Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [ChIP-seq]

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: Chromatin was prepared from 0-14 hour old embryos that were wildtype, Cp190[0], CTCF[0] or double[0] (i.e. CTCF[0] and Cp190[0]), in biological triplicates. Chromatin was also prepared from wildtype (WT), Cp190[KO] and su(Hw)[KO] mutant third instar larval central nervous systems (CNSs) in biological duplicates. ChIP-seq was performed with antibodies recognizing CTCF or Cp190. Multiplexed ChIP-seq libraries were sequenced paired-end on 2 (for embryo ChIP) or 1 (for larval CNS ChIP) lanes of a HiSeq4000 instrument.