Chromosome-level organization of the regulatory genome in the Drosophila nervous system [Hi-C]

Here we present evidence for a new level of genome folding, whereby distant domains megabases apart fuse to form meta-domains. Within meta-domains, certain gene promoters pair with structural intergenic elements in the distant TAD. These long-range associations occur in a large fraction of Drosophila neurons, but support transcription in only a subset of cells in the nervous system. Most of the associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that one of these factors, GAF, plays a direct role in this process. Overall design: Drosophila melanogaster and Drosophila virilis dissected central nervous systems (CNSs) or CNS cell types (neuroblasts, glia or neurons) isolated from staged Drosophila melanogaster embryos were subjected to Hi-C.