- The basal factor TFIIE is an important component of the RNA polymerase II transcription machinery. In our efforts to determine the role of TFIIE in the transcription process, we have begun to define the interactions between TFIIE and other basal transcription factors. Here we report that TFIIE binds selectively to the nonphosphorylated form of RNA polymerase II (IIa) and that this interaction is mediated by the 56-kD subunit of TFIIE. Additional binding studies reveal that TFII can interact with TBP as well as TFIID and that this interaction is mediated primarily via the 56-kD subunit. Our studies indicate that TFIIE also interacts with both subunits of TFIIF and with TFIIH, a multisubunit basal factor reported to catalyze RNA polymerase II CTD phosphorylation. Protein affinity assays demonstrate that TFIIE binds directly to ERCC-3, a DNA repair protein associated with TFIIH. More importantly, TFIIE affinity resin can selectively isolate transcriptionally competent TFIIH from a partially purified preparation and thereby may recruit TFIIH to the transcription complex in vivo. These multiple interactions between TFIIE, Pol II and TFIIH support a model in which TFIIE plays a role in promoter clearance as well as in the recruitment of proteins required for transcription-coupled DNA repair.