Crosslinked, sonicated lysates were spun down to remove debris and protein-DNA complexes were immuno-precipitated. Immuno-complexes were washed, and protein-DNA complexes were eluted. After reversing crosslinks overnight at 65 C, the complexes were treated with RNase and proteinase K. DNA was isolated by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. Air-dried input and ChIP DNA was resuspended in nuclease-free water. ChIP and input DNA was end-repaired (End-It DNA End Repair, Epicentre #ER0720), had 'A' nucleotides added to the 3' ends of blunt ends (Klenow Fragement, NEB #M0212L), and ligated to adapters with 'T' overhangs using T4 DNA Ligase (Enzymatics #L6030-HC-L). Libraries were size-selected at ~350 bp (DNA fragment plus adapters) from a 2% agarose gel, gel extracted (QIAgen Gel extraction kit), and LM-PCR amplified (NEB Phusion High Fidelity PCR Master Mix, #M0531S) with 18 cycles. Libraries were then purified off AMPure XP magnetic beads to remove adapter dimers. All libraries were checked for the absence of adapter dimers by agarose gel and for the presence of quantitative ChIP enrichment at positive control loci prior to sequencing. Library concentrations were determined by PicoGreen assay.