CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [Hi-C]

CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. Hi-C experiments on dissected larval CNSs of wildtype controls and CTCF[0] mutants that completely lack CTCF revealed that CTCF forms hundreds of physical boundaries in fly chromosomes. 60 wildtype (WT, corresponding to the Drosophila w[1118] reference strain) and CTCF[0] mutant third instar larval CNSs were dissected in biological triplicate and Hi-C libraries were prepared. Hi-C libraries were also prepared from single whole-bodied female flies that were WT or CTCF[0] mutant.