Abstract
Polycomb 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.
Highlights
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development
Using a five-component PRC2 containing human EZH1, ectoderm development (EED), suppressor of zeste 12 (SUZ12), RBAP48, and AEBP2 (Fig. 1a), we determined a structure at 4.1-Å resolution (Supplementary Fig. 1)
To obtain a PRC2:EZH1–nucleosome structure, we first purified a PRC2:EZH1 with a longer JARID2 fragment containing residues 1–367 that includes a ubiquitin-interaction domain[33,34]. We incubated this complex with nucleosomes containing ten base pair DNA overhangs on either end of a 601 nucleosome-positioning sequence and a histone octamer containing two modifications: histone H3 mutated to methionine at lysine 27 (H3K27M) and histone H2A monoubiquitinated at lysine 119 (H2AUb)
Summary
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. Mutation of three basic amino acids in the C2 domain of SUZ12 disrupted dimerization of the four-component PRC2, reduced CpG island DNA-binding activity, and reduced H3K27 trimethylation at some developmental genes, providing a possible biological role for PRC2 dimerization[26] Despite these studies, it is not understood molecularly how dimers form in the context of PRC2 containing full-length SUZ12, EED, and EZH1/2 in addition to RBAP48, and how dimers interact with chromatin. This structure captures a PRC2:EZH1 dimer on a nucleosome containing H3K27M, with each PRC2: EZH1 in the dimer exhibiting an extensive structural rearrangement compared to the monomeric, nucleosome-free form This structure of a PRC2 dimer shows both the upper catalytic and lower regulatory lobes and reveals a dramatically different conformation of PRC2. We show that PRC2:EZH1 dimers more effectively promote compaction of nucleosome arrays, suggesting that dimerization helps to coalesce chromatin into silent domains
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