SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues

We have developed SpyChIP, a method that depends on covalent isopeptide bond formation, to identify sites of cell type-specific transcription factor (TF) occupancy in native physiological contexts without tissue dissociation or nuclei sorting. Using SpyChIP, we characterized the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two non-overlapping domains of the Drosophila haltere imaginal disc, revealing extensive region-specific Ubx-DNA binding events. The application of cell type-specific covalent bond formation to ChIP sets the stage for carrying out many other cell type-specific analyses and genetic manipulations in vivo that were previously unachievable. The 3xFLAG tag was inserted into the endogenous Hox genes Scr and Ubx. A 3xFLAG-Scr(YPWM*) allele, which encodes a mutant 3xFLAG-Scr protein unable to interact with the Hox cofactor Exd, was also generated. ChIP-seq (2 biological replicates) against various 3xFLAG-tagged Hox proteins was performed, and the wild type animals, which lacks the 3xFLAG tag, was used as negative control. ChIP-seq was also performed against the homeodomain TF Dll.