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Faculty: John Denu, PhD

Dept: Professor, Biomolecular Chemistry
Contact: 2178 Wisconsin Institute for Discovery
Training Areas: Molecular and Cellular Pharmacology

Research Interests

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.

Other projects involve understanding the mechanism of catalysis and regulation for the CBP/p300 and MYST families of histone/protein acetyltransferases, as well as the dual specificity protein phosphatases that down-regulate mitogenic signal tranduction through dephosphorylation of the MAP kinases. Mutations in several of these enzyme families can cause miss-regulation of gene transcription and lead to such diseases as cancer. Through these studies will come an understanding of biological function and enzyme mechanism, which will undoubtedly lead to the design of rational therapeutics that target these novel enzymes or the pathways they regulate.

Honors & Awards

John Denu, PhD, and Catherine Fox, PhD, both professors in the Department of Biomolecular Chemistry, recently received a two year Collaborative Research Award in the amount of $240,000 from the National Institutes of Health to examine the epigenetic mechanisms that regulate chromosome duplication, a process fundamental to cell proliferation. Fox's lab focuses on understanding how a protein complex critical to chromosome duplication functions. Denu's laboratory, particularly over the last several years as Denu has served as the director of the Epigenetics Theme in the Wisconsin Institute of Discovery, has established new technologies for probing this epigenetic code at the biochemical level. This award will allow the laboratories of Denu and Fox to team up and define the epigenetic mechanisms that ORC uses to duplicate chromosomes.

John Denu, PhD, professor, Department of Biomolecular Chemistry, has been asked to serve on the editorial board of the Journal of Biological Chemistry. His renewable board appointment began in fall 2013 and will run through 2018.

Selected Publications

(Find publications on PubMed)

  • Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ, Westphall MS, Pagliarini DJ, Prolla TA, Assadi-Porter F, Roy S, Denu JM, and Coon JJ (2013). Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol Cell. 2013 Jan 10;49:186-99. Epub 2012 Nov 29. PMID: 23201123
  • Dominy JE Jr, Lee Y, Jedrychowski MP, Chim H, Jurczak MJ, Camporez JP, Ruan HB, Feldman J, Pierce K, Mostoslavsky R, Denu JM, Clish CB, Yang X, Shulman GI, Gygi SP, Puigserver P (2013). The deacetylase Sirt6 activates the acetyltransferase GCN5 and suppresses hepatic gluconeogenesis. Mol Cell. 2012 Dec 28;48:900-13. Epub 2012 Nov 8.PMID:23142079
  • Feldman JL, Dittenhafer-Reed KE, and Denu JM (2012). Sirtuin catalysis and regulation. J Biol Chem. 2012 Dec 14;287(51):42419-27. Epub 2012 Oct 18. Review. PMID:23086947
  • Denu JM and Gottesfeld JM. Minireview series on sirtuins: from biochemistry to health and disease. J Biol Chem. 2012 Dec 14;287(51):42417-8. doi: 10.1074/jbc.R112.428862. Epub 2012 Oct 18. No abstract available.PMID: 23086946
  • Wagner EK, Nath N, Flemming R, Feltenberger JB, and Denu JM. Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry. 2012 Oct 16;51(41):8293-306. doi: 10.1021/bi3009278. Epub 2012 Oct 2. PMID: 22994852
  • Wagner EK, Albaugh BN, and Denu JM (2012). High-throughput strategy to identify inhibitors of histone-binding domains. Methods Enzymol. 2012;512:161-85. PMID: 2910207
  • Oliver SS, Musselman CA, Srinivasan R, Svaren JP, Kutateladze TG, and Denu JM(2012). Multivalent recognition of histone tails by the PHD fingers of CHD5. Biochemistry. 2012 Aug 21;51(33):6534-44. Epub 2012 Aug 8. PMID: 22834704
  • Denu JM (2012). Fortifying the link between SIRT1, resveratrol, and mitochondrial function. Cell Metab. 15:566-7. PMID: 22560207
  • Yu W, Dittenhafer-Reed KE, and Denu JM (2012). SIRT3 Protein Deacetylates Isocitrate Dehydrogenase 2 (IDH2) and Regulates Mitochondrial Redox Status. J Biol Chem. 287:14078-86. PMID: 22416140
  • Smith BC, Anderson MA, Hoadley KA, Keck JL, Cleland WW, and Denu JM (2012). Structural and Kinetic Isotope Effect Studies of Nicotinamidase (Pnc1) from Saccharomyces cerevisiae. Biochemistry. 51:243-56. PMID: 22229411
  • Hallows WC, Yu W, and Denu JM (2011). Regulation of glycolytic enzyme phosphoglycerate mutase-1 by Sirt1-mediated deacetylation. J Biol Chem. 287:3850-3858. PMID: 22157007
  • Albaugh BN, Arnold KM, Lee S, and Denu JM (2011). Autoacetylation of the histone acetyltransferase Rtt109. J Biol Chem. 286:24694-701. PMID: 21606491
  • Chen D, Vollmar M, Rossi MN, Phillips C, Kraehenbuehl R, Slade D, Mehrotra PV, von Delft F, Crosthwaite SK, Gileadi O, Denu JM, and Ahel I (2011). Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J Biol Chem. 286:13261-71. PMID: 21257746
  • Hallows WC, Yu W, Smith BC, Devries MK, Ellinger JJ, Someya S, Shortreed MR, Prolla T, Markley JL, Smith LM, Zhao S, Guan KL, and Denu JM (2011). Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. Mol Cell. 41:139-49. Devires, Mark K [corrected to Devries, Mark K]. PMID: 21255725
  • Oliver SS and Denu JM (2011). Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a "histone language". Chembiochem. 12:299-307. PMID: 21243717
  • Albaugh BN, Arnold KM, and Denu JM (2011). KAT(ching) metabolism by the tail: insight into the links between lysine acetyltransferases and metabolism. Chembiochem. 12(2):290-8. PMID: 21243716
  • Dittenhafer-Reed KE, Feldman JL, and Denu JM (2011). Catalysis and mechanistic insights into sirtuin activation. Chembiochem. 12:281-9. PMID: 21243715
  • Arnold KM, Lee S, and Denu JM (2011). Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex. Biochemistry. 50.:727-37. PMID: 21182309