To determine the interactome of RNA Polymerase II (RNAPII), HA-tagged RPB3 was stably expressed in U2OS cells. The cells were harvested followed by the native stepwise isolation of chromatin-associated RNAPII complexes. HA-RPB3 was immunoprecipitated and interacting proteins analyzed by quantitative mass spectrometry. U2OS cells expressing no HA-tagged protein were used for comparison.