Alternative splicing decouples local from global PRC2 activity

PRC2 mediates epigenetic maintenance of gene silencing in eukaryotes via methylation of H3K27. This complex interacts with sets of accessory factors forming two distinct subtypes (PRC2.1 and PRC2.2) that differ in their action and chromatin targeting mechanisms. However, the underlying molecular mechanisms orchestrating PRC2 assembly are not yet understood. Here, we report the identification of an alternative splicing event involving that alternative splicing of the PRC2 core component SUZ12 exon 4 which generates two isoforms coexisting in the same cell in virtually all tissues and developmental stages. Skipping this exon generates a previously uncharacterized isoform (SUZ12S) that forces the formation of the PRC2.1 subtype and favors PRC2 dimerization. Our results suggest that while SUZ12L is needed for maintenance of global H3K27 methylation levels, While SUZ12S is necessary and sufficient to ensure correct repression of Polycomb target genes via promoter-proximal H3K27me3 deposition, the full-length SUZ12L isoform is needed for maintenance of global H3K27 methylation levels. Lastly, we show that mouse embryonic stem cells lacking either of the two isoforms display impaired exit from pluripotency upon differentiation stimulus. Our findings thus reveal evidence for the existence of a physiological mechanism regulating PRC2 assembly and higher order interactions, with an impact on H3K27 methylation and gene repression.