Cells were processed using the truChIP Chromatin Shearing Kit (Covaris, 520127) following manufacturer's instructions. 20 million nuclei were sonicated in 1mL tubes using a Covaris M220 to obtain chromatin frgament size of 250-500bp. Sonicated chromatin was centrifuged at 14,000 rpm at 4ºC for 10 minutes and the supernatant was isolated for subsequent steps. In parallel, Drosophila S2 cells were fixed, lysed and sonicated as described above. For quantitative ChIP analysis E14 mESC input chromatin was mixed with Drosophila S2 chromatin (0.05% of total chromatin) after sonication. Chromatin associated to each histone mark was obtained by incubating sonicated chromatin with the corresponding antibody. Libraries were costructed using the KAPA Hyperprep kit following manufacturer's instruction, except that 1.25 µM of Illumina compatible indexed adapters (Pentabase) were ligated to A-tailed DNA.