Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC]

While Drosophila has widespread contact domains, most domain boundaries are formed independently of CTCF by unclear mechanisms. We genetically ablate the ubiquitous boundary-associated factor Cp190 and examine impacts on genome folding and developmental gene regulation in Drosophila embryos. We find that Cp190 is widely required to form fly domain boundaries that are distal from transcribed gene promoters, while promoter proximal boundaries are unaffected by Cp190 loss. Overall design: About 100 2-6 hour old embryos that were wildtype, Cp190[0], CTCF[0] or double[0] (i.e. CTCF[0] and Cp190[0]) mutants were mechanically disrupted and fixed in biological quadruplicates, and Hi-C libraries were prepared using MseI and Csp6I as restriction enzymes. Multiplexed Hi-C libraries were sequenced paired-end on HiSeq4000 instruments.