Silencing mediated by Polycomb repressor complexes (PRCs) in embryonic stem cells (ESCs) can be accompanied by histone marks typical of active genes and RNA polymerase II (RNAPII) presence. A study by Pombo and colleagues analyzes this correlation between seemingly antagonistic Polycomb and RNAPII complexes, referred to as chromatin bivalency, at the genome-wide level. ChIP-seq analyses of PRC repression markers and RNAPII states in ESCs revealed that PRC targets exhibit a range of RNAPII variants. Silent, developmental PRC target genes were generally only associated with RNAPII with phosphorylated Ser5 in the C-terminal tail of RNAPII's largest subunit (RNAPII-S5p) at promoters and throughout coding regions. RNAPII-S5p produced transcripts that did not mature into mRNA and were not translated. Derepression of PRC target genes correlated with RNAPII-S5p levels, suggesting both physical and functional synergy between PRCs and RNAPII-S5p. A group of active genes was also associated with PRC binding, and many of these genes have roles in metabolism. These active PRC targets switch between PRC-repressed (S5p only) and PRC-active (S5p, S2p, S7p) states within the ESC population. It is thought that fluctuation from the PRC-repressed state to the active state occurs to variable extents across different PRC targets, resulting in different expression levels. (Cell Stem Cell 10, 157–170, 2012)