Cryo-EM uncovers polycomb interactions

Polycomb family enzymes include the chromatin modifiers PRC1 and PRC2, which are involved in gene repression. Although the catalytic functions of these complexes are well known, their functional relationship is not. Kasinath et al. used cryoelectron microscopy (cryo-EM) to visualize the interactions between nucleosomes containing ubiquitinated histone H2A, the product of PRC1, and the PRC2-activating cofactors JARID2 and AEBP2, providing the molecular basis for PRC1-dependent recruitment of PRC2. They also show that JARID2 and AEBP2 partially overcome the inhibitory effect of PRC2 by two trimethyl lysine transcription marks on histones. This work suggests that PRC2 regulation involves an intricate interplay between PRC2 cofactors and histone posttranslational modifications.

Science, this issue p. eabc3393

Histone modification activity of the polycomb repressive complexes 1 and 2 (PRC1 and PRC2) is critical for the establishment and maintenance of gene expression patterns and, thus, to the maintenance of cell identity. Distinct classes of cofactor proteins are known to regulate the functional activity and interplay of these two complexes, but we presently lack a comprehensive, mechanistic understanding of this process. Furthermore, PRC2 cofactors like AEBP2 and JARID2 also play a role in mediating the cross-talk between different histone posttranslational modifications and PRC2 recruitment and activitya function that is important for the regulated control of gene expression.

PRC1 is an E3 ubiquitin ligase responsible for the monoubiquitination of histone H2A (H2AK119ub1), a histone mark recognized by PRC2 and linked to its genomic recruitment. We used cryoelectron microscopy (cryo-EM) and biochemical activity assays to probe the role played by PRC2 cofactors JARID2 and AEBP2 in the recognition of H2AK119ub1 and the regulation of PRC2 activity. We extended our cryo-EM and biochemical activity analysis to examine the possible role played by JARID2 and AEBP2 in the cross-talk between the histone H3K4me3, H3K36me3 modifications linked to transcriptionally active regions, and PRC2 activity.

We find that JARID2 recognizes both the ubiquitin moiety in H2AK119ub1 and the conserved histone H2A-H2B acidic patch. We also observe that the tandem zinc fingers of AEBP2 interact with ubiquitin and the histone H2A-H2B surface on the other side of the nucleosome. Biochemical assays show a secondary activation of PRC2 by JARID2 and AEBP2 on H2AK119ub1-containing nucleosomes besides the primary EED-mediated allosteric activation of PRC2 by methylated JARID2. Furthermore, we also find that the joint presence of JARID2 and AEBP2 partially reduces the inhibition of PRC2 methyltransferase activity by the transcriptionally active histone posttranslational modifications H3K4me3 and H3K36me3. Cryo-EM visualization of PRC2 that contains JARID2 and AEBP2 interacting with a H3K4me3-containing nucleosome shows the coexistence of states in which the histone H3 tail is either absent or engaged and reaching the catalytic site in PRC2, which provides a physical basis for the partial activity of the complex on H3K4me3-containing nucleosomes.

Our studies indicate that cofactors JARID2 and AEBP2 play a crucial role in both the recruitment and activation of PRC2 through their recognition of H2AK119ub1, which is generated by PRC1. Additionally, our work suggests that JARID2 and AEBP2 are likely to play a key role in regulating PRC2 activity on genomic regions with active transcription marks. The examination of the genomic distribution in embryonic stem cells of PRC2 core proteins together with JARID2 and AEBP2 will be important to further define their role in the tight regulation of PRC2 activity.

Although core PRC2 is a weak enzyme, it is allosterically activated by JARID2 and AEBP2. The presence of monoubiquitinated histone H2A, the product of PRC1 activity, is recognized by both JARID2 and AEBP2 through interactions that likely mediate recruitment of PRC2 to polycomb sites in the genome and further activate the methyltransferase activity of PRC2 on K27 of histone H3.

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 cryoelectron 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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JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications - Science Magazine