Non-core subunits of the PRC2 complex are collectively required for its target site specificity

The Polycomb repressive complex 2 (PRC2) catalyzes H3K27 methylation across the genome, which through involvement in transcriptional regulation is critical in establishment of cell identity. Because of its essential function during development and in cancer, understanding the establishment of genome-wide H3K27 methylation patterns has been the focus of intense investigation. PRC2 methylation activity is abundant and dispersed throughout the genome, but highest activity is specifically directed to a subset of target regions that are stably occupied by the complex and highly enriched for H3K27me3. Here we show, by systematically knocking out single and multiple non-core subunits of the PRC2 complex in mouse embryonic stem cells (mESCs), that they each contribute in directing PRC2 activity to targets sites. Furthermore, combined knockout of six non-core subunits reveal that, while dispensable for global H3K27 methylation levels, the non-core PRC2 subunits are collectively required for focusing H3K27me3 activity to specific sites in the genome. Overall design: H3K27me3, SUZ12, JARID2, PCL2 and Flag enrichment profiles (ChIPseq) analyzed in mouse ES cells which are wildtype, knockout for one or multiple PRC2 subunits (SUZ12, AEBP2, EPOP, JARID2, PCL1, PCL2, PCL3), or expressing Flag-tagged SUZ12 fragment in SUZ12 KO cells or Flag-tagged PRC2 subunit (AEBP2, EPOP, JARID or PCL2) in cells with combined knockout of all non-core PRC2 subunits. RNAseq analysis in mouse ES cells which are wildtype or knockout for one or multiple PRC2 subunits (SUZ12, AEBP2, EPOP, JARID2, PCL1, PCL2, PCL3).