The development of an embryo from a single fertilized cell is orchestrated by a large set of key regulatory genes whose activities need to be precisely controlled. Proteins from the Polycomb group (PcG) family maintain the inactive state of these genes by modifying the surrounding histone H3 tails. Here we report that these inactive genes contact other PcG-rich regions within otherwise active environments in the cell nucleus, suggesting the presence of repressive microenvironments. PcG positive genes interact independently from neighboring genes, depending on their linear distance and more global chromosome folding characteristics, with only moderate changes during embryonic development.