Combinatorial Interactions Are Required for the Efficient Recruitment of Pho Repressive Complex (PhoRC) to Polycomb Response Elements

Abstract

Polycomb Group (PcG) proteins are epigenetic repressors that control metazoan development and cell differentiation. In Drosophila, PcG proteins form five distinct complexes targeted to genes by Polycomb Response Elements (PREs). Of all PcG complexes PhoRC is the only one that contains a sequence-specific DNA binding subunit (PHO or PHOL), which led to a model that places PhoRC at the base of the recruitment hierarchy. Here we demonstrate that in vivo PHO is preferred to PHOL as a subunit of PhoRC and that PHO and PHOL associate with PREs and a subset of transcriptionally active promoters. Although the binding to the promoter sites depends on the quality of recognition sequences, the binding to PREs does not. Instead, the efficient recruitment of PhoRC to PREs requires the SFMBT subunit and crosstalk with Polycomb Repressive Complex 1. We find that human YY1 protein, the ortholog of PHO, binds sites at active promoters in the human genome but does not bind most PcG target genes, presumably because the interactions involved in the targeting to Drosophila PREs are lost in the mammalian lineage. We conclude that the recruitment of PhoRC to PREs is based on combinatorial interactions and propose that such a recruitment strategy is important to attenuate the binding of PcG proteins when the target genes are transcriptionally active. Our findings allow the appropriate placement of PhoRC in the PcG recruitment hierarchy and provide a rationale to explain why YY1 is unlikely to serve as a general recruiter of mammalian Polycomb complexes despite its reported ability to participate in PcG repression in flies.

Author Summary

Polycomb Group (PcG) proteins are epigenetic repressors essential for development and cell differentiation. PcG proteins form five complexes targeted to specific genes by Polycomb Response Elements (PREs). How PcG complexes are recruited to PREs is poorly understood. Here we investigate the recruitment of PhoRC, a seemingly simple case of a complex that contains a sequence-specific DNA binding subunit: PHO (or the related protein PHOL). Unexpectedly, we find that the sequence specific binding of PHO is not a primary determinant for recruitment of PhoRC to PRE, which depends on the non-DNA binding subunit SFMBT and cross-talk with another PcG complex, PRC1. The binding of PhoRC is helped by PRC1 and, in turn, may stabilize the binding of PRC1. We propose that the recruitment based on combinatorial interactions enables the conditional binding of PcG proteins, which is important for switching the state of the target genes from repressed to active. The critical role of the cross-talk between PhoRC and PRC1 is further supported by the finding that in mammals, where the protein domains linking the two complexes are missing, the PHO ortholog YY1 has no implication in PcG repression, despite 100% conservation between DNA binding domains of YY1 and PHO.