RNA: Cells were harvested in Isol-RNA lysis reagent (5 PRIME) and purified according to the manufacturer's instructions. ChIP-seq: Crosslinking: For MED1/TRAP220, SMC1, P300, HDAC2, HDAC3 and NCoR ChIP-seq: Cells were crosslinked by 2 mM disuccinimidyl glutarate (DSG) for 20-30 min at RT followed by 1% formaldehyde for 10 min at RT. Crosslinking was quenched by addition of 0.125M glycine for 10 min. For CTCF and histone mark ChIP-seq: Cells were crosslinked in formaldehyde only as described above. Sonication: For MED1/TRAP220, SMC1, CTCF and histone marks: Crosslinked cells were scraped in ChIP lysis buffer (0.1% SDS, 1% Triton X-100, 0.15M NaCl, 1mM EDTA, 20mM Tris, pH=8) and sonicated for 40 cycles (approximately 10-12 million crosslinked cells in 1.5 ml lysis buffer was sonicated in 15 ml tubes, 30 sec on, 30 sec off, maximum intensity) in a Bioruptor (Diagenode). For P300, HDAC2, HDAC3 and NCoR: Crosslinked cells were scraped in high SDS lysis buffer (1% SDS, 20mM EDTA, 50mM Tris, pH=8) and rotated 2h at 4C to release nuclei. A buffer change was done on pelleted nuclei to the ChIP lysis buffer described above before sonication for 7 cycles (nuclei from approximately 10-12 million crosslinked cells in 0.3 ml lysis buffer was sonicated in 1.5 ml tubes, 30 sec on, 30 sec off, maximum intensity) in a Bioruptor (Diagenode). Immunoprecipitation was performed overnight using specific antibodies. After washing, IP’ed chromatin was decrosslinked overnight at 65 °C and DNA was purified by phenol-chloroform extraction. Crosslinking of cells for Hi-C and PCHi-C: Approximately 50-80 millions of 3T3-L1 cells were crosslinked for 10 min by 2% formaldehyde in PBS. Crosslinking was quenched by addition of 0.125M glycine. Cells were incubated at room temperature for 5 min and then on ice for 15 min. Crosslinked cells were washed once in cold PBS, and the cell pellets were flash frozen in liquid nitrogen and stored at -80°C. mRNA-seq: Libraries were prepared from purified RNA (TruSeq Illumina mRNA prep kit) and sequenced according to the manufacturer’s instructions (HiSeq v4 Illumina SR sequencing kit). ChIP-seq: Libraries were prepared from the purified DNA using the NEB ChIPseq prep kit and samples were sequenced according to the manufacturer’s instructions (HiSeq v4 Illumina SR sequencing kit). Hi-C : Hi-C library generation was carried out with in-nucleus ligation as described previously (Nagano et al., 2015). PCHi-C: Capture Hi-C of promoters was carried out with SureSelect target enrichment (SureSelectXT Custom 3-5.9Mb library), using the custom-designed biotinylated RNA bait library and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies). Between 500 ng to 1 µg of Hi-C library were captured. After library enrichment, a post-capture PCR amplification step was carried out using PE PCR 1.0 and PE PCR 2.0 primers with 4 PCR amplification cycles. RNA-seq, ChIP-seq, Hi-C, PCHi-C