Colorado State University

Our lab studies the interface between the ubiquitin-proteasome pathway and transcriptional regulation. Modification of components of the transcription machinery by ubiquitin can serve as a regulatory switch that both activate and limit gene expression. We are using a variety of biochemical and genetic approaches to define the molecular mechanisms that underlie these seemingly opposite processes. Ubiquitin (Ub) is a small protein of 76 amino acids. It is ubiquitous among all eukaryotes and it is highly conserved from yeast to man. The covalent attachment of Ub to other proteins, i.e., ubiquitination, is used as a regulatory signal in a broad spectrum of biological processes. These include targeting proteins for proteasomal degradation, intracellular trafficking, transcription activation, DNA damage repair, and chromatin remodeling. These different outcomes are due in part to the versatility of the Ub modification, which can vary in the number of Ub molecules attached and, if polyubiquitin chains are formed, the linkage between ubiquitins in the chain. Moreover, like phosphorylation, ubiquitination is reversible. Proteins are subject to ubiquitination and deubiquitination, and the balance between these competing processes determines the fate of the substrate. For most genes, transcription has long been regarded as the dominant regulatory process for production of a functional protein. Rather unexpectedly, recent discoveries have indicated that the Ub-proteasome pathway (UPP) is intimately involved in transcriptional regulation. Studies from many laboratories revealed that a variety of transcription activators are mono- or polyubiquitinated, and in some cases, their regulation involves a transition from one state to the other. Furthermore, although histones were among the first proteins found to be ubiquitinated, it was demonstrated only recently that ubiquitinated histone H2A is a hallmark of repressed chromatin, and that dynamic ubiquitination and deubiquitination of histone H2B is required for gene activation. An understanding of the mechanisms that link ubiquitination with transcription has been hindered by our very limited knowledge of the machinery that establishes and maintains specific (poly)Ub signals; moreover, the Ub receptors that recognize ubiquitinated transcription activators and histones are largely unknown. Our long-term interest is to understand how Ub and Ub-proteasome pathways interface with transcriptional regulation. Currently we are studying functions of a particularly interesting deubiquitinating enzyme called Uch37. We discovered that Uch37 is a shared subunit of both the proteasome and the INO80 chromatin remodeling complex, providing a unique link between these two processes. In addition, we are using a combination of genetics and proteomics approaches to identify new players at the crossroads of UPP and transcription. These studies will provide mechanistic insights into activation and inactivation of some of the most tightly controlled transcription factors, such as c-Myc and Estrogen Receptor α.