Canonical and variant PRC1 functionally converge on PRC2 targets to regulate transcriptional programs during mouse limb development

The developing limb is a classical model system for studying genetic aspects of pattern formation and mechanisms underlying tissue differentiation. The transition from early to differentiated cell fates during limb bud development requires the precise spatial and temporal regulation of gene activation and silencing programs. However, how transcriptional silencing of early genes is achieved remains poorly understood. Here, we investigate the role of the Polycomb Repressive Complexes (PRC1 and PRC2) in this transcriptional transition in the developing mouse forelimb. We show that the progression from early (E10) to late (E12.5 distal) forelimb stages is associated with shifts in promoter-proximal SUZ12 occupancy at early developmental genes. Conditional inactivation of Eed results in derepression and ectopic distal expression of early genes, which occurs despite the persistence of RING1B and H2AK119Ub. We further identified that SUZ12/RING1B co-occupied targets were also bound by RYBP-containing variant PRC1, indicating parallel recruitment of canonical and variant PRC1. Functional analyses of the combined inactivation of EED and RING1B reveal severe limb malformations and significant gene derepression, exceeding the effects of single EED or RING1B inactivation. Together, our findings demonstrate that the functional convergence of canonical and variant PRC1 at key developmental loci is required to maintain robust transcriptional silencing and regulate transitions in gene expression programs required for proper limb morphogenesis.