Hi-C libraries of two biological replicates were generated utilizing the recently published in situ Hi-C methodology with minor modifications (45 (link)). The genomes were digested with either DpnII (NEB) or HinfI (NEB) and 5΄ overhangs were filled in with Biotin-16-dUTP (Jena Bioscience). HiC libraries were sequenced at the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) sequencing facility and the HudsonAlpha Genomic Services Laboratory. Paired reads were mapped to the genome, processed and matrix resolution was calculated as described previously (45 (link)). To call significant interactions, contact matrixes were first normalized by ICE and processed by Fit-Hi-C at 1 kb resolution for all interaction distances between 3 kb and 1 Mb (46 (link),47 (link)). Interaction calls from Fit-Hi-C were further filtered by their probability of occurring in a random generated list of interactions. Using this secondary filtering step, we obtained lists of interactions below a secondary false discovery rate (FDR < 0.001). To ensure Fit-Hi-C calls were accurate across replicates and/or experimental conditions, KR normalized reads (and further normalized by total sequencing depth) from HinfI and DpnII were plotted and the spearman correlation was calculated.