Crosslinked cells were treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) and nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) and subjected to sonication. IP was performed using Rad21 antibody(Abcam, #ab992) or CTCF antibody (Millipore, #07-729). IP and Input DNA were de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns. ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645)