Chromatin immunoprecipitation (ChIP) was performed as previously described (Heintzman et al., 2007). Briefly, 10-20 million of cultured cells and ~0.2 g of frozen tissue samples were cross-linked in 1% formaldehyde at room temperature for 10 and 25 minutes, respectively. Cross-linked samples were sonicated until chromatin fragments were of 200-600 bp in length. Chromatin immunoprecipitation was carried out using 3-5 µg of antibody and 200 µg of chromatin preparation in RIPA buffer at 4 degree overnight. After five washes in RIPA and one wash with 1xTE buffer, chromatins were eluted and reverse cross-linked at 65 C overnight. DNA was purified after phenol extraction. Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).