Abstract: RNA polymerase II is a multisubunit enzyme that requires many auxiliary factors for its activity. Over the years, these factors have been identified using both biochemical and genetic approaches. Recently, the systematic characterization of protein complexes by TAP and mass spectroscopy has allowed the identification of new components of well-established complexes, including the RNA pol II holoenzyme. Krogan et al. (1) have described in yeast a novel and highly conserved factor, Iwr1p, that physically interacts with most of the RNA pol II subunits. Here we show that Iwr1p genetically interacts with components of the basal transcription machinery and plays a role in both the basal and regulated transcription. We report that the mutation of the IWR1 gene is able to bypass the otherwise essential requirement for the TBP-binding factor NC2, which occurs with different components of the basal transcription machinery, including TFIIA and subunits of the mediator complex. Deletion of the IWR1 gene leads to an altered expression of specific genes, including phosphate-responsive genes and SUC2. Our results show that Iwr1p is a nucleo-cytoplasmic shuttling protein and suggest that Iwr1p acts early in the formation of the pre-initiation complex by mediating the interaction of certain activators with the basal transcription apparatus.