Chromatin immunoprecipitation was performed as previously described (Karimi et al Cell Stem Cell 2011) . Ten million TT2 and feeder depleted C3H/HeJ cells were harvested for nChIP-seq using antibodies against H3K4me3 (Abcam ab1012, 5 uL) and H3K9me3 (Active Motif 39161, 5 μl). Illumina library construction was performed as described in Brind'Amour et al, Nature communications, 2015.