Opposing function of AEBP2 isoforms fine-tune PRC2 catalytic activity

Polycomb repressive complex 2 (PRC2) represses genes through catalyzing H3K27me3, a histone modification essential for maintenance of cellular identity. The complex's catalytic activity, chromatin localization, and propagation along chromatin are modulated by accessory proteins such as AEBP2, MTF2, JARID2, and PALI, which is specifically required for mouse embryogenesis. AEBP2 exists in distinct isoforms: a short isoform that enhances PRC2 catalytic activity and promotes H3K27me3 spreading, facilitating robust gene repression, and a long isoform whose function has remained unclear. Here, we report that the N-terminal region of the long isoform contains conserved DE-motifs unique to this isoform that inhibit PRC2 activity, including both H3K27 methylation and EZH2 automethylation, suggesting that these motifs interfere with the automethylation loop proximal to the SET domain. Notably, re-expression of the long isoform in Mtf2/Jarid2/Aebp2 triple-knockout mouse embryonic stem cells failed to restore H3K27me3 and caused defective differentiation. These findings uncover an isoform-specific regulatory mechanism by which AEBP2 controls PRC2 activity and contributes to a broader understanding of the dynamic regulation of PRC2 during development.