Publications

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

Selected recent publications

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.

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.