The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [delSBD-ChIP-Rx]

Polycomb group proteins maintain gene expression patterns established during early development, with Polycomb Repressive Complex 2 (PRC2) methyltransferase a key regulator of cell differentiation, identity and plasticity. Consequently, extensive somatic mutations in PRC2, including gain- or loss- of function (GOF or LOF), are observed in human cancers. The regulation of chromatin structure by PRC2 is critically dependent on its EZH2 (Enhancer of Zeste Homolog 2) subunit, which catalyzes the methylation of histone H3 lysine 27 (H3K27). Recent structural studies of PRC2 revealed extensive conformational changes in the non-catalytic EZH2 N-terminal SANT-Binding Domain (SBD) during PRC2 activation, though the functional significance remains unclear. Here, we investigate how the SBD regulates PRC2 function. The domain is highly conserved in metazoans, dispensable for PRC2 assembly and chromatin localization, yet required for genome-wide histone H3K27 methylation. Further, we show that an intact SBD is necessary for the proliferation of EZH2-addicted lymphomas, and its deletion in the presence of EZH2 GOF mutations inhibits cancer cell growth. These observations provide new insights to the regulation of PRC2 activity in normal development and malignancy. EZH2, SUZ12, H3K27me3, H3K27me2 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD. MTF2, JARID2 ChIP-seq experiment of A1 (WT) mESCs, EZH2 KO and EZH2 ΔSBD. Cut and Run experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF) RNA-seq experiment of Lymphoma Karpas-422 cells, with shEZH2, and rescue with EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF), 72 hours after EZH2-KO induction. H3K27me3 ChIP-Rx experiment with S2 chromatin spike-in of A1 (WT) mESC with the expression of EZH2-Y641 (GOF) and EZH2-ΔSBD-Y641N (ΔSBD-GOF)