at the Wisconsin Institute for Discovery

Publications

Selected Recent Publications

 

 

Click here for a PubMed search of recent publications from the Denu Lab

2020

  • Klein MA, Lie C, Kuznetsov V, Feltenberger JB, Tang W, Denu JM. Mechanism of Activation for the Sirtuin 6 Protein Deacylase. J Biol Chem 2020, 295 (5), 1385-1399
  • Haws SA, Yu D, Ye C, Wille CK, Nguyen LC, Krautkramer KA, Tomasiewicz JL, Yang SE, Miller BR, Liu WH, Igarashi K, Sridharan R, Tu BP, Cryns VL, Lamming DW, Denu JM. Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistance. Mol Cell 2020

2019

  • Thomas SP, Haws SA, Borth LE, Denu JM. A practical guide for analysis of histone post-translational modification by mass spectrometry: Best practices and pitfalls. Methods 2019
  • Dieterich IA, Lawton AJ, Peng Y, Yu Q, Rhoads, TW, Overmyer, KA, Cui Y, Armstrong EA,  Howell PR, Burhans MS, Li L, Denu JM, Anderson RM, Puglielli L.  Acetyl-CoA flux regulates the proteome and acetyl-proteome to maintain intracellular metabolic crosstalk. Nature Communications 2019, 10(1).
  • Lindahl A, Lawton A, Baeza J, Dowell J, Denu J: Site-Specific Lysine Acetylation Stoichiometry Across Subcellular Compartments. Methods in Molecular Biology 2019, 1983: 79-106.
  • Miller KN, Clark JP, Martin SA, Howell PR, Burhans MS, Haws SA, Johnson NB, Rhoads TW, Pavelec DM, Eliceiri KW, Roopra AS, Ntambi JM, Denu JM, Parks BW, Anderson RM: PGC-1a Integrates a Metabolism and Growth Network Linked to Caloric Restriction. Aging cell 2019, 18(5):e12999

2018

  • Kuznetsov V, Haws S, Fox C, Denu J: General method for rapid purification of native chromatin fragments. Journal of Biological Chemistry 2018, 293 (31): 12271-82.
  • Ferrer CM, Alders M, Postma AV, Park S, Klein MA, Cetinbas M, Pajkrt E, Glas A, van Koningsbruggen S, Christoffels VM, Mannens MMAM, Knegt L, Etchegaray JP, Sadreyev RI, Denu JM, Mostoslavsky G, van Maarle MC, Mostoslavsky R: An Inactivating Mutation in the Histone Deacetylase SIRT6 Causes Human Perinatal Lethality. Genes & development 2018, 32(5-6):373-388
  • Latorre-Muro P, Baeza J, Armstrong EA, Hurtado-Guerrero R, Corzana F, Wu LE, Sinclair DA, López-Buesa P, Carrodeguas JA, Denu JM: Dynamic Acetylation of Phosphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions. Molecular cell 2018, 71(5): 718-732

2017

  • Lee J, Yang B, Lindahl A, Damaschke N, Boersma M, Huang W, Corey E, Jarrard D, Denu J: Identifying Dysregulated Epigenetic Enzyme Activity in Castrate-Resistant Prostate Cancer Development. ACS Chemical Biology. 2017, 12(11): 2804-14.
  • Krautkramer KA, Rey FE, Denu JM: Chemical Signaling Between Git Microbiota and Host Chromatin: What is You Gut Really Saying? The Journal of Biological Chemistry 2017. 292(21): 8582-8593
  • Krautkramer KA, Dhillon RS, Denu JM, Casey HV: Metabolic Programming of the Epigenome: Host and Git Microbial Metabolite Interactions with Host Chromatin. Translational research: the journal of laboratory and clinical  medicine 2017. 189: 30-50

2016

  • Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Veronica E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN Jr, Denu JM: Reader Domain Specificity and Lysine Demethylase-4 Family Function. Nature communications 2016.
  • Baeza J, Smallegan MJ, Denu JM: Mechanisms and Dynamics of Protein Acetylation in Mitochondria. Trends in biochemical sciences 2016.
  • Su Z, Denu JM: Reading the Combinatorial Histone Language. ACS chemical biology 2016, 11 (3): 564-574.
  • Yu W, Denu RA, Krautkramer KA, Grindle KM, Yang DT, Asimakopoulos F, Hematti P, Denu JM: Loss of SIRT3 Provides Growth Advantage for B Cell Malignancies. The Journal of biological chemistry 2016, 291 (7): 3268-79.
  • Krautkramer K, Kreznar J, Romano K, Vivas E, Barrett-Wilt G, Rabaglia M, Keller M, Attie A, Rey F, Denu J: Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Molecular cell. 2016, 64 (5): 982-92.
  • Dummer AM, Su Z, Cherney R, Choic K, Denu J, Zhao X, Fox CA: Binding of the Fkh1 Forehead Associated Domain to a Phosphopeptide within the Mph1 DNA Helicase Regulates Mating-Type Switching in Budding Yeast. PLoS genetics 2016, 12(6)
  • Hullinger R, Li M, Wang J, Peng Y, Dowell JA, Bomba-Warczak E, Mitchell HA, Burger C, Chapman ER, Denu JM, Li L, Puglielli L: Increased Expression of AT-1/SLC33A1 Causes an Autistic-like Phenotype in Mice by Affecting Dendritic Branching and Spine Formation. Journal of experimental medicine 2016, 213(7):1267-84
  • Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA: A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. Molecular and cellular proteomics 2016, 15(7):2462-75
  • Rensvold JW, Krautkramer KA, Dowell JA, Denu JM, Pagliarini DJ: Iron Deprivation Induces Transcriptional Regulation of Mitchondrial Biogenesis. Journal of biological chemistry 2016, 291(40): 20827-37

2015

  • Kugel S, Feldman JL, Klein MA, Silberman DM, Sebastian C, Mermel C, Dobersch C, Clark AR, Getz G, Denu JM, Mostoslavsky R: Identification of and Molecular Basis for SIRT6 Loss-Of-Function Point Mutations in Cancer. Cell reports 2015, 13 (3): 479-88.
  • Krautkramer KA, Reiter L, Denu JM and Dowell JA: Quantification of SAHA-dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. Journal of proteome research 2015, 14(8): 3252-62
  • Su Z and Denu JM: MARCC (Matrix-Assisted Reader Chromatin Capture): An antibody-free method to enrich and analyze combinatorial nucleosome modifications. Current Protocols in Molecular Biology 2015, 111:21.32.1-21.32.21
  • Feldman JL, Dittenhafer-Reed KE, Kudo N, Thelen JN, Ito A, Yoshida M, Denu JM: Kinetic and Structural Basis for Acyl-Group Selectivity and NAD+ Dependence in Sirtuin-Catalyzed Deaceylation. Biochemistry 2015, 54(19):3037-50
  • Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Fotuhi Siahpirani A, Kemmerer ZA, Prolla TA, Roy S, Coon JJ, Denu JM: SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching. Cell metabolism 2015, 21(4):637-46
  • Fan J, Krautkramer KA, Feldman JL, Denu JM: Metabolic regulation of histone post-translational modifications. ACS Chemical Biology 2015, 10(1):95-108
  • Baeza J, Smallegan MJ, Denu JM: Site-specific reactivity of nonenzymatic lysine acetylation. ACS Chemical Biology 2015, 10(1):122-128

2014

  • Baeza J, Dowell JA, Smallegan MJ, Fan J, Amador-Noguez D, Khan Z, Denu JM: Stoichiometry of site-specific lysine acetylation in an entire proteome. The Journal of biological chemistry 2014, 289(31):21326-21338.
  • Su Z, Boersma MD, Lee J, Oliver SS, Liu S, Garcia BA, Denu JM: ChIP-less analysis of chromatin states. Epigenetics & Chromatin 2014, 7:7.
  • Prolla TA, Denu JM: NAD(+) Deficiency in Age-Related Mitochondrial Dysfunction. Cell metabolism 2014, 19(2):178-180.
  • Gough SM, Lee F, Yang F, Walker RL, Zhu YJ, Pineda M, Onozawa M, Chung YJ, Bilke S, Wagner EK et al: NUP98-PHF23 is a chromatin modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD domain histone reader function. Cancer discovery 2014, 4(5): 564-77.

2013

  • Still AJ, Floyd BJ, Hebert AS, Bingman CA, Carson JJ, Gunderson DR, Dolan BK, Grimsrud PA, Dittenhafer-Reed KE, Stapleton DS et al: Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation. The Journal of biological chemistry 2013, 288(36):26209-26219.
  • Peek CB, Affinati AH, Ramsey KM, Kuo HY, Yu W, Sena LA, Ilkayeva O, Marcheva B, Kobayashi Y, Omura C et al: Circadian clock NAD+ cycle drives mitochondrial oxidative metabolism in mice. Science 2013, 342(6158):1243417.
  • Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ et al: Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Molecular cell 2013. 49(1):186-199.
  • Feldman JL, Baeza J, Denu JM: Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. The Journal of biological chemistry 2013. 288(43):31350-31356.

2012

  • Yu W, Dittenhafer-Reed KE, Denu JM: SIRT3 protein deacetylates isocitrate dehydrogenase 2 (IDH2) and regulates mitochondrial redox status. The Journal of biological chemistry 2012. 287(17):14078-14086.
  • Wagner EK, Nath N, Flemming R, Feltenberger JB, Denu JM: Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry 2012. 51(41):8293-8306.
  • Wagner EK, Albaugh BN, Denu JM: High-throughput strategy to identify inhibitors of histone-binding domains. Methods in enzymology 2012. 512:161-185.
  • Smith BC, Anderson MA, Hoadley KA, Keck JL, Cleland WW, Denu JM: Structural and kinetic isotope effect studies of nicotinamidase (Pnc1) from Saccharomyces cerevisiae. Biochemistry 2012. 51(1):243-256.
  • Oliver SS, Musselman CA, Srinivasan R, Svaren JP, Kutateladze TG, Denu JM: Multivalent recognition of histone tails by the PHD fingers of CHD5. Biochemistry 2012. 51(33):6534-6544.
  • Musselman CA, Ramirez J, Sims JK, Mansfield RE, Oliver SS, Denu JM, Mackay JP, Wade PA, Hagman J, Kutateladze TG: Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression. Proceedings of the National Academy of Sciences of the United States of America 2012. 109(3):787-792.
  • Hallows WC, Yu W, Denu JM: Regulation of glycolytic enzyme phosphoglycerate mutase-1 by Sirt1 protein-mediated deacetylation. The Journal of biological chemistry 2012. 287(6):3850-3858.
  • Feldman JL, Dittenhafer-Reed KE, Denu JM: Sirtuin catalysis and regulation. The Journal of biological chemistry 2012. 287(51):42419-42427.
  • Denu JM, Gottesfeld JM: Minireview series on sirtuins: from biochemistry to health and disease. The Journal of biological chemistry 2012. 287(51):42417-42418.
  • Denu JM: Fortifying the link between SIRT1, resveratrol, and mitochondrial function. Cell metabolism 2012. 15(5):566-567.

2011

  • Smith BC, Settles B, Hallows WC, Craven MW, Denu JM: SIRT3 substrate specificity determined by peptide arrays and machine learning. ACS chemical biology 2011, 6(2):146-157.
  • Peterson FC, Chen D, Lytle BL, Rossi MN, Ahel I, Denu JM, Volkman BF: Orphan macrodomain protein (human C6orf130) is an O-acyl-ADP-ribose deacylase: solution structure and catalytic properties. The Journal of biological chemistry 2011, 286(41):35955-35965.
  • Pan PW, Feldman JL, Devries MK, Dong A, Edwards AM, Denu JM: Structure and biochemical functions of SIRT6. The Journal of biological chemistry 2011, 286(16):14575-14587.
  • Mansfield RE, Musselman CA, Kwan AH, Oliver SS, Garske AL, Davrazou F, Denu JM, Kutateladze TG, Mackay JP: Plant homeodomain (PHD) fingers of CHD4 are histone H3-binding modules with preference for unmodified H3K4 and methylated H3K9. The Journal of biological chemistry 2011, 286(13):11779-11791.
  • Kasamatsu A, Nakao M, Smith BC, Comstock LR, Ono T, Kato J, Denu JM, Moss J: Hydrolysis of O-acetyl-ADP-ribose isomers by ADP-ribosylhydrolase 3. The Journal of biological chemistry 2011, 286(24):21110-21117.
  • Hallows WC, Yu W, Smith BC, Devries MK, Ellinger JJ, Someya S, Shortreed MR, Prolla T, Markley JL, Smith LM et al: Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. Molecular cell 2011, 41(2):139-149.
  • Chen D, Vollmar M, Rossi MN, Phillips C, Kraehenbuehl R, Slade D, Mehrotra PV, von Delft F, Crosthwaite SK, Gileadi O et al: Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. The Journal of biological chemistry 2011, 286(15):13261-13271.
  • Arnold KM, Lee S, Denu JM: Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex. Biochemistry 2011, 50(5):727-737.
  • Albaugh BN, Arnold KM, Lee S, Denu JM: Autoacetylation of the histone acetyltransferase Rtt109. The Journal of biological chemistry 2011, 286(28):24694-24701.

2010

  • Someya S, Yu W, Hallows WC, Xu J, Vann JM, Leeuwenburgh C, Tanokura M, Denu JM, Prolla TA: Sirt3 mediates reduction of oxidative damage and prevention of age-related hearing loss under caloric restriction. Cell 2010, 143(5):802-812.
  • Kolonko EM, Albaugh BN, Lindner SE, Chen Y, Satyshur KA, Arnold KM, Kaufman PD, Keck JL, Denu JM: Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone. Proceedings of the National Academy of Sciences of the United States of America 2010, 107(47):20275-20280.
  • Garske AL, Oliver SS, Wagner EK, Musselman CA, LeRoy G, Garcia BA, Kutateladze TG, Denu JM: Combinatorial profiling of chromatin binding modules reveals multisite discrimination. Nature chemical biology 2010, 6(4):283-290.
  • Albaugh BN, Kolonko EM, Denu JM: Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex. Biochemistry 2010, 49(30):6375-6385.