Regulation of TFIIH ATPase and kinase activities by TFIIE during active initiation complex formation

The general transcription factor TFIIE, together with other general transcription factors, is essential for transcription initiation by RNA polymerase II. TFIIE stimulates the TFIIH-dependent kinase activity that phosphorylates the carboxy-terminal domain of the largest subunit of RNA polymerase II, and possesses a helicase activity. Here we show that human TFIIH has DNA-dependent ATPase activity and we characterize the stimulatory effect of TFIIE on both the ATPase and kinase activities. We demonstrate that extensive phosphorylation of RNA polymerase II occurs in a TFIIE-dependent manner in both the absence and presence of DNA but, in the latter case, only at a late stage of preinitiation complex assembly. We also show that TFIIH specifically phosphorylates three general transcription factors, human TFIID tau (TBP), TFIIE-alpha and TFIIF-alpha (RAP74).