Protein Extraction and Western Blotting

Normal rabbit IgG and rabbit polyclonal antibodies to INTS3, Actin, NABP2, INTS9, INTS11, CUL9, COBRA1 (NELFB), JunB, and HA were obtained from Bethyl Laboratories, Inc. Other rabbit antibodies used include NABP2, NABP1 (Proteintech), Pol II (N-20, Santa Cruz), Spt5 (N-20, Santa Cruz), Histone H2A (Abcam), Histone H3 (Abcam), Histone H2B (Millipore), Histone H4 (gift from CD Allis), INIP (gift from W Wang), Lamin A/C (Cell Signaling), and Cyclin A. The mouse monoclonal Pol II antibody 8WG16 (Millipore) was also used (Supplementary information, Figure S1). Cell lysates were generated in lysis buffer (50 mM Tris, pH 8.0, 1 mM EDTA, 50 mM NaF, 0.5% Triton X-100, and either 150 or 250 mM NaCl, as indicated) supplemented with protease and phosphatase inhibitors. CSK (100 mM NaCl, 300 mM Sucrose, 3 mM MgCl₂, and 10 mM PIPES, pH 6.8) extractions were generated as indicated. Select samples were generated by sonication (Bioruptor; Diagenode) in buffer containing 1 U/μl benzonase. Western blotting was performed as described previously^{32 (link)}.