Preparation of cross-linked chromatin free of RNA, sonication, and immunoprecipitation was performed as previously described (Vicent et al., 2014). For Pol II, ChIP was performed as described (Di Vona et al., 2015). DNA was quantified with Qubit HS kit (Invitrogen). Sequencing libraries were constructed from 1 ng of immunoprecipitated and input DNA using the Ovation Ultralow DR Multiplex System 1-8 and 9-16 kit (NuGen). To minimize false positives calling, several input libraries were sequenced to reach saturation with a coverage of 4 reads/bp for the human genome for each condition. The T47D ChIPs for TFIIIC, BDP1, RPC39, and H3K18ac were done in two separate biological repeats and pulled together. T47D ChIP for CTCF+S was done in a single biological experiment and compare with previously published CTCF ChIP data in absence of serum ((Le Dily et al., 2014)). RNA pol II ChIP was performed in a single biological experiment.