scholarly journals Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jorine M. Eeftens ◽  
Manya Kapoor ◽  
Davide Michieletto ◽  
Clifford P. Brangwynne
Keyword(s):  
Phase Separation ◽  
Cell Function ◽  
Eukaryotic Cell ◽  
Epigenetic Changes ◽  
Equilibrium Concept ◽  
Chromatin Compaction ◽  
Heterochromatin Formation ◽  
Polycomb Proteins ◽  
Time Integral ◽  
Polycomb Complex

AbstractOrganization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function. Phase-separation has been implicated in heterochromatin formation, but it is unclear how phase-separated condensates can contribute to stable repression, particularly for heritable epigenetic changes. Polycomb complex PRC1 is key for heterochromatin formation, but the multitude of Polycomb proteins has hindered our understanding of their collective contribution to chromatin repression. Here, we show that PRC1 forms multicomponent condensates through hetero-oligomerization. They preferentially seed at H3K27me3 marks, and subsequently write H2AK119Ub marks. We show that inducing Polycomb phase-separation can cause chromatin compaction, but polycomb condensates are dispensable for maintenance of the compacted state. Our data and simulations are consistent with a model in which the time integral of Polycomb phase-separation is progressively recorded in repressive histone marks, which subsequently drive compaction. These findings link the equilibrium thermodynamics of phase-separation with the fundamentally non-equilibrium concept of epigenetic memory.

scholarly journals Epigenetic memory as a time integral over prior history of Polycomb phase separation

2020 ◽  
Author(s):  
Jorine M. Eeftens ◽  
Manya Kapoor ◽  
Clifford P. Brangwynne
Keyword(s):  
Phase Separation ◽  
Cell Function ◽  
Eukaryotic Cell ◽  
Prior History ◽  
Epigenetic Memory ◽  
Chromatin Compaction ◽  
Heterochromatin Formation ◽  
Polycomb Proteins ◽  
Time Integral ◽  
Associated Proteins

ABSTRACTStructural organization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function. Heterochromatin is a more compact form of chromatin, and is associated with characteristic post-translational histone modifications and chromatin binding proteins. Phase-separation has recently been suggested as a mechanism for heterochromatin formation, through condensation of heterochromatin associated proteins. However, it is unclear how phase-separated condensates can contribute to stable and robust repression, particularly for heritable epigenetic changes. The Polycomb complex PRC1 is known to be key for heterochromatin formation, but the multitude of Polycomb proteins has hindered our understanding of their collective contribution to chromatin repression. Here, we take a quantitative live cell imaging approach to show that PRC1 proteins form multicomponent condensates through hetero-oligomerization. They preferentially seed at H3K27me3 marks, and subsequently write H2AK119Ub marks. Using optogenetics to nucleate local Polycomb condensates, we show that Polycomb phase separation can induce chromatin compaction, but phase separation is dispensable for maintenance of the compacted state. Our data are consistent with a model in which the time integral of historical Polycomb phase separation is progressively recorded in repressive histone marks, which subsequently drive chromatin compaction. These findings link the equilibrium thermodynamics of phase separation with the fundamentally non-equilibrium concept of epigenetic memory.

scholarly journals The hyaluronate synthase from a eukaryotic cell line

1993 ◽  
Vol 290 (3) ◽  
pp. 791-795 ◽  
Author(s):  
L Klewes ◽  
E A Turley ◽  
P Prehm
Keyword(s):  
Monoclonal Antibodies ◽  
Phase Separation ◽  
Affinity Chromatography ◽  
Cell Line ◽  
Aqueous Phase ◽  
Plasma Membranes ◽  
Eukaryotic Cell ◽  
Molecular Masses ◽  
Triton X ◽  
Hyaluronate Synthase

The hyaluronate synthase complex was identified in plasma membranes from B6 cells. It contained two subunits of molecular masses 52 kDa and 60 kDa which bound the precursor UDP-GlcA in digitonin solution and partitioned into the aqueous phase, together with nascent hyaluronate upon Triton X-114 phase separation. The 52 kDa protein cross-reacted with poly- and monoclonal antibodies raised against the streptococcal hyaluronate synthase and the 60 kDa protein was recognized by monoclonal antibodies raised against a hyaluronate receptor. The 52 kDa protein was purified to homogeneity by affinity chromatography with monoclonal anti-hyaluronate synthase.

scholarly journals Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation

2018 ◽  
Vol 294 (5) ◽  
pp. 1451-1463 ◽  
Author(s):  
Roubina Tatavosian ◽  
Samantha Kent ◽  
Kyle Brown ◽  
Tingting Yao ◽  
Huy Nguyen Duc ◽  
...  
Keyword(s):  
Phase Separation ◽  
Polycomb Group ◽  
Site Directed Mutagenesis ◽  
Developmental Defects ◽  
Heterochromatin Formation ◽  
Intrinsically Disordered ◽  
Polycomb Protein ◽  
Condensate Formation

Polycomb group (PcG) proteins repress master regulators of development and differentiation through organization of chromatin structure. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the cell nucleus, and these condensates are the physical sites of PcG-targeted gene silencing via formation of facultative heterochromatin. However, the physiochemical principles underlying the formation of PcG condensates remain unknown, and their determination could shed light on how these condensates compact chromatin. Using fluorescence live-cell imaging, we observed that the Polycomb repressive complex 1 (PRC1) protein chromobox 2 (CBX2), a member of the CBX protein family, undergoes phase separation to form condensates and that the CBX2 condensates exhibit liquid-like properties. Using site-directed mutagenesis, we demonstrated that the conserved residues of CBX2 within the intrinsically disordered region (IDR), which is the region for compaction of chromatin in vitro, promote the condensate formation both in vitro and in vivo. We showed that the CBX2 condensates concentrate DNA and nucleosomes. Using genetic engineering, we report that trimethylation of Lys-27 at histone H3 (H3K27me3), a marker of heterochromatin formation produced by PRC2, had minimal effects on the CBX2 condensate formation. We further demonstrated that the CBX2 condensate formation does not require CBX2–PRC1 subunits; however, the condensate formation of CBX2–PRC1 subunits depends on CBX2, suggesting a mechanism underlying the assembly of CBX2–PRC1 condensates. In summary, our results reveal that PcG condensates assemble through liquid–liquid phase separation (LLPS) and suggest that phase-separated condensates can organize PcG-bound chromatin.

scholarly journals The mechanism of kinesin inhibition by kinesin-binding protein

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Joseph Atherton ◽  
Jessica JA Hummel ◽  
Natacha Olieric ◽  
Julia Locke ◽  
Alejandro Peña ◽  
...  
Keyword(s):  
Cell Function ◽  
Binding Protein ◽  
Eukaryotic Cell ◽  
Motor Domain ◽  
Tetratricopeptide Repeat ◽  
Kinesin Motor ◽  
Temporal Regulation ◽  
Cryo Electron Microscopy ◽  
Local Environments ◽  
Binding Surface

Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin-binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment, and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP–kinesin motor domain complex. KBP is a tetratricopeptide repeat-containing, right-handed α-solenoid that sequesters the kinesin motor domain’s tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain, and selected structure-guided mutations disrupt KBP inhibition of kinesin transport in cells. The KBP-interacting motor domain surface contains motifs exclusively conserved in KBP-interacting kinesins, suggesting a basis for kinesin selectivity.

A Review of epigenetics in psychiatry: focus on environmental risk factors

2020 ◽  
Vol 32 (1) ◽  
pp. 57-64
Author(s):  
Jessica Keverne ◽  
Elisabeth B. Binder
Keyword(s):  
Risk Factors ◽  
Psychiatric Disorders ◽  
Environmental Risk ◽  
Cell Function ◽  
Epigenetic Modifications ◽  
Environmental Risk Factors ◽  
Epigenetic Changes ◽  
Cell Type Specificity ◽  
Environmental Signals ◽  
Genetic And Environmental Factors

Abstract Epigenetic modifications play a key role in development and cell type specificity. These modifications seem to be particularly critical for brain development, where mutations in epigenetic enzymes have been associated with neurodevelopmental disorders as well as with the function of post-mitotic neurons. Epigenetic modifications can be influenced by genetic and environmental factors, both known major risk factors for psychiatric disorders. Epigenetic modifications may thus be an important mediator of the effects of genetic and environmental risk factors on cell function. This review summarizes the different types of epigenetic regulation and then focuses on the mechanisms transducing environmental signals, especially adverse life events that are major risk factors for psychiatric disorders, into lasting epigenetic changes. This is followed by examples of how the environment can induce epigenetic changes that relate to the risk of psychiatric disorders.

The complex role of EZH2 in the tumor microenvironment: opportunities and challenges for immunotherapy combinations

2020 ◽  
Vol 12 (15) ◽  
pp. 1415-1430
Author(s):  
Jing Qiu ◽  
Shikhar Sharma ◽  
Robert A Rollins ◽  
Thomas A Paul
Keyword(s):  
Tumor Microenvironment ◽  
Cell Fate ◽  
Cell Function ◽  
Immune Dysfunction ◽  
Lymphoid Cells ◽  
Epigenetic Changes ◽  
Immune Effector ◽  
Effector Functions ◽  
Tumor Immunogenicity

Immune dysfunction in the tumor microenvironment occurs through epigenetic changes in both tumor cells and immune cells that alter transcriptional programs driving cell fate and cell function. Oncogenic activation of the histone methyltransferase EZH2 mediates gene expression changes, governing tumor immunogenicity as well as differentiation, survival and activation states of immune lineages. Emerging preclinical studies have highlighted the potential for EZH2 inhibitors to reverse epigenetic immune suppression in tumors and combine with immune checkpoint therapies. However, EZH2 activity is essential for the development of lymphoid cells, performing critical immune effector functions within tumors. In this review, we highlight the complexity of EZH2 function in immune regulation which may impact the implementation of combination with immunotherapy agents in clinic.

Polycomb proteins in hematologic malignancies

Blood ◽  
2010 ◽  
Vol 116 (25) ◽  
pp. 5465-5475 ◽  
Author(s):  
Daniel Martin-Perez ◽  
Miguel A. Piris ◽  
Margarita Sanchez-Beato
Keyword(s):  
Stem Cell ◽  
Cell Function ◽  
Chromatin Modification ◽  
Hematologic Malignancies ◽  
Polycomb Group ◽  
Major Mechanism ◽  
Polycomb Proteins ◽  
Frequent Event ◽  
Health And Disease

Abstract The Polycomb group (PcG) of proteins is a major mechanism of epigenetic regulation that has been broadly linked to cancer. This system can repress gene expression by chromatin modification and is essential for establishing cell identity. PcG proteins are important for stem cell function and differentiation and have a profound impact during hematopoiesis. In recent years, several published studies have deepened our knowledge of the biology of the PcG in health and disease. In this article, we review the current understanding of the mechanisms of PcG-mediated repression and their relation to DNA methylation, and we discuss the role of the PcG system in hematopoiesis and hematologic malignancies. We suggest that alteration of different PcG members is a frequent event in leukemia and lymphomas that confers the stem cell properties on tumor cells. Thus, drugs targeting Polycomb complexes could be useful for treating patients with these diseases.

scholarly journals Xist IncRNA forms silencing granules that induce heterochromatin formation and repressive complexes recruitment by phase separation

2018 ◽  
Author(s):  
Andrea Cerase ◽  
Alexandros Armaos ◽  
Fernando Cid ◽  
Philip Avner ◽  
Gian Gaetano Tartaglia
Keyword(s):  
Phase Separation ◽  
Heterochromatin Formation

scholarly journals A lipid bound actin meshwork organizes liquid phase separation in model membranes

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Alf Honigmann ◽  
Sina Sadeghi ◽  
Jan Keller ◽  
Stefan W Hell ◽  
Christian Eggeling ◽  
...  
Keyword(s):  
Phase Separation ◽  
Eukaryotic Cell ◽  
Membrane Curvature ◽  
Actin Binding ◽  
Lipid Phase ◽  
Membrane Composition ◽  
Actin Cortex ◽  
Dense Membrane ◽  
Experimental Findings ◽  
Membrane Components

The eukaryotic cell membrane is connected to a dense actin rich cortex. We present FCS and STED experiments showing that dense membrane bound actin networks have severe influence on lipid phase separation. A minimal actin cortex was bound to a supported lipid bilayer via biotinylated lipid streptavidin complexes (pinning sites). In general, actin binding to ternary membranes prevented macroscopic liquid-ordered and liquid-disordered domain formation, even at low temperature. Instead, depending on the type of pinning lipid, an actin correlated multi-domain pattern was observed. FCS measurements revealed hindered diffusion of lipids in the presence of an actin network. To explain our experimental findings, a new simulation model is proposed, in which the membrane composition, the membrane curvature, and the actin pinning sites are all coupled. Our results reveal a mechanism how cells may prevent macroscopic demixing of their membrane components, while at the same time regulate the local membrane composition.

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