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

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. RNA-sequencing of CNSs of CTCF[0] mutants that completely lack CTCF identified putative targets that are expressed in altered patterns. We find that CTCF recruits Centrosomal protein 190 kDa (Cp190) to CTCF's binding sites to co-regulate a substantial fraction of common genes that we find are also altered in CNSs of Cp190[KO] mutants carrying a CRISPR/Cas9-mediated deletion of the Cp190 open reading frame. Overall design: Wildtype (WT, corresponding to the Drosophila w[1118] reference strain), CTCF[0] and Cp190[KO] mutant third instar larval central nervous systems were dissected and stranded mRNA-sequencing libraries were prepared in biological triplicate.