One histone modification which is significantly altered in Brg1-knockout ES cells is histone H3 lysine-27 trimethylation (H3K27me3) (Ho et al., 2011), which is a repressive mark deposited by Polycomb repressive complex 2 (PRC2). Many Brg1-dependent STAT3 targets, as well as genes that are co-activated by Brg1 and Oct4 or Sox2, gain aberrant H3K27me3 upon Brg1 deletion, even though PRC2 components are not upregulated and the overall level of H3K27me3 remains constant. The ectopic H3K27me3 domains are localized near promoters and transcription start sites (TSSs) where Brg1 peaks are normally located, suggesting a direct opposition between BAF and PRC2. Consistent with their functional antagonism, the genome-wide binding of Brg1 is largely mutually exclusive with Suz12, a PRC2 component (Ho et al., 2009a), and the ectopic H3K27me3 marks in Brg1-deleted cells can be suppressed by knockdown of Suz12 (Ho et al., 2011). This antagonistic relationship is conserved in flies, where homeotic transformations caused by PcG mutations can be suppressed by compensating trithorax mutations (Tamkun et al., 1992; Elfring et al., 1994; Kennison and Tamkun, 1988). However, the interaction seems more complex in
