Chromatin immunoprecipitation (ChIP) was performed based on the protocol as previously described (Lee et al., 2006), with modifications and adaptations. Briefly, a Diagenode bioruptor was used for sonication of formaldehyde-crosslinked cells on high for 30s on/ 30s off for 45 cycles in sonication buffer (20mM Tris-HCl; 150mM NaCl; 2mM EDTA; 0.1mM SDS; 1% Triton X-100; protease inhibitor (Thermo-scientific)). The Diagenode IP-star was also used for automation of the ChIP protocol in all but ST7_Suz12GT_K27, according to the manufacturer’s specifications. After purification of DNA, samples were used for to prepare libraries for Illumina sequencing. Library preparation is performed essentially as previously described (Schmidt et al., 2009); the amplification and size selection steps are reversed in order, and size selection was performed using Agencourt Ampure XP beads. Sequencing was run on an Illumina Hi-Seq (barcoded).