Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C]

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. About 100 2-6 hour old embryos that were wildtype, Cp190[0], or SF1[KO] mutants were mechanically disrupted and fixed in biological triplicates, and Hi-C libraries were prepared using MseI and Csp6I as restriction enzymes. Multiplexed Hi-C libraries were subjected to two successive rounds of capture using 5'-biotinylated 120 nt oligos with viewpoints in HOX genes and control loci. Capture-C libraries were then sequenced 150 bp paired-end on a Novaseq 6000 instrument.