Interaction between acidic transcriptional activation domains of herpes simplex virus activator protein VP16 and transcriptional initiation factor IID

This chapter discusses the interaction between acidic transcriptional activation domains of herpes simplex virus activator protein VP16 and transcriptional initiation factor IID (TFIID). The chapter describes the use of protein affinity chromatography to identify interactions between acidic activation domains and TFIID. This chapter describes most of the technical details involved in using protein affinity chromatography to probe the structure of multiprotein complexes. The chapter focuses primarily on those technical considerations that are unique for RNA polymerase II and its interacting factors. Of major importance is the biochemical and genetic criteria that are useful for evaluating whether an observed interaction is likely to be specific and biologically important. Evidence suggests that transcription in vivo is carried out by RNA polymerase II holoenzyme containing most or the entire general initiation factors, as well as many other polypeptides. The interaction of activators with any one of these polypeptides in RNA polymerase II holoenzyme may recruit RNA polymerase II to the promoter and lead to transcriptional activation.