Proteomics reveals a physical and functional link between hepatocyte nuclear factor 4α and transcription factor IID

Proteomic analyses have contributed substantially to our understanding of diverse cellular processes. Improvements in the sensitivity of mass spectrometry approaches are enabling more in-depth analyses of protein-protein networks and, in some cases, are providing surprising new insights into well established, longstanding problems. Here, we describe such a proteomic analysis that exploits MudPIT mass spectrometry and has led to the discovery of a physical and functional link between the orphan nuclear receptor hepatocyte nuclear factor 4a (HNF4α) and transcription factor IID (TFIID). A systematic characterization of the HNF4α-TFIID link revealed that the HNF4α DNA-binding domain binds directly to the TATA box-binding protein (TBP) and, through this interaction, can target TBP or TFIID to promoters containing HNF4α-binding sites in vitro. Supporting the functional significance of this interaction, an HNF4α mutation that blocks binding of TBP to HNF4α interferes with HNF4α transactivation activity in cells. These findings identify an unexpected role for the HNF4α DNA-binding domain in mediating key regulatory interactions and provide new insights into the roles of HNF4α and TFIID in RNA polymerase II transcription.