PRC1 facilitates stage-specific enhancer-promoter contacts during Drosophila development

Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are highly conserved epigenetic factors that collaborate at multiple levels to maintain their target genes in a repressed state. However, recent reports suggest that PRC1 binds a subset of active promoters and enhancers devoid of the PRC2-mediated H3K27me3 repressive mark in both Drosophila and mammals. Here, we characterize the 3D epigenome of Drosophila Eye-antennal imaginal discs (EDs) and identify a large set of PRC1-bound promoters and enhancers that show preferential interactions in 3D. These PRC1-centered contacts are generally not pre-formed in embryos and coincide with increased PRC1 binding at the larval stage, a concomitant increase in expression during development and mis-regulation in PRC1 mutants. A detailed analysis of the dachshund locus indicates that PRC1-anchored chromatin loops are not only repressive structures, but might also be required for gene activation. Finally, a meta-analysis of RING1B binding profiles and 3D contacts during mouse neural differentiation suggests that this function might be conserved in mammals. These data suggest that, in addition to its known function in gene silencing, PRC1 binding to enhancers and promoters favors stage-specific 3D contacts to facilitate transcription of key developmental genes. Characterization of the 3D epigenetic landscape of the Polycomb Repressive Complex 1 (PRC1) during Drosophila development using ChIP-Seq, RNA-Seq and Hi-C methods. Please note that the *merge* processed files were generated by merging all the replicates and are linked to the corresponding rep1 sample records.