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. 2021 Jan 22;371(6527):eabc3393.
doi: 10.1126/science.abc3393.

JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications

Vignesh Kasinath  1 , Curtis Beck  2 , Paul Sauer  3   4 , Simon Poepsel  5   6 , Jennifer Kosmatka  2 , Marco Faini  7 , Daniel Toso  3 , Ruedi Aebersold  7   8 , Eva Nogales  1   2   4   9
Affiliations

JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications

Vignesh Kasinath et al. Science. .

Abstract

Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) cooperate to determine cell identity by epigenetic gene expression regulation. However, the mechanism of PRC2 recruitment by means of recognition of PRC1-mediated H2AK119ub1 remains poorly understood. Our PRC2 cryo-electron microscopy structure with cofactors JARID2 and AEBP2 bound to a H2AK119ub1-containing nucleosome reveals a bridge helix in EZH2 that connects the SET domain, H3 tail, and nucleosomal DNA. JARID2 and AEBP2 each interact with one ubiquitin and the H2A-H2B surface. JARID2 stimulates PRC2 through interactions with both the polycomb protein EED and the H2AK119-ubiquitin, whereas AEBP2 has an additional scaffolding role. The presence of these cofactors partially overcomes the inhibitory effect that H3K4me3 and H3K36me3 exert on core PRC2 (in the absence of cofactors). Our results support a key role for JARID2 and AEBP2 in the cross-talk between histone modifications and PRC2 activity.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

Fig. 1.
Fig. 1.. Cryo-EM structure of PRC2-AEBP2-JARID2 bound to a H2AK119ub1 nucleosome.
(A) Schematic representation of the proteins in the PRC2-AEBP2-JARID2 complex. Newly modeled regions in EZH2, JARID2, and AEBP2 that contribute to the interaction with the nucleosome are marked by dashed boxes. (B) Coomassie-stained gel showing all of the PRC2-core subunits, cofactors JARID2 and AEBP2, and histone proteins in the sample used for structural studies. (C) (Top) Cryo-EM density map for PRC2-AJ1–450 bound to an H2AK119ub1-containing nucleosome. (Bottom) Atomic model of PRC2-AJ1–450 bound to an H2AK119ub1-containing nucleosome, with EZH2 (SANT1) highlighted in gold, EZH2 (SANT2) in hot pink, EZH2 (SET) in blue, EED in light blue, RBAP48 in light purple, SUZ12 in green, JARID2 in magenta, AEBP2 in red, ubiquitin in orange, histone H3 in light pink, H2A in salmon, H4 and H2B in khaki, and nucleosome DNA in cyan. The image shown is a composite map where the PRC2 and nucleosome core correspond to the local resolution-filtered map from multibody refinement, whereas the ubiquitin, JARID2 UIM, and AEBP2 zinc finger densities correspond to the local resolution-filtered map from the consensus refinement. This color coding also applies to movie S1.
Fig. 2.
Fig. 2.. Interaction of EZH2 with the histone H3 tail and nucleosomal DNA.
(A) (Top) Cartoon representation of the newly defined EZH2 bridge helix (amino acids 497 to 513) that interacts with nucleosomal DNA and the H3 tail. (Left) Cryo-EM structure of the PRC2-AEBP2-JARID2 complex bound to an H2AK119ub1-containing nucleosome. The zoom out shows the bridge helix, with residues interacting with the EZH2 (SET) domain, nucleosomal DNA, and the histone tail depicted in stick representation. (Right) Helix wheel diagram for the bridge helix that shows the distribution of positively charged residues on the nucleosomal DNA interacting face (cyan), positive and hydrophobic residues on the EZH2 (SET) interacting face (blue), and the residues interacting with the backbone of the H3 tail (pink). aa, amino acids. (B) (Left) Density map of the histone H3 tail (amino acids 21 to 40) (contour level: 0.024) with the corresponding atomic model. Clear density for residues R26 and K27, which have been previously observed, as well as density for K23, K36, K37, and V35 allow us to define the full extent of interaction between EZH2 (SET) and the histone H3 tail. (Right) Extensive electrostatic and van der Waals interactions between the residues in EZH2 (SET) (blue; shown in green stick representation) and the histone H3 tail (black; shown in pink stick representation) guide the H3 tail into the catalytic site. (C) Close-up view of the interaction of EZH2 (SET and CXC) with the histone H3 tail (stick representation with corresponding cryo-EM density in transparency), which shows residues involved in either direct or indirect interaction with the histone H3 tail and nucleosome DNA that are also frequently found mutated in cancers as orange spheres [COSMIC database (57)]. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
Fig. 3.
Fig. 3.. JARID2 and AEBP2 interact with ubiquitin and the H2A-H2B surface.
(A) Cryo-EM density (contour level: 0.007) and model of JARID2 (amino acids 22 to 56) (magenta) showing how this segment of JARID2 is sandwiched between ubiquitin and the histone surface. The JARID2 UIM (amino acids 24 to 41) forms an alpha helix that interacts with both ubiquitin and nucleosomal DNA. JARID2 (amino acids 42 to 56), which contains positively charged arginine and lysine residues, sits on top of the conserved H2A-H2B acidic patch. The blue spheres with dashed lines connecting them indicate the H2AK119C-G76C conjugation. (B) The tandem C2H2 zinc fingers of AEBP2 (amino acids 50 to 116) interact with ubiquitin, the H2A-H2B surface, and nucleosomal DNA. The second AEBP2 zinc finger (amino acids 85 to 116) interacts extensively with an H2A-H2B surface that contains a mixture of positively and negatively charged residues (blue and orange balls, respectively).
Fig. 4.
Fig. 4.. HMTase activity of different PRC2 complexes on modified nucleosomes.
(A) Bar graph showing the comparison of end-point, cumulative HMTase activity (H3K27me1/me2/me3) of PRC2-core, PRC2-AEBP2, PRC2-JARID2 (amino acids 106 to 450), PRC2-AEBP2ΔZn-JARID2 (amino acids 1 to 450), and PRC2-AEBP2-JARID2 (amino acids 1 to 450) on unmodified nucleosomes (gray), H3K4me3-containing (orange), H3K36me3-containing (green), and H2AK119ub1-containing nucleosomes (magenta). The differences in end-point measurements that are statistically significant are indicated by the P values. (B) Western blot analysis comparing the H3K27me3 production for unmodified nucleosomes versus the H3K4me3-containing, H3K36me3-containing, and H2AK119ub1-containing nucleosomes.
Fig. 5.
Fig. 5.. Location of H3K36 at the PRC2-nucleosomal DNA interface.
Close-up view of the location of histone H3K36 and its interactions with nucleosomal DNA and PRC2. Bulky residues in PRC2 close to H3K36 are shown in stick representation, with the orange sphere indicating the potential space available for alternative conformations of the H3K36 side chain. On the right is the cryo-EM density (contour level: 0.024) with the atomic model shown, illustrating the distances between the H3K36 terminal amine group and the nearest bulky residues.
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