Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2)

Abstract

The polycomb repressive complex 2 (PRC2) is the major methyltransferase for H3K27 methylation, a modification critical for maintaining repressed gene expression programs throughout development. It has been previously shown that PRC2 maintains histone methylation patterns during DNA replication in part through its ability to bind to H3K27me3. However, the mechanism by which PRC2 recognizes H3K27me3 is unclear. Here we show that the WD40 domain of EED, a PRC2 component, is a methyllysine histone-binding domain. The crystal structures of apo-EED and EED in complex respectively with five different trimethyllysine histone peptides reveal that EED binds these peptides via the top face of its β-propeller architecture. The ammonium group of the trimethyllysine is accommodated by an aromatic cage formed by three aromatic residues, while its aliphatic chain is flanked by a fourth aromatic residue. Our structural data provide an explanation for the preferential recognition of the Ala-Arg-Lys-Ser motif-containing trimethylated H3K27, H3K9, and H1K26 marks by EED over lower methylation states and other histone methyllysine marks. More importantly, we found that binding of different histone marks by EED differentially regulates the activity and specificity of PRC2. Whereas the H3K27me3 mark stimulates the histone methyltransferase activity of PRC2, the H1K26me3 mark inhibits PRC2 methyltransferase activity on the nucleosome. Moreover, H1K26me3 binding switches the specificity of PRC2 from methylating H3K27 to EED. In addition to determining the molecular basis of EED-methyllysine recognition, our work provides the biochemical characterization of how the activity of a histone methyltransferase is oppositely regulated by two histone marks.methyllysine-binding domain | WD40 repeat-containing protein | X-ray crystallography

Corepressor Protein CDYL Functions as a Molecular Bridge between Polycomb Repressor Complex 2 and Repressive Chromatin Mark Trimethylated Histone Lysine 27

“…Recently, two studies reported that EED, a component of PRC2, specifically binds to H3K27me3 via its C-terminal WD40 repeats and is responsible for the propagation of H3K27me3 to neighboring nucleosomes (44,45). We found that CDYL exhibits much stronger binding affinity for H3K27me3 than EED.…”

“…EED is therefore thought to be responsible for the propagation of H3K27me3 marks to neighboring nucleosomes or the sister chromatid (44,45). Researchers have noted, however, that the affinity of EED for H3K27me3 is significantly weaker than that of HP1 and Pc chromodomains for the H3K9me3 or H3K27me3 peptides, suggesting additional readers may contribute to the recruitment of PRC2 to pre-existing H3K27me3 (45). We compared the binding affinity of CDYL and EED for H3K27me3 through semi-quantitative histone peptide binding assays.…”

Structure of the MeCP2–TBLR1 complex reveals a molecular basis for Rett syndrome and related disorders

“…S3E). This mode of recognition differs from other WD40 domain peptide interactions involving basic motifs, such as recognition of modified arginine and lysine residues in histone tails, where aromatic cages stabilize the positive charges (30,31) (Fig. S4B).…”

Crystal structure of human nuclear pore complex component NUP43

“…Most of the loop residues are invisible and the length of the loop varies among Nup43 orthologs. In contrast, another loop between b1A and b1B (resi [19][20][21][22][23][24][25][26][27][28][29][30], exhibits an ordered conformation in the crystal structure. It is solvent accessible and protrudes at the bottom surface which might allow it to contact the helix region of hNup85, as implied by the cryo-EM structure of Nup107 complex (Fig.…”