Profiling of PRC1 and PRC2 occupancy reveals the preponderant role of PRC1 in regulating the limb development program [RNA-seq]

The Polycomb Repressive Complexes (PRC) are key players in the regulation of tissue-specific gene expression through their ability to epigenetically silence developmental genes. They are subdivided into two multicomponent complexes, PRC1 and PRC2, functioning through post-translational modifications of histone tails. A large body of work has revealed functional interactions between PRC1 and PRC2, whereby trimethylation of lysine 27 on histone H3 (H3K27me3) by PRC2 contributes to the recruitment of canonical PRC1 (cPRC1). In parallel, a PRC2-independent binding of PRC1 has been uncovered and referred to as non-canonical PRC1 or variant PRC1 (vPRC1). Moreover, PRC1-dependent ubiquitination of lysine 119 on histone H2A is involved in recruiting PRC2/propagating PRC2-dependent H3K27 trimethylation. While it was initially assumed that cPRC1 and vPRC1 bind distinct targets, subsequent evidences pointed to cPRC1 and vPRC1 sharing a significant subset of their targets. In turn, this raises the question of PRC2/cPRC1 contribution to gene regulation. Here, we show that, in the developing limb, PRC2 inactivation barely affects PRC1 occupancy, consistent with the fact that the majority of PRC2-bound loci can also be bound by vPRC1 (RYBP-PRC1), both in wild type and PRC2 mutant limbs. Consistent with this, we found that loci bound by CBX2, a PRC1 subunit involved in the recognition of H3K27me3 and thereby recruitment of cPRC1, are, for the vast majority, also bound by vPRC1. Intriguingly, analysis of PRC2 mutant limbs revealed that while a large part of CBX2 occupancy is lost in absence of PRC2 function, as expected from the absence of H3K27me3, there is a significant number of loci retaining CBX2 binding and even few loci gaining CBX2 binding. Importantly, these loci corresponds to developmental genes and include most genes known as playing a key role in limb morphogenesis. Based on the importance of vPRC1 in gene silencing, our findings explain why PRC2 inactivation affects rather moderately the limb genetic program and questions the specific functional role of cPRC1/PRC2 in gene regulation.