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The bound complexes were pulled down with magnetic protein-A beads (New England Biolabs, Beverly, MA).
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DNA was immunoprecipitated using anti-RNAPII phosphor-S2 (AbCam no. ab5095, AbCam Cambridge, MA USA), anti-H3K27me3 (Cell Signaling no. 9756S, Danvers, MA, USA), or anti-CTCF (Santa Cruz Biotechnology no. sc-15914, Santa Cruz, CA, USA) antibody bound complexes were then pulled down using magnetic Dynabeads Protein A (Life Technologies, Carlsbad, CA, USA).
Antibody bound protein complexes were pulled down by adding 15 μl pre-washed Protein-A agarose and incubated 45 min at 4°C.
The structures for the inhibitor bound complexes were retrieved from Protein Data Bank with PDB codes: 1AJX [32] for AHA001 bound complex, 1HVR [33] for XK263 bound complex and 1HXW [34] for ABT538 bound complex.
Immune complexes were pulled down by gentle centrifugation at 1000 rpm for 2 minutes at 4°C.
Antigen Ab complexes were pulled down using protein-A beads.
Protein-antibody complexes were pulled down by adding beads to the solution for 2 hr.
The protein antibody complexes were pulled down by adding protein A/G-Sepharose beads.
RNA-protein complexes were pulled down and analyzed by western blot (Pierce).
Antibody chromatin complexes were pulled down with protein G-Dynabeads (Thermo Fisher Scientific), washed, and then eluted.
Lysate was incubated overnight with the appropriate antibody and immune complexes were pulled down with Protein G Sepharose (Sigma).
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