PRC2-associated chromatin contacts in the developing limb reveal a possible mechanism for the atypical role of PRC2 in HoxA gene expression

Preventing inappropriate gene expression in time and space is as fundamental as triggering the activation of tissue/cell-type specific factors at the correct developmental stage and in the correct cells. Here, we study the impact of Polycomb Repressive Complex 2 (PRC2) function on HoxA gene regulation. We analyze chromatin conformation of the HoxA cluster and its regulatory regions and show that in addition to the well-known role of PRC2 in silencing Hox genes via direct binding, its function is required for the changes in HoxA long-range interactions distinguishing proximal limb from distal limb. This effect stems from the differential PRC2 occupancy over the HoxA cluster and, at least in part, from the ability of PRC2-bound loci to engage in long-range contacts. Unexpectedly, PRC2 also impacts chromatin conformation in a way that promotes enhancer-promoter contacts required for proper HoxA expression, pointing to a dual role of PRC2 in gene regulation. ChIP analysis of SUZ12, RING1B and H3K27ac in proximal and distal limb tissue at E12.5