Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction

AbstractPolycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell.

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Faculty Opinions recommendation of The histone H3 lysine 9 methyltransferases G9a and GLP regulate polycomb repressive complex 2-mediated gene silencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718228225.793499412 ◽

2014 ◽

Author(s):

Anne Ferguson-Smith ◽

Celia Delahaye

Keyword(s):

Gene Silencing ◽

Histone H3 ◽

Polycomb Repressive Complex ◽

Polycomb Repressive Complex 2

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Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

Molecular Cell ◽

10.1016/j.molcel.2014.06.005 ◽

2014 ◽

Vol 55 (3) ◽

pp. 347-360 ◽

Cited By ~ 262

Author(s):

Eva Madi Riising ◽

Itys Comet ◽

Benjamin Leblanc ◽

Xudong Wu ◽

Jens Vilstrup Johansen ◽

...

Keyword(s):

Gene Silencing ◽

Cpg Islands ◽

Polycomb Repressive Complex ◽

Polycomb Repressive Complex 2 ◽

Genome Wide

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Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

10.1101/2021.07.16.452543 ◽

2021 ◽

Author(s):

Abdoallah Sharaf ◽

Mallika Vijayanathan ◽

Miroslav Obornik ◽

iva Mozgova

Keyword(s):

Developmental Regulation ◽

Structural Diversity ◽

Polycomb Group ◽

Catalytic Subunit ◽

Set Domain ◽

Polycomb Repressive Complex ◽

Polycomb Repressive Complex 2 ◽

Domains Of Life ◽

Domain Protein ◽

Phylogenetic Profiling

Polycomb Repressive Complex 2 (PRC2) is involved in establishing transcriptionally silent chromatin states through its ability to methylate lysine 27 of histone H3 by the catalytic subunit Enhancer of zeste [E(z)]. Polycomb group (PcG) proteins play a crucial role in the maintenance of cell identity and in developmental regulation. Previously, the diversity of PRC2 subunits within some eukaryotic lineages has been reported and its presence in early eukaryotic evolution has been hypothesized. So far however, systematic survey of the presence of PRC2 subunits in species of all eukaryotic lineages is missing. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. In detail, we investigate the SET-domain protein sequences and their evolution across the four domains of life and particularly focus on the structural diversity of the SET-domain subfamily containing E(z), the catalytic subunit of PRC2. We show that PRC2 subunits are already present in early eukaryotic lineages, strengthening the support for PRC2 emergence prior to diversification of eukaryotes. We identify a common presence of E(z) and ESC, suggesting that Su(z)12 may have emerged later and/or may be dispensable from the evolutionarily conserved functional core of PRC2. Furthermore, our results broaden our understanding of the E(z) evolution within the SET-domain protein family, suggesting possibilities of function evolution. Through this, we shed light on a possible emerging point of the PRC2 and the evolution of its function in eukaryotes.

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Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid

Nucleic Acids Research ◽

10.1093/nar/gkaa073 ◽

2020 ◽

Vol 48 (6) ◽

pp. 2969-2981 ◽

Cited By ~ 2

Author(s):

Patrick R Heenan ◽

Xueyin Wang ◽

Anne R Gooding ◽

Thomas R Cech ◽

Thomas T Perkins

Keyword(s):

Gene Silencing ◽

Single Molecule ◽

Molecular Mechanisms ◽

Cpg Island ◽

Specific Binding ◽

Gc Content ◽

Polycomb Repressive Complex ◽

Apparent Dissociation Constant ◽

Polycomb Repressive Complex 2 ◽

Epigenetic Gene Silencing

Abstract Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the resulting images showed PRC2, consisting of five subunits (EZH2, EED, SUZ12, AEBP2 and RBBP4), bound to a 2.5-kb DNA with an apparent dissociation constant ($K_{\rm{D}}^{{\rm{app}}}$) of 150 ± 12 nM. PRC2 did not show sequence-specific binding to a region of high GC content (76%) derived from a CpG island embedded in such a long DNA substrate. At higher concentrations, PRC2 compacted DNA by forming DNA loops typically anchored by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold increase in the local bending of DNA’s helical backbone without evidence of DNA wrapping around the protein. We suggest that the bending and looping of DNA by PRC2, independent of PRC2’s methylation activity, may contribute to heterochromatin formation and therefore epigenetic gene silencing.

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Faculty Opinions recommendation of Origin of the polycomb repressive complex 2 and gene silencing by an E(z) homolog in the unicellular alga Chlamydomonas.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.3288956.2975055 ◽

2010 ◽

Author(s):

Anton Wutz

Keyword(s):

Gene Silencing ◽

Unicellular Alga ◽

Polycomb Repressive Complex ◽

Polycomb Repressive Complex 2

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Downregulation of the Polycomb-Associated Methyltransferase Ezh2 during Maturation of Hippocampal Neurons Is Mediated by MicroRNAs Let-7 and miR-124

International Journal of Molecular Sciences ◽

10.3390/ijms21228472 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8472

Author(s):

Laura Guajardo ◽

Rodrigo Aguilar ◽

Fernando J. Bustos ◽

Gino Nardocci ◽

Rodrigo A. Gutiérrez ◽

...

Keyword(s):

Gene Silencing ◽

Hippocampal Neurons ◽

Gene Sequence ◽

Histone H3 ◽

Catalytic Subunit ◽

Maturation Process ◽

Polycomb Repressive Complex 2 ◽

Ezh2 Expression ◽

Epigenetic Gene Silencing ◽

Mature Neurons

Ezh2 is a catalytic subunit of the polycomb repressive complex 2 (PRC2) which mediates epigenetic gene silencing through depositing the mark histone H3 lysine 27 trimethylation (H3K27me3) at target genomic sequences. Previous studies have demonstrated that Enhancer of Zeste Homolog 2 (Ezh2) was differentially expressed during maturation of hippocampal neurons; in immature neurons, Ezh2 was abundantly expressed, whereas in mature neurons the expression Ezh2 was significantly reduced. Here, we report that Ezh2 is downregulated by microRNAs (miRs) that are expressed during the hippocampal maturation process. We show that, in mature hippocampal neurons, lethal-7 (let-7) and microRNA-124 (miR-124) are robustly expressed and can target cognate motifs at the 3′-UTR of the Ezh2 gene sequence to downregulate Ezh2 expression. Together, these data demonstrate that the PRC2 repressive activity during hippocampal maturation is controlled through a post-transcriptional mechanism that mediates Ezh2 downregulation in mature neurons.

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Inhibition of Polycomb Repressive Complex 2 activity reduces trimethylation of H3K27 and affects development in Arabidopsis seedlings

BMC Plant Biology ◽

10.1186/s12870-019-2057-7 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Veronica Ruta ◽

Chiara Longo ◽

Alessandra Boccaccini ◽

Valentina Noemi Madia ◽

Francesco Saccoliti ◽

...

Keyword(s):

Transcriptional Repression ◽

Transcriptional Control ◽

Catalytic Subunit ◽

Human Leukemia ◽

Polycomb Repressive Complex ◽

Polycomb Repressive Complex 2 ◽

Human Leukemia Cells ◽

Suitable Target ◽

Dose Dependent Fashion ◽

Dose Dependent

Abstract Background Polycomb repressive complex 2 (PRC2) is an epigenetic transcriptional repression system, whose catalytic subunit (ENHANCER OF ZESTE HOMOLOG 2, EZH2 in animals) is responsible for trimethylating histone H3 at lysine 27 (H3K27me3). In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. Results We show here that the 1,5-bis (3-bromo-4-methoxyphenyl)penta-1,4-dien-3-one compound (RDS 3434), previously reported as an EZH2 inhibitor in human leukemia cells, is active on the Arabidopsis catalytic subunit of PRC2, since treatment with the drug reduces the total amount of H3K27me3 in a dose-dependent fashion. Consistently, we show that the expression level of two PRC2 targets is significantly increased following treatment with the RDS 3434 compound. Finally, we show that impairment of H3K27 trimethylation in Arabidopsis seeds and seedlings affects both seed germination and root growth. Conclusions Our results provide a useful tool for the plant community in investigating how PRC2 affects transcriptional control in plant development.

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