Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody. Libraries were prepared according to manufacturer’s instructions (Illumina). Briefly, immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicentre), tailed with deoxyadenine using Klenow exo minus (NEB), and ligated to custom adapters with T4 Rapid DNA Ligase (Enzymatics). Fragments of 350 ± 50 bp were size-selected using Agencourt AMPure XP beads, and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 DNA polymerase (NEB). Libraries were quantified by qPCR using primers annealing to the adaptor sequence and sequenced at a concentration of 10 pM on an Illumina HiSeq 2000.