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. 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.