Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with MNase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cells were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures. Libraries were constructed according to the Illumina Tru-seq protocol.