John M. Denu

Mechanisms of chromatin dynamics, epigenetic, metabolism and signaling

The laboratory investigates the mechanism and biological function of reversible protein modifications involved in modulating signal transduction, chromatin dynamics and gene activation. Histones are one of the best examples of protein function regulated by modification, and are the target of an array of modifications including acetylation, phosphorylation and methylation. The dynamic and specific nature of these modifications has led to the proposal that there is a “Histone Code”, which when decoded would allow us to understand, for instance, what is required to maintain “silenced” or “active” chromatin. In general, histone acetylation (catalyzed by histone acetyltransferases) correlates with gene transcription, while hypo-acetylation (catalyzed by protein deacetylases) correlates with repression. To begin to understand this signaling code, we must first understand the mechanisms and regulation of the enzymes responsible for these modifications. A large component of our work is to understand the major enzyme families that catalyze these reactions.

Chromatin remodeling enzymes rely on co-enzymes derived from metabolic pathways, suggesting coordination between nuclear events and metabolic networks. A unique example of this link is the recently described NAD+-dependent protein/histone deacetylases. The founding member of this family, yeast Sir2 (silent information regulator 2), is involved in gene silencing, chromosomal stability, and ageing. Sir2-like enzymes catalyze a reaction in which the cleavage of NAD+, and histone/protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence on NAD+ and the generation of this potential second messenger offer new clues in understanding the function and regulation for nuclear, cytoplasmic and mitochondrial Sir2-like enzymes. Questions we are currently attempting to answer with this project: What is the physiological basis for the NAD+ -dependence? What are the cellular, acetylated-protein substrates for the various Sir2 homologues? What is the function of O-acetyl-ADP-ribose? What is the relationship between Sir2 enzyme function and metabolism? How are Sir2 enzymes regulated? How does Sir2 catalyze this unique reaction? To address these questions we are using a breadth of approaches that involve biochemistry, genetics, proteomics, enzymology, and use of a mammalian tissue culture system and yeast as a genetically tractable system to explore biological function.