Chromatin immunoprecipitation (ChIP) assays were performed as previously described (37 (link),38 (link)). For ChIP-qPCR, 5 μg chromatin was immunoprecipitated with 1 μg of the indicated anti-CIITA antibody overnight at 4°C. Enrichment was determined using a 5-point genomic DNA standard curve and plotted as percentage of input chromatin or percentage of HLA-DRA enrichment. Standard error of the mean was used to represent experimental variation from three independent biological experiments. All ChIP primers used in this study are listed in Supplemental Table S2. For ChIP-seq, 30 μg chromatin was immunoprecipitated with 5 μg of anti-CIITA antibody ‘B’ generated in our lab (39 (link)), anti-H3K27ac (Millipore, 07-360), or anti-H3K4me3 (Millipore, 07-473) antibody overnight at 4°C. For anti-CIITA antibodies from Rockland Immunochemicals Inc. (100-401-249) and Diagenode (C15410062), 10 μg of antibody was prebound to 30 μl of Protein A beads and incubated overnight at 4°C with 30 μg of chromatin. Antibody–chromatin complexes were captured with Protein A beads (Invitrogen), cross-links reversed and DNA purified. Five percent of each chromatin suspension was removed prior to the immunoprecipitation and used as the Input fraction.