Chromatin Immunoprecipitation (ChIP) Protocol

ChIP was performed, as previously described.^{9 (link)} Cells were cross-linked with 1% formaldehyde for 10 min and quenched with 125 mM glycine (Sigma-Aldrich) for 5 min. Cross-linked samples were lysed at 4 °C for 10 min and sonicated to generate chromatin fragments with an average size of 200–800 bp. Chromatin from 1 × 10⁶ cells was immunoprecipitated with Protein G Dynabeads and anti-RNApII (clone 4H8) and anti-Ser2 RNApII antibodies (both from Abcam, Waterloo, NSW, Australia). Cross-links in immunoprecipitated samples were reversed by incubating with 200 mM NaCl and 10 mg/ml of Proteinase K at 65 °C for 16 h and purified using the Qiagen PCR purification kit. Samples were analysed using qPCR with primers described in Supplementary Table SI.