Chromatin loops are an ancestral hallmark of the animal regulatory genome [DAP-seq]

We characterised the genome organization in non-bilaterian animals (sponge Ephydatia muelleri, ctenophores Mnemiopsis leidyi and Hormiphora californensis, placozoans Trichoplax adhaerens and Cladtertia collaboinventa, and cnidarian Nematostella vectensis) and close unicellular relatives (ichthyosporeans Sphaeroforma arctica, filasterean Capsaspora owczarzaki and choanoflagellate Salpingoeca rosetta) by combining high-resolution chromosome conformation capture (Micro-C) with profiling of chromatin marks (ChIP-seq), accessible genomic regions (ATAC-seq) and gene expression (MARS-seq). DAP-seq libraries were generated from native genomic DNA fragments or PCR-amplified DNA fragments lacking DNA methylation, which were bound by N-terminal HALO-tagged fusion proteins of CTEP1 and CTEP2.