Total RNA and DNA were extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion). 3ug Ribosomal RNA was depleted from total DNaseI-treated RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre). Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified as described for strand-specific sequencing. Native ChIP for H3K4me3 (antibody: cat. 07-473, lot 2019729, Millipore) was conducted. ChIP-seq libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina). 100 bp paired end sequencing for RNA-seq and 50 bp single end sequencing for ChIP-seq were performed by the Biomedical Sequencing Facility (BSF) in Vienna using the Illumina HiSeq 2000 platform.