Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2

Abstract

Polycomb repressive complex 2 (PRC2) silences gene expression through trimethylation of K27 of histone H3 (H3K27me3) via its catalytic SET domain. A missense mutation in the substrate of PRC2, histone H3K27M, is associated with certain pediatric brain cancers and is linked to a global decrease of H3K27me3 in the affected cells thought to be mediated by inhibition of PRC2 activity. We present here the crystal structure of human PRC2 in complex with the inhibitory H3K27M peptide bound to the active site of the SET domain, with the methionine residue located in the pocket that normally accommodates the target lysine residue. The structure and binding studies suggest a mechanism for the oncogenic inhibition of H3K27M. The structure also reveals how binding of repressive marks, like H3K27me3, to the EED subunit of the complex leads to enhancement of the catalytic efficiency of the SET domain and thus the propagation of this repressive histone modification.

Structure of the PRC2 complex and application to drug discovery

“…The complex crystal structures of all three groups contain EZH2, EED and the VEFS domain of SUZ12. They show that the PRC2 complex has at least two states: a basal state, as shown for PRC2 in the absence of a stimulatory peptide, and a stimulated state in which the same complex contains either the stimulatory H3K27me3 peptide or a stimulatory JARID2-K116me3 peptide [93,94] . These complexes were further stabilized by binding of SAH cofactor and a substrate-trapping H3K27M peptide in the catalytic cleft.…”

“…Recently, three PRC2 structures were determined: PRC2 of the thermophilic fungus Chaetomium thermophilum (ctPRC2) in a stimulated and basal state [93] , human PRC2 in a stimulated state [94] and a human/chameleon (Anolis carolinensis) hybrid PRC2 [Hs/AcPRC2] in complex with a pyridine-based PRC2 inhibitor [95] . Although human and fungal PRC2 have low sequence conservation, they share a similar overall structure.…”

“…These complexes were further stabilized by binding of SAH cofactor and a substrate-trapping H3K27M peptide in the catalytic cleft. H3K27M is an oncogenic mutant histone that binds the EZH2 subunit and inhibits active PRC2 by blocking its methyltransferase activity [94] .…”

“…The catalytic module is composed of SUZ12(VEFS) and the four C-terminal domains of EZH2, consisting of the motif connecting SANT1 and SANT2 (MCSS), SANT2 (in fungal PRC2 SANT2-like domain), the cysteine-rich domain (CXC), and the Su(var)3-9, enhancer of zeste, trithorax domain (SET). The SET domain is positioned above EED and SUZ12(VEFS) and adjacent to the SRM [93,94] .…”

“…Thus, the first and last of the domains from the EZH2 N-terminal fragment interact to close the ring that EZH2 forms around the EED subunit [94] . The EBD and BAM domains pack against the bottom and side of the EED.…”