ChIP was performed using a ChIP-IT kit from Active Motif (Carlsbad, CA), following the manufacturer’s recommended protocol with minor modifications as described in supplementary methods. Antibodies used were: anti-H3K4me3 (17-614, Millipore), anti-H3K27me3 (07-449, Millipore), anti-V5 (R960-25, Life Technologies), anti-FLAG (M2. Sigma Aldrich) and anti RNA Polymerase II (CTD4H8, Santa Cruz). ChIP DNA (10 ng) was end-repaired and phosphorylated using T4 polymerase, Klenow, and T4 Polynucleotide Kinase. An A-overhang was introduced using exo-Klenow and then ligated to Illumina paired-end adapters with DNA ligase. Ligated products were size selected on a Caliper LabChip XT to a mean size of 240bp +/- 20%. The libraries were amplified with Illumina PCR Primer InPE1.0, PCR Primer InPE2.0 and PCR Primer Indexes and sequenced on Illumina GAIIx or MiSeq sequencers under a single-end run protocol.