ES cells were fixed with 1% formaldehyde, lysed in cell lysis buffer with proteinase inhibitor cocktail and PMSF. Chromatin was sonicated in a Bioruptor and fragments of ~200-500 base pairs were diluted with RIPA buffer and immunoprecipitated with anti-HA polyclonal antibody (ChIP-grade ab 9110; Abcam) coupled to magnetic beads coated with anti-rabbit immunoglobulin (overnight, 4ºC). Beads were washed extensively and precipitates eluted, reverse crosslinked, and DNA was purified on Qiagen columns. DNA libraries were prepared for sequencing using Trueseq DNA Sample Preparation kit (Illumina) protocols