Molecular architecture of human Polycomb repressive complex 2

Department of Molecular and Cell Biology , University of California , Berkeley , United States.
eLife Sciences (Impact Factor: 9.32). 10/2012; 1(1):e00005. DOI: 10.7554/eLife.00005
Source: PubMed


Polycomb Repressive Complex 2 (PRC2) is essential for gene silencing, establishing transcriptional repression of specific genes by tri-methylating Lysine 27 of histone H3, a process mediated by cofactors such as AEBP2. In spite of its biological importance, little is known about PRC2 architecture and subunit organization. Here, we present the first three-dimensional electron microscopy structure of the human PRC2 complex bound to its cofactor AEBP2. Using a novel internal protein tagging-method, in combination with isotopic chemical cross-linking and mass spectrometry, we have localized all the PRC2 subunits and their functional domains and generated a detailed map of interactions. The position and stabilization effect of AEBP2 suggests an allosteric role of this cofactor in regulating gene silencing. Regions in PRC2 that interact with modified histone tails are localized near the methyltransferase site, suggesting a molecular mechanism for the chromatin-based regulation of PRC2 activity. DOI:

1 Follower
35 Reads
  • Source
    • "Two structural features distinguish our EZH2 structure from catalytically competent conformations of other SET domain methyltransferases: the post-SET domain projects away from its expected position (Figure 3A), resulting in an incomplete cofactor binding site, and the I-SET domain is shifted towards the post-SET domain, which closes the histone binding groove and blocks the entrance of the substrate lysine channel (Figure 2 and Figure S10). While these features may be related to crystal lattice contacts which are numerous both at the post-SET and I-SET domains, there is evidence that at least some of the atypical features of our crystallized conformation (inactive trajectory of the post-SET) may be populated in the PRC2 complex in solution (Figure 3C) [53]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Polycomb repressive complex 2 (PRC2) is an important regulator of cellular differentiation and cell type identity. Overexpression or activating mutations of EZH2, the catalytic component of the PRC2 complex, are linked to hyper-trimethylation of lysine 27 of histone H3 (H3K27me3) in many cancers. Potent EZH2 inhibitors that reduce levels of H3K27me3 kill mutant lymphoma cells and are efficacious in a mouse xenograft model of malignant rhabdoid tumors. Unlike most SET domain methyltransferases, EZH2 requires PRC2 components, SUZ12 and EED, for activity, but the mechanism by which catalysis is promoted in the PRC2 complex is unknown. We solved the 2.0 Å crystal structure of the EZH2 methyltransferase domain revealing that most of the canonical structural features of SET domain methyltransferase structures are conserved. The site of methyl transfer is in a catalytically competent state, and the structure clarifies the structural mechanism underlying oncogenic hyper-trimethylation of H3K27 in tumors harboring mutations at Y641 or A677. On the other hand, the I-SET and post-SET domains occupy atypical positions relative to the core SET domain resulting in incomplete formation of the cofactor binding site and occlusion of the substrate binding groove. A novel CXC domain N-terminal to the SET domain may contribute to the apparent inactive conformation. We propose that protein interactions within the PRC2 complex modulate the trajectory of the post-SET and I-SET domains of EZH2 in favor of a catalytically competent conformation.
    PLoS ONE 12/2013; 8(12):e83737. DOI:10.1371/journal.pone.0083737 · 3.23 Impact Factor
  • Source
    • "Clearly, further structural and mechanistic advances are needed to define how these remarkably conserved partner inputs control the efficiency of PRC2 output. Importantly, the recent report of EM-derived PRC2 architecture (Ciferri et al., 2012) provides the first full structural framework for analyzing PRC2 inner workings. This multilobed structure places portions of EED and SU(Z)12 in close proximity to the EZH2 SET domain—prime locations to impact PRC2 enzymatic function. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Chromatin modification by Polycomb proteins provides an essential strategy for gene silencing in higher eukaryotes. Polycomb repressive complexes (PRCs) silence key developmental regulators and are centrally integrated in the transcriptional circuitry of stem cells. PRC2 trimethylates histone H3 on lysine 27 (H3K27me3), and PRC1-type complexes ubiquitylate histone H2A and compact polynucleosomes. How PRCs are deployed to select and silence genomic targets is the subject of intense investigation. We review advances on targeting, modulation, and functions of PRC1 and PRC2 and progress on defining the transcriptional steps they impact. Recent findings emphasize PRC1 targeting independent of H3K27me3, nonenzymatic PRC1-mediated compaction, and connections between PRCs and noncoding RNAs. Systematic analyses of Polycomb complexes and associated histone modifications during DNA replication and mitosis have also emerged. The stage is now set to reveal fundamental epigenetic mechanisms that determine how Polycomb target genes are silenced and how Polycomb silence is preserved through cell-cycle progression.
    Molecular cell 03/2013; 49(5):808-24. DOI:10.1016/j.molcel.2013.02.013 · 14.02 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Chromatin remodelers have been implicated in the regulation of histone-modifying complexes. However, the underlying mechanism remains poorly understood. The Rpd3S histone deacetylase complex is recruited by elongating RNA polymerase II to remove histone acetylation at coding regions in a manner that is dependent on methylation of lysine 36 on histone 3 (H3K36me), and Rpd3S prefers dinucleosomes. Here, we show that the binding of Rpd3S to dinucleosomes and its catalytic activity are sensitive to the length of nucleosomal linker in a nonlinear fashion. Intriguingly, we found that H3K36me on one nucleosome stimulates Rpd3S to deacetylate the neighboring nucleosomes when those two nucleosomes are within an optimal distance. Finally, we demonstrate that chromatin remodelers enhance Rpd3S activity by altering nucleosomal spacing, suggesting that chromatin remodelers prime chromatin configuration to fine-tune subsequent histone modification reactions. This mechanism is important for accurate temporal control of chromatin dynamics during the transcription elongation cycle.
    Molecular cell 09/2013; 41(2). DOI:10.1016/j.molcel.2013.08.024 · 14.02 Impact Factor
Show more