JARID2 and AEBP2 regulate PRC2 activity in the presence of H2A ubiquitination or other histone modifications

Abstract

The Polycomb repressive complexes PRC1 and PRC2 functionally interact to coordinate cell type identity by the epigenetic regulation of gene expression. It has been proposed that PRC2 is recruited to genomic loci via the recognition of PRC1-mediated mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub1), but the mechanism of this process remains poorly understood. Here, we report the cryo-EM structure of human PRC2 with cofactors JARID2 and AEBP2 bound to a nucleosome substrate containing H2AK119ub1. We find that JARID2 and AEBP2 each interact with one of the two ubiquitin molecules in the nucleosome. A ubiquitin-interaction motif (UIM) in JARID2 is sandwiched between ubiquitin and the histone H2A-H2B acidic patch. Simultaneously, the tandem zinc-fingers of AEBP2 interact with the second ubiquitin and the histone H2A-H2B surface on the opposite side of the nucleosome. JARID2 plays a dual role in the H2AK119ub1 dependent stimulation of PRC2 through interactions with both EED via its K116 trimethylation and with the H2AK119-ubiquitin. AEBP2, on the other hand, appears to primarily serve as a scaffold contributing to the interaction between PRC2 and the H2AK119ub1 nucleosome. Our structure also provides a detailed visualization of the EZH2-nucleosome interface, revealing a segment of EZH2 (named "bridge helix") that is stabilized as it bridges the EZH2(SET) domain, the H3 tail and the nucleosomal DNA. In addition to the role played by AEBP2 and JARID2 in PRC2 regulation by H2AK119ub1 recognition, we also observe that the presence of these cofactors partially overcomes the inhibitory effect that H3K4-and H3K36trimethylation have on core PRC2. Together, our results reveal the central role played by cofactors JARID2 and AEBP2 in orchestrating the crosstalk between histone post-translational modifications and PRC2 methyltransferase activity.

Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3

“…Moreover, this interaction sets the register for a network of interactions of the H3 N-terminus with the EZH2 surface that permits H3K27 to reach into the active site ( Figure 1D,F ). Consistent with our findings here, an independent recent study of a cryo-EM structure of PRC2 with co-factors JARID2 and AEBP2 bound to a mononucleosome with monoubiquitylated H2A ( Kasinath et al, 2020 ) identified very similar interactions of EZH2 with the nucleosomal DNA and the H3 N-terminus. Different forms of PRC2 that contain different accessory proteins and dock in different ways on chromatin therefore contact the substrate H3 N-terminus in the nucleosome through similar interactions.…”

“…The "bridge helix" ( Kasinath et al, 2020 ) which based on this study is likely constituted of the EZH2 residues 497–511, is located above V35 of the H3 tail. As can be seen when observing the density-modified map ( Terwilliger et al, 2020 ) of EZH2 sub -Nuc sub at lower threshold, it presumably engages in interactions with the nucleosomal DNA, the H3 tail and EZH2, as described in greater detail in Kasinath et al, 2020 . ( C ) The bottom view of EZH2 sub -Nuc sub cryo-EM density and model shows details of the vicinity of K36 with the corresponding density for the H3 tail, EZH2 and nucleosomal DNA.…”

“… ( A ) The front view of EZH2 sub -Nuc sub cryo-EM density and model shows details of the EZH2 CXC interaction with nucleosomal DNA. ( B ) The top view of EZH2 sub -Nuc sub cryo-EM shows a tubular density into which based on recent findings of the N ogales lab ( Kasinath et al, 2020 ) an α-helix was built. The "bridge helix" ( Kasinath et al, 2020 ) which based on this study is likely constituted of the EZH2 residues 497–511, is located above V35 of the H3 tail.…”

“…( B ) The top view of EZH2 sub -Nuc sub cryo-EM shows a tubular density into which based on recent findings of the N ogales lab ( Kasinath et al, 2020 ) an α-helix was built. The "bridge helix" ( Kasinath et al, 2020 ) which based on this study is likely constituted of the EZH2 residues 497–511, is located above V35 of the H3 tail. As can be seen when observing the density-modified map ( Terwilliger et al, 2020 ) of EZH2 sub -Nuc sub at lower threshold, it presumably engages in interactions with the nucleosomal DNA, the H3 tail and EZH2, as described in greater detail in Kasinath et al, 2020 .…”

“…The orange square indicates the region shown as a zoom-in in ( E ). ( D ) The back view of EZH2 sub -Nuc sub cryo-EM density and model shows details of the location of K36 and the "bridge helix" ( Kasinath et al, 2020 ). ( E ) Zoom-in views of H3K36 and its chemical environment.…”