Experiments were performed with 3.3 million cells and 3 microgram antibody per ChIP. Crosslinking was performed on the culture plates for 20 min and ChIP’ed DNA was purified by Qiaquick PCR purification Kit (QIAGEN). Total RNA was isolated using Trizol (Invitrogen) and subjected to chloroform extraction, isopropanol precipitation and ethanol washing according to the manufacturer's recommendations. 100µg total RNA was subjected to two rounds of poly(A) selection using the Oligotex mRNA Mini Kit (Qiagen), followed by DNaseI treatment (Qiagen). 100-200ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 seconds and purified using the RNAeasy Minelute Kit (Qiagen). The fragmented mRNA was used as template for cDNA synthesis using 5µg random hexamers using Superscript III Reverse Transcriptase (Invitrogen) according to the manufacturer's recommendations. Ds-cDNA was synthesized in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified using the Minelute Reaction Cleanup Kit (Qiagen). Quality control was performed by qPCR. DNA samples from ChIP-Seq and RNA-Seq were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Integrity of DNA libraries was confirmed by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing was performed with the Illumina Genome Analyzer IIx (GAIIx) or HiSeq 2000 sequencing platform according to standard Illumina protocols.