For ChIP-seq experiments, lysates were clarified from sonicated nuclei and cohesin-DNA complexes were isolated with antibody. HiC was performed as described (Rao et al., 2014) using MboI enzyme. For RNA-Seq, RNA was extracted using the RNeasy Mini Kit and treated with DNaseI. ChIP-Seq liibraries were prepared as follows: From 5 to 15 ng of immunoprecipitated chromatin (as quantitated by fluorometry) were electrophoresed on an agarose gel and independent sample-specific fractions of 100–200 bp were taken. Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. HiC libraries were performed as described (Rao et al., 2014) using MboI enzyme. For RNA-seq libraries, RNA was extracted as described and treated with DNaseI (Ambion). polyA+RNA was purified with the Dynabeads mRNA purification kit (Invitrogen), randomly fragmented and converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation Guide" (Part # 15008136 Rev. A). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.