Alternative splicing decouples local from global PRC2 activity

The Polycomb repressive complex 2 (PRC2) mediates epigenetic maintenance of gene silencing in eukaryotes via methylation of histone H3 at lysine 27 (H3K27). This complex interacts with sets of accessory factors to form two distinct subtypes, PRC2.1 and PRC2.2, that differ in their actions and chromatin targeting mechanisms. The underlying molecular mechanisms orchestrating PRC2 assembly are not yet fully understood. Here, we report that alternative splicing (AS) of the PRC2 core component SUZ12 generates an uncharacterised isoform SUZ12-S, which co-exists with the canonical SUZ12-L isoform in the same cell in virtually all tissues and developmental stages. We show that SUZ12-S drives PRC2.1 subtype formation and favours PRC2 dimerisation. While SUZ12-S is necessary and sufficient to ensure correct repression of Polycomb target genes via promoter-proximal H3K27me3 deposition, SUZ12-L is needed for maintaining global H3K27 methylation levels. Lastly, we show that mouse embryonic stem cells (ESCs) lacking either of the two isoforms have a slower exit from pluripotency upon differentiation stimulus. Our findings thus reveal a physiological mechanism regulating PRC2 assembly and higher-order interactions, with impacts on H3K27 methylation and gene repression.