.S, and S.R.
ISSN:	0092-8674 1097-4172
DOI:	10.1016/j.cell.2019.08.037