Insulators, Not Polycomb Response Elements, Are Required for Long-Range Interactions between Polycomb Targets in Drosophila melanogaster

Abstract

The genomic binding sites of Polycomb group (PcG) complexes have been found to cluster, forming Polycomb “bodies” or foci in mammalian or fly nuclei. These associations are thought to be driven by interactions between PcG complexes and result in enhanced repression. Here, we show that a Polycomb response element (PRE) with strong PcG binding and repressive activity cannot mediate trans interactions. In the case of the two best-studied interacting PcG targets in Drosophila, the Mcp and the Fab-7 regulatory elements, we find that these associations are not dependent on or caused by the Polycomb response elements they contain. Using functional assays and physical colocalization by in vivo fluorescence imaging or chromosome conformation capture (3C) methods, we show that the interactions between remote copies of Mcp or Fab-7 elements are dependent on the insulator activities present in these elements and not on their PREs. We conclude that insulator binding proteins rather than PcG complexes are likely to be the major determinants of the long-range higher-order organization of PcG targets in the nucleus.

ACKNOWLEDGMENTS

We thank Christian Sigrist, Amy Csink, and Julio Vazquez for plasmids. Jackie Guiard helped produce the Flipper transgenic lines.

This work was supported in part by funds to V.P. from the Swiss National Science Foundation and from Rutgers University, to P.G. from the Russian Foundation for Basic Research (project 10-04-00474-a) and the Ministry of Science and Education of the Russian Federation (project 02.740.11.0289), and to O.K. from the Molecular and Cell Biology Program of the Russian Academy of Sciences.