For H3K36me3, H3K79me2 and Pol II ChIP-seq experiments: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed with IP-Star (Diagenode) buffer. Chromatin was sonicated on the Bioruptor (Diagenode) to an average size of 0.2-1 kb. ChIP was performed on chromatin from approximately 5 million cells with 3 μg of antibody (above) using the IP-Star Automated System (Diagenode), and 2.5% of chromatin was used for each whole cell extract (WCE). Following reversal of crosslinks, sample and WCE DNA was purified. ChIP DNA was dissolved in water and placed on the SPRI-TE (Beckman Coulter) for Illumina sample preparation. For H3K9ac, H3K56ac and LEO1 ChIP-seq experiements: approximately 5x10^7 formaldehyde-crosslinked ESCs were lysed and prepared for ChIP-seq according to the protocol described by Black et al., (2013) (PMID: 23871696). For H3K9ac, H3K56ac and LEO1 ChIP-seq experiments: libraries were constructued according to the protocol described by TruSeq ChIP Sample ptreparation from Illumina Part# 15023092 Rev.B, Cat# IP-202-9001DOC.