John M. Denu - Publications

Affiliations: 
Biomolecular Chemistry University of Wisconsin, Madison, Madison, WI 
Area:
Chromatin and epigenetics
Website:
http://www.bmolchem.wisc.edu/labs/denu/labMembers/denuJ.html

159 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Gregg T, Sdao SM, Dhillon RS, Rensvold JW, Lewandowski SL, Pagliarini DJ, Denu JM, Merrins MJ. Obesity-dependent CDK1 signaling stimulates mitochondrial respiration at complex I in pancreatic β-cells. The Journal of Biological Chemistry. PMID 30700550 DOI: 10.1074/jbc.RA118.006085  0.44
2018 Kasahara K, Krautkramer KA, Org E, Romano KA, Kerby RL, Vivas EI, Mehrabian M, Denu JM, Bäckhed F, Lusis AJ, Rey FE. Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model. Nature Microbiology. PMID 30397344 DOI: 10.1038/s41564-018-0272-x  0.44
2018 Yang Z, Qian S, Scheid RN, Lu L, Chen X, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J, Zhong X. EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nature Genetics. PMID 30082787 DOI: 10.1038/s41588-018-0187-8  0.32
2018 Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, ... ... Denu JM, et al. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. Elife. 7. PMID 30039798 DOI: 10.7554/eLife.37816  0.44
2018 Qian S, Lv X, Scheid RN, Lu L, Yang Z, Chen W, Liu R, Boersma MD, Denu JM, Zhong X, Du J. Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nature Communications. 9: 2425. PMID 29930355 DOI: 10.1038/s41467-018-04836-y  0.32
2017 Krautkramer KA, Dhillon RS, Denu JM, Carey HV. Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin. Translational Research : the Journal of Laboratory and Clinical Medicine. PMID 28919341 DOI: 10.1016/j.trsl.2017.08.005  0.44
2017 Krautkramer KA, Rey FE, Denu JD. Chemical signaling between gut microbiota and host chromatin: What is your gut really saying? The Journal of Biological Chemistry. PMID 28389558 DOI: 10.1074/jbc.R116.761577  0.44
2017 Sanders D, Qian S, Fieweger R, Lu L, Dowell JA, Denu JM, Zhong X. Histone lysine-to-methionine mutations reduce histone methylation and cause developmental pleiotropy. Plant Physiology. PMID 28202597 DOI: 10.1104/pp.16.01499  0.44
2016 Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, Keller MP, Attie AD, Rey FE, Denu JM. Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Molecular Cell. 64: 982-992. PMID 27889451 DOI: 10.1016/j.molcel.2016.10.025  0.44
2016 Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN, Denu JM. Reader domain specificity and lysine demethylase-4 family function. Nature Communications. 7: 13387. PMID 27841353 DOI: 10.1038/ncomms13387  0.44
2016 Rensvold JW, Krautkramer KA, Dowell JA, Denu JM, Pagliarini DJ. Iron Deprivation Induces Transcriptional Regulation of Mitochondrial Biogenesis. The Journal of Biological Chemistry. PMID 27497435 DOI: 10.1074/jbc.M116.727701  0.44
2016 Gregg T, Poudel C, Schmidt BA, Dhillon RS, Sdao SM, Truchan NA, Baar EL, Fernandez LA, Denu JM, Eliceiri KW, Rogers JD, Kimple ME, Lamming DW, Merrins MJ. Pancreatic β cells from Mice Offset Age-Associated Mitochondrial Deficiency with Reduced KATP Channel Activity. Diabetes. PMID 27284112 DOI: 10.2337/db16-0432  1
2016 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. The Journal of Experimental Medicine. PMID 27242167 DOI: 10.1084/jem.20151776  0.44
2016 Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. A novel quantitative mass spectrometry platform for determining site-specific protein O-GlcNAcylation dynamics. Molecular & Cellular Proteomics : McP. PMID 27114449 DOI: 10.1074/mcp.O115.049627  0.44
2016 Baeza J, Smallegan MJ, Denu JM. Mechanisms and Dynamics of Protein Acetylation in Mitochondria. Trends in Biochemical Sciences. PMID 26822488 DOI: 10.1016/j.tibs.2015.12.006  1
2015 Su Z, Denu JM. Reading the combinatorial histone language. Acs Chemical Biology. PMID 26675328 DOI: 10.1021/acschembio.5b00864  1
2015 Yu W, Denu RA, Kruatkramer 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. PMID 26631723 DOI: 10.1074/jbc.M115.702076  1
2015 Kugel S, Feldman JL, Klein MA, Silberman DM, Sebastián C, Mermel C, Dobersch S, Clark AR, Getz G, Denu JM, Mostoslavsky R. Identification of and Molecular Basis for SIRT6 Loss-of-Function Point Mutations in Cancer. Cell Reports. 13: 479-88. PMID 26456828 DOI: 10.1016/j.celrep.2015.09.022  1
2015 Su Z, Denu JM. MARCC (Matrix-Assisted Reader Chromatin Capture): An Antibody-Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. 111: 21.32.1-21.32.21. PMID 26131849 DOI: 10.1002/0471142727.mb2132s111  1
2015 Krautkramer KA, Reiter L, Denu JM, Dowell JA. Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. Journal of Proteome Research. PMID 26120868 DOI: 10.1021/acs.jproteome.5b00245  1
2015 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 Deacylation. Biochemistry. 54: 3037-50. PMID 25897714 DOI: 10.1021/acs.biochem.5b00150  1
2015 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. 21: 637-46. PMID 25863253 DOI: 10.1016/j.cmet.2015.03.007  1
2015 Fan J, Krautkramer KA, Feldman JL, Denu JM. Metabolic regulation of histone post-translational modifications. Acs Chemical Biology. 10: 95-108. PMID 25562692 DOI: 10.1021/cb500846u  1
2015 Baeza J, Smallegan MJ, Denu JM. Site-specific reactivity of nonenzymatic lysine acetylation. Acs Chemical Biology. 10: 122-8. PMID 25555129 DOI: 10.1021/cb500848p  1
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. 289: 21326-38. PMID 24917678 DOI: 10.1074/jbc.M114.581843  1
2014 Su Z, Boersma MD, Lee JH, Oliver SS, Liu S, Garcia BA, Denu JM. ChIP-less analysis of chromatin states. Epigenetics & Chromatin. 7: 7. PMID 24872844 DOI: 10.1186/1756-8935-7-7  1
2014 Gough SM, Lee F, Yang F, Walker RL, Zhu YJ, Pineda M, Onozawa M, Chung YJ, Bilke S, Wagner EK, Denu JM, Ning Y, Xu B, Wang GG, Meltzer PS, et al. NUP98-PHF23 is a chromatin-modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD histone reader function. Cancer Discovery. 4: 564-77. PMID 24535671 DOI: 10.1158/2159-8290.CD-13-0419  1
2014 Prolla TA, Denu JM. NAD+ deficiency in age-related mitochondrial dysfunction. Cell Metabolism. 19: 178-80. PMID 24506863 DOI: 10.1016/j.cmet.2014.01.005  1
2014 Sahar S, Masubuchi S, Eckel-Mahan K, Vollmer S, Galla L, Ceglia N, Masri S, Barth TK, Grimaldi B, Oluyemi O, Astarita G, Hallows WC, Piomelli D, Imhof A, Baldi P, ... Denu JM, et al. Circadian control of fatty acid elongation by SIRT1 protein-mediated deacetylation of acetyl-coenzyme A synthetase 1. The Journal of Biological Chemistry. 289: 6091-7. PMID 24425865 DOI: 10.1074/jbc.M113.537191  1
2013 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. 288: 31350-6. PMID 24052263 DOI: 10.1074/jbc.C113.511261  1
2013 Peek CB, Affinati AH, Ramsey KM, Kuo HY, Yu W, Sena LA, Ilkayeva O, Marcheva B, Kobayashi Y, Omura C, Levine DC, Bacsik DJ, Gius D, Newgard CB, Goetzman E, ... ... Denu JM, et al. Circadian clock NAD+ cycle drives mitochondrial oxidative metabolism in mice. Science (New York, N.Y.). 342: 1243417. PMID 24051248 DOI: 10.1126/science.1243417  1
2013 Still AJ, Floyd BJ, Hebert AS, Bingman CA, Carson JJ, Gunderson DR, Dolan BK, Grimsrud PA, Dittenhafer-Reed KE, Stapleton DS, Keller MP, Westphall MS, Denu JM, Attie AD, Coon JJ, et al. Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation. The Journal of Biological Chemistry. 288: 26209-19. PMID 23864654 DOI: 10.1074/jbc.M113.483396  0.44
2013 Zhou X, Fan LX, Sweeney WE, Denu JM, Avner ED, Li X. Sirtuin 1 inhibition delays cyst formation in autosomal-dominant polycystic kidney disease. The Journal of Clinical Investigation. 123: 3084-98. PMID 23778143 DOI: 10.1172/JCI64401  1
2013 Wickert LE, Blanchette JB, Waldschmidt NV, Bertics PJ, Denu JM, Denlinger LC, Lenertz LY. The C-terminus of human nucleotide receptor P2X7 is critical for receptor oligomerization and N-linked glycosylation. Plos One. 8: e63789. PMID 23691096 DOI: 10.1371/journal.pone.0063789  1
2013 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, et al. Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Molecular Cell. 49: 186-99. PMID 23201123 DOI: 10.1016/j.molcel.2012.10.024  1
2012 Dominy JE, 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, et al. The deacetylase Sirt6 activates the acetyltransferase GCN5 and suppresses hepatic gluconeogenesis. Molecular Cell. 48: 900-13. PMID 23142079 DOI: 10.1016/j.molcel.2012.09.030  1
2012 Feldman JL, Dittenhafer-Reed KE, Denu JM. Sirtuin catalysis and regulation. The Journal of Biological Chemistry. 287: 42419-27. PMID 23086947 DOI: 10.1074/jbc.R112.378877  1
2012 Denu JM, Gottesfeld JM. Minireview series on sirtuins: from biochemistry to health and disease. The Journal of Biological Chemistry. 287: 42417-8. PMID 23086946 DOI: 10.1074/jbc.R112.428862  1
2012 Wagner EK, Nath N, Flemming R, Feltenberger JB, Denu JM. Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry. 51: 8293-306. PMID 22994852 DOI: 10.1021/bi3009278  1
2012 Wagner EK, Albaugh BN, Denu JM. High-throughput strategy to identify inhibitors of histone-binding domains. Methods in Enzymology. 512: 161-85. PMID 22910207 DOI: 10.1016/B978-0-12-391940-3.00008-1  1
2012 Oliver SS, Musselman CA, Srinivasan R, Svaren JP, Kutateladze TG, Denu JM. Multivalent recognition of histone tails by the PHD fingers of CHD5. Biochemistry. 51: 6534-44. PMID 22834704 DOI: 10.1021/bi3006972  1
2012 Denu JM. Fortifying the link between SIRT1, resveratrol, and mitochondrial function. Cell Metabolism. 15: 566-7. PMID 22560207 DOI: 10.1016/j.cmet.2012.04.016  1
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. 287: 14078-86. PMID 22416140 DOI: 10.1074/jbc.M112.355206  1
2012 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. 51: 243-56. PMID 22229411 DOI: 10.1021/bi2015508  1
2012 Musselman CA, Ramírez 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. 109: 787-92. PMID 22215588 DOI: 10.1073/pnas.1113655109  1
2012 Hallows WC, Yu W, Denu JM. Regulation of glycolytic enzyme phosphoglycerate mutase-1 by Sirt1 protein-mediated deacetylation. The Journal of Biological Chemistry. 287: 3850-8. PMID 22157007 DOI: 10.1074/jbc.M111.317404  1
2011 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. 286: 35955-65. PMID 21849506 DOI: 10.1074/jbc.M111.276238  1
2011 Oliver SS, Denu JM. Disrupting the reader of histone language. Angewandte Chemie (International Ed. in English). 50: 5801-3. PMID 21618372 DOI: 10.1002/anie.201101414  1
2011 Albaugh BN, Arnold KM, Lee S, Denu JM. Autoacetylation of the histone acetyltransferase Rtt109. The Journal of Biological Chemistry. 286: 24694-701. PMID 21606491 DOI: 10.1074/jbc.M111.251579  1
2011 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. 286: 21110-7. PMID 21498885 DOI: 10.1074/jbc.M111.237636  1
2011 Pan PW, Feldman JL, Devries MK, Dong A, Edwards AM, Denu JM. Structure and biochemical functions of SIRT6. The Journal of Biological Chemistry. 286: 14575-87. PMID 21362626 DOI: 10.1074/jbc.M111.218990  1
2011 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. 286: 11779-91. PMID 21278251 DOI: 10.1074/jbc.M110.208207  1
2011 Chen D, Vollmar M, Rossi MN, Phillips C, Kraehenbuehl R, Slade D, Mehrotra PV, von Delft F, Crosthwaite SK, Gileadi O, Denu JM, Ahel I. Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. The Journal of Biological Chemistry. 286: 13261-71. PMID 21257746 DOI: 10.1074/jbc.M110.206771  1
2011 Hallows WC, Yu W, Smith BC, Devries MK, Devires MK, Ellinger JJ, Someya S, Shortreed MR, Prolla T, Markley JL, Smith LM, Zhao S, Guan KL, Denu JM. Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. Molecular Cell. 41: 139-49. PMID 21255725 DOI: 10.1016/j.molcel.2011.01.002  1
2011 Oliver SS, Denu JM. Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a "histone language". Chembiochem : a European Journal of Chemical Biology. 12: 299-307. PMID 21243717 DOI: 10.1002/cbic.201000474  1
2011 Albaugh BN, Arnold KM, Denu JM. KAT(ching) metabolism by the tail: insight into the links between lysine acetyltransferases and metabolism. Chembiochem : a European Journal of Chemical Biology. 12: 290-8. PMID 21243716 DOI: 10.1002/cbic.201000438  1
2011 Dittenhafer-Reed KE, Feldman JL, Denu JM. Catalysis and mechanistic insights into sirtuin activation. Chembiochem : a European Journal of Chemical Biology. 12: 281-9. PMID 21243715 DOI: 10.1002/cbic.201000434  1
2011 Arnold KM, Lee S, Denu JM. Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex. Biochemistry. 50: 727-37. PMID 21182309 DOI: 10.1021/bi101355a  1
2011 Smith BC, Settles B, Hallows WC, Craven MW, Denu JM. SIRT3 substrate specificity determined by peptide arrays and machine learning. Acs Chemical Biology. 6: 146-57. PMID 20945913 DOI: 10.1021/cb100218d  1
2010 Shimazu T, Hirschey MD, Hua L, Dittenhafer-Reed KE, Schwer B, Lombard DB, Li Y, Bunkenborg J, Alt FW, Denu JM, Jacobson MP, Verdin E. SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metabolism. 12: 654-61. PMID 21109197 DOI: 10.1016/j.cmet.2010.11.003  1
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. 143: 802-12. PMID 21094524 DOI: 10.1016/j.cell.2010.10.002  1
2010 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. 107: 20275-80. PMID 21057107 DOI: 10.1073/pnas.1009860107  1
2010 Albaugh BN, Kolonko EM, Denu JM. Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex. Biochemistry. 49: 6375-85. PMID 20560668 DOI: 10.1021/bi100381y  1
2010 Ariyannur PS, Moffett JR, Madhavarao CN, Arun P, Vishnu N, Jacobowitz DM, Hallows WC, Denu JM, Namboodiri AM. Nuclear-cytoplasmic localization of acetyl coenzyme a synthetase-1 in the rat brain. The Journal of Comparative Neurology. 518: 2952-77. PMID 20533355 DOI: 10.1002/cne.22373  1
2010 Arun P, Madhavarao CN, Moffett JR, Hamilton K, Grunberg NE, Ariyannur PS, Gahl WA, Anikster Y, Mog S, Hallows WC, Denu JM, Namboodiri AM. Metabolic acetate therapy improves phenotype in the tremor rat model of Canavan disease. Journal of Inherited Metabolic Disease. 33: 195-210. PMID 20464498 DOI: 10.1007/s10545-010-9100-z  1
2010 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. 6: 283-90. PMID 20190764 DOI: 10.1038/nchembio.319  1
2010 Tong L, Denu JM. Function and metabolism of sirtuin metabolite O-acetyl-ADP-ribose. Biochimica Et Biophysica Acta. 1804: 1617-25. PMID 20176146 DOI: 10.1016/j.bbapap.2010.02.007  1
2009 Musselman CA, Mansfield RE, Garske AL, Davrazou F, Kwan AH, Oliver SS, O'Leary H, Denu JM, Mackay JP, Kutateladze TG. Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications. The Biochemical Journal. 423: 179-87. PMID 19624289 DOI: 10.1042/BJ20090870  1
2009 Smith BC, Hallows WC, Denu JM. A continuous microplate assay for sirtuins and nicotinamide-producing enzymes. Analytical Biochemistry. 394: 101-9. PMID 19615966 DOI: 10.1016/j.ab.2009.07.019  1
2009 Hallows WC, Smith BC, Lee S, Denu JM. Ure(k)a! Sirtuins Regulate Mitochondria. Cell. 137: 404-6. PMID 19410538 DOI: 10.1016/j.cell.2009.04.036  1
2009 Tong L, Lee S, Denu JM. Hydrolase regulates NAD+ metabolites and modulates cellular redox. The Journal of Biological Chemistry. 284: 11256-66. PMID 19251690 DOI: 10.1074/jbc.M809790200  1
2009 Smith BC, Denu JM. Chemical mechanisms of histone lysine and arginine modifications. Biochimica Et Biophysica Acta. 1789: 45-57. PMID 18603028 DOI: 10.1016/j.bbagrm.2008.06.005  1
2008 Berndsen CE, Tsubota T, Lindner SE, Lee S, Holton JM, Kaufman PD, Keck JL, Denu JM. Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75. Nature Structural & Molecular Biology. 15: 948-56. PMID 19172748 DOI: 10.1038/nsmb.1459  1
2008 Berndsen CE, Denu JM. Catalysis and substrate selection by histone/protein lysine acetyltransferases. Current Opinion in Structural Biology. 18: 682-9. PMID 19056256 DOI: 10.1016/j.sbi.2008.11.004  1
2008 Smith BC, Hallows WC, Denu JM. Mechanisms and molecular probes of sirtuins. Chemistry & Biology. 15: 1002-13. PMID 18940661 DOI: 10.1016/j.chembiol.2008.09.009  1
2008 Lee S, Tong L, Denu JM. Quantification of endogenous sirtuin metabolite O-acetyl-ADP-ribose. Analytical Biochemistry. 383: 174-9. PMID 18812159 DOI: 10.1016/j.ab.2008.08.033  1
2008 Garske AL, Craciun G, Denu JM. A combinatorial H4 tail library for exploring the histone code. Biochemistry. 47: 8094-102. PMID 18616348 DOI: 10.1021/bi800766k  1
2008 Hallows WC, Albaugh BN, Denu JM. Where in the cell is SIRT3?--functional localization of an NAD+-dependent protein deacetylase. The Biochemical Journal. 411: e11-3. PMID 18363549 DOI: 10.1042/BJ20080336  1
2008 Milne JC, Denu JM. The Sirtuin family: therapeutic targets to treat diseases of aging. Current Opinion in Chemical Biology. 12: 11-7. PMID 18282481 DOI: 10.1016/j.cbpa.2008.01.019  1
2008 Kowieski TM, Lee S, Denu JM. Acetylation-dependent ADP-ribosylation by Trypanosoma brucei Sir2. The Journal of Biological Chemistry. 283: 5317-26. PMID 18165239 DOI: 10.1074/jbc.M707613200  1
2007 Smith BC, Denu JM. Mechanism-based inhibition of Sir2 deacetylases by thioacetyl-lysine peptide. Biochemistry. 46: 14478-86. PMID 18027980 DOI: 10.1021/bi7013294  1
2007 Smith BC, Denu JM. Acetyl-lysine analog peptides as mechanistic probes of protein deacetylases. The Journal of Biological Chemistry. 282: 37256-65. PMID 17951578 DOI: 10.1074/jbc.M707878200  1
2007 Comstock LR, Denu JM. Synthesis and biochemical evaluation of O-acetyl-ADP-ribose and N-acetyl analogs. Organic & Biomolecular Chemistry. 5: 3087-91. PMID 17878966 DOI: 10.1039/b710231c  1
2007 Garske AL, Smith BC, Denu JM. Linking SIRT2 to Parkinson's disease. Acs Chemical Biology. 2: 529-32. PMID 17708669 DOI: 10.1021/cb700160d  1
2007 Denu JM. Vitamins and aging: pathways to NAD+ synthesis. Cell. 129: 453-4. PMID 17482537 DOI: 10.1016/j.cell.2007.04.023  1
2007 Smith BC, Denu JM. Sir2 deacetylases exhibit nucleophilic participation of acetyl-lysine in NAD+ cleavage. Journal of the American Chemical Society. 129: 5802-3. PMID 17439123 DOI: 10.1021/ja070162w  1
2007 Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, Denu JM, Kaufman PD. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Molecular Cell. 25: 703-12. PMID 17320445 DOI: 10.1016/j.molcel.2007.02.006  1
2007 Berndsen CE, Selleck W, McBryant SJ, Hansen JC, Tan S, Denu JM. Nucleosome recognition by the Piccolo NuA4 histone acetyltransferase complex. Biochemistry. 46: 2091-9. PMID 17274630 DOI: 10.1021/bi602366n  1
2007 Berndsen CE, Albaugh BN, Tan S, Denu JM. Catalytic mechanism of a MYST family histone acetyltransferase. Biochemistry. 46: 623-9. PMID 17223684 DOI: 10.1021/bi602513x  1
2006 Tyler RC, Bitto E, Berndsen CE, Bingman CA, Singh S, Lee MS, Wesenberg GE, Denu JM, Phillips GN, Markley JL. Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family. Biochemistry. 45: 14325-36. PMID 17128971 DOI: 10.1021/bi0612059  1
2006 Smith BC, Denu JM. Sirtuins caught in the act. Structure (London, England : 1993). 14: 1207-8. PMID 16905094 DOI: 10.1016/j.str.2006.07.004  1
2006 Hallows WC, Lee S, Denu JM. Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases. Proceedings of the National Academy of Sciences of the United States of America. 103: 10230-5. PMID 16790548 DOI: 10.1073/pnas.0604392103  1
2006 Grubisha O, Rafty LA, Takanishi CL, Xu X, Tong L, Perraud AL, Scharenberg AM, Denu JM. Metabolite of SIR2 reaction modulates TRPM2 ion channel. The Journal of Biological Chemistry. 281: 14057-65. PMID 16565078 DOI: 10.1074/jbc.M513741200  1
2006 Smith BC, Denu JM. Sir2 protein deacetylases: evidence for chemical intermediates and functions of a conserved histidine. Biochemistry. 45: 272-82. PMID 16388603 DOI: 10.1021/bi052014t  1
2006 Garske AL, Denu JM. SIRT1 top 40 hits: use of one-bead, one-compound acetyl-peptide libraries and quantum dots to probe deacetylase specificity. Biochemistry. 45: 94-101. PMID 16388584 DOI: 10.1021/bi052015l  1
2005 Grubisha O, Smith BC, Denu JM. Small molecule regulation of Sir2 protein deacetylases. The Febs Journal. 272: 4607-16. PMID 16156783 DOI: 10.1111/j.1742-4658.2005.04862.x  1
2005 Denu JM. The Sir 2 family of protein deacetylases. Current Opinion in Chemical Biology. 9: 431-40. PMID 16122969 DOI: 10.1016/j.cbpa.2005.08.010  1
2005 Berndsen CE, Denu JM. Assays for mechanistic investigations of protein/histone acetyltransferases. Methods (San Diego, Calif.). 36: 321-31. PMID 16085424 DOI: 10.1016/j.ymeth.2005.03.002  1
2005 Denu JM. Vitamin B3 and sirtuin function. Trends in Biochemical Sciences. 30: 479-83. PMID 16039130 DOI: 10.1016/j.tibs.2005.07.004  1
2005 Borra MT, Smith BC, Denu JM. Mechanism of human SIRT1 activation by resveratrol. The Journal of Biological Chemistry. 280: 17187-95. PMID 15749705 DOI: 10.1074/jbc.M501250200  1
2004 Borra MT, Langer MR, Slama JT, Denu JM. Substrate specificity and kinetic mechanism of the Sir2 family of NAD+-dependent histone/protein deacetylases. Biochemistry. 43: 9877-87. PMID 15274642 DOI: 10.1021/bi049592e  1
2004 Schmidt MT, Smith BC, Jackson MD, Denu JM. Coenzyme specificity of Sir2 protein deacetylases: implications for physiological regulation. The Journal of Biological Chemistry. 279: 40122-9. PMID 15269219 DOI: 10.1074/jbc.M407484200  1
2004 Grzyska PK, Kim Y, Jackson MD, Hengge AC, Denu JM. Probing the transition-state structure of dual-specificity protein phosphatases using a physiological substrate mimic. Biochemistry. 43: 8807-14. PMID 15236589 DOI: 10.1021/bi049473z  1
2004 Borra MT, Denu JM. Quantitative assays for characterization of the Sir2 family of NAD(+)-dependent deacetylases. Methods in Enzymology. 376: 171-87. PMID 14975305 DOI: 10.1016/S0076-6879(03)76011-X  1
2003 Kim Y, Rice AE, Denu JM. Intramolecular dephosphorylation of ERK by MKP3. Biochemistry. 42: 15197-207. PMID 14690430 DOI: 10.1021/bi035346b  1
2003 Jackson MD, Schmidt MT, Oppenheimer NJ, Denu JM. Mechanism of nicotinamide inhibition and transglycosidation by Sir2 histone/protein deacetylases. The Journal of Biological Chemistry. 278: 50985-98. PMID 14522996 DOI: 10.1074/jbc.M306552200  1
2003 Jackson MD, Fjeld CC, Denu JM. Probing the function of conserved residues in the serine/threonine phosphatase PP2Calpha. Biochemistry. 42: 8513-21. PMID 12859198 DOI: 10.1021/bi034074+  1
2003 North BJ, Marshall BL, Borra MT, Denu JM, Verdin E. The human Sir2 ortholog, SIRT2, is an NAD+-dependent tubulin deacetylase. Molecular Cell. 11: 437-44. PMID 12620231 DOI: 10.1016/S1097-2765(03)00038-8  1
2003 Denu JM. Linking chromatin function with metabolic networks: Sir2 family of NAD(+)-dependent deacetylases. Trends in Biochemical Sciences. 28: 41-8. PMID 12517451 DOI: 10.1016/S0968-0004(02)00005-1  1
2003 Kim Y, Denu JM. Protein Tyrosine Phosphatase Structure and Mechanisms Handbook of Cell Signaling. 1: 653-657. DOI: 10.1016/B978-012124546-7/50470-8  1
2002 Dutnall RN, Denu JM. Methyl magic and HAT tricks. Nature Structural Biology. 9: 888-91. PMID 12447351 DOI: 10.1038/nsb1202-888  1
2002 Boyer LA, Langer MR, Crowley KA, Tan S, Denu JM, Peterson CL. Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes. Molecular Cell. 10: 935-42. PMID 12419236 DOI: 10.1016/S1097-2765(02)00634-2  1
2002 Rafty LA, Schmidt MT, Perraud AL, Scharenberg AM, Denu JM. Analysis of O-acetyl-ADP-ribose as a target for Nudix ADP-ribose hydrolases. The Journal of Biological Chemistry. 277: 47114-22. PMID 12370179 DOI: 10.1074/jbc.M208997200  1
2002 Ludlam WH, Taylor MH, Tanner KG, Denu JM, Goodman RH, Smolik SM. The acetyltransferase activity of CBP is required for wingless activation and H4 acetylation in Drosophila melanogaster. Molecular and Cellular Biology. 22: 3832-41. PMID 11997517 DOI: 10.1128/MCB.22.11.3832-3841.2002  1
2002 Langer MR, Fry CJ, Peterson CL, Denu JM. Modulating acetyl-CoA binding in the GCN5 family of histone acetyltransferases. The Journal of Biological Chemistry. 277: 27337-44. PMID 11994311 DOI: 10.1074/jbc.M203251200  1
2002 Todd JL, Rigas JD, Rafty LA, Denu JM. Dual-specificity protein tyrosine phosphatase VHR down-regulates c-Jun N-terminal kinase (JNK). Oncogene. 21: 2573-83. PMID 11971192 DOI: 10.1038/sj.onc.1205344  1
2002 Bashor C, Denu JM, Brennan RG, Ullman B. Kinetic mechanism of adenine phosphoribosyltransferase from Leishmania donovani. Biochemistry. 41: 4020-31. PMID 11900545 DOI: 10.1021/bi0158730  1
2002 Jackson MD, Denu JM. Structural identification of 2'- and 3'-O-acetyl-ADP-ribose as novel metabolites derived from the Sir2 family of beta -NAD+-dependent histone/protein deacetylases. The Journal of Biological Chemistry. 277: 18535-44. PMID 11893743 DOI: 10.1074/jbc.M200671200  1
2002 Denu JM, Tanner KG. Redox regulation of protein tyrosine phosphatases by hydrogen peroxide: detecting sulfenic acid intermediates and examining reversible inactivation. Methods in Enzymology. 348: 297-305. PMID 11885283 DOI: 10.1016/S0076-6879(02)48648-X  1
2002 Schumacher MA, Todd JL, Rice AE, Tanner KG, Denu JM. Structural basis for the recognition of a bisphosphorylated MAP kinase peptide by human VHR protein Phosphatase. Biochemistry. 41: 3009-17. PMID 11863439 DOI: 10.1021/bi015799l  1
2002 Borra MT, O'Neill FJ, Jackson MD, Marshall B, Verdin E, Foltz KR, Denu JM. Conserved enzymatic production and biological effect of O-acetyl-ADP-ribose by silent information regulator 2-like NAD+-dependent deacetylases. The Journal of Biological Chemistry. 277: 12632-41. PMID 11812793 DOI: 10.1074/jbc.M111830200  1
2001 Jackson MD, Denu JM. Molecular reactions of protein phosphatases--insights from structure and chemistry. Chemical Reviews. 101: 2313-40. PMID 11749375  0.44
2001 Kumano M, Carroll DJ, Denu JM, Foltz KR. Calcium-mediated inactivation of the MAP kinase pathway in sea urchin eggs at fertilization. Developmental Biology. 236: 244-57. PMID 11456458 DOI: 10.1006/dbio.2001.0328  1
2001 Langer MR, Tanner KG, Denu JM. Mutational analysis of conserved residues in the GCN5 family of histone acetyltransferases. The Journal of Biological Chemistry. 276: 31321-31. PMID 11397810 DOI: 10.1074/jbc.M103839200  1
2001 Roth SY, Denu JM, Allis CD. Histone acetyltransferases. Annual Review of Biochemistry. 70: 81-120. PMID 11395403 DOI: 10.1146/annurev.biochem.70.1.81  1
2001 Rigas JD, Hoff RH, Rice AE, Hengge AC, Denu JM. Transition state analysis and requirement of Asp-262 general acid/base catalyst for full activation of dual-specificity phosphatase MKP3 by extracellular regulated kinase. Biochemistry. 40: 4398-406. PMID 11284696 DOI: 10.1021/bi002951v  1
2001 Jackson MD, Denu JM. Molecular reactions of protein phosphatases - Insights from structure and chemistry Chemical Reviews. 101: 2313-2340. DOI: 10.1021/cr000247e  1
2000 Tanner KG, Langer MR, Denu JM. Kinetic mechanism of human histone acetyltransferase P/CAF Biochemistry. 39: 15652. PMID 11112555  0.44
2000 Tanner KG, Landry J, Sternglanz R, Denu JM. Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. Proceedings of the National Academy of Sciences of the United States of America. 97: 14178-82. PMID 11106374 DOI: 10.1073/pnas.250422697  1
2000 Tanner KG, Langer MR, Denu JM. Kinetic mechanism of human histone acetyltransferase P/CAF. Biochemistry. 39: 11961-9. PMID 11009610 DOI: 10.1021/bi001272h  1
2000 Cheung P, Tanner KG, Cheung WL, Sassone-Corsi P, Denu JM, Allis CD. Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Molecular Cell. 5: 905-15. PMID 10911985  1
2000 Tanner KG, Langer MR, Kim Y, Denu JM. Kinetic mechanism of the histone acetyltransferase GCN5 from yeast. The Journal of Biological Chemistry. 275: 22048-55. PMID 10811654 DOI: 10.1074/jbc.M002893200  1
2000 Kim Y, Tanner KG, Denu JM. A continuous, nonradioactive assay for histone acetyltransferases. Analytical Biochemistry. 280: 308-14. PMID 10790315 DOI: 10.1006/abio.2000.4546  1
2000 Fjeld CC, Rice AE, Kim Y, Gee KR, Denu JM. Mechanistic basis for catalytic activation of mitogen-activated protein kinase phosphatase 3 by extracellular signal-regulated kinase. The Journal of Biological Chemistry. 275: 6749-57. PMID 10702230 DOI: 10.1074/jbc.275.10.6749  1
1999 Fjeld CC, Denu JM. Kinetic analysis of human serine/threonine protein phosphatase 2Calpha. The Journal of Biological Chemistry. 274: 20336-43. PMID 10400656 DOI: 10.1074/jbc.274.29.20336  1
1999 Todd JL, Tanner KG, Denu JM. Extracellular regulated kinases (ERK) 1 and ERK2 are authentic substrates for the dual-specificity protein-tyrosine phosphatase VHR. A novel role in down-regulating the ERK pathway. The Journal of Biological Chemistry. 274: 13271-80. PMID 10224087 DOI: 10.1074/jbc.274.19.13271  1
1998 Denu JM, Dixon JE. Protein tyrosine phosphatases: mechanisms of catalysis and regulation. Current Opinion in Chemical Biology. 2: 633-41. PMID 9818190  1
1998 Bell SD, Denu JM, Dixon JE, Ellington AD. RNA molecules that bind to and inhibit the active site of a tyrosine phosphatase. The Journal of Biological Chemistry. 273: 14309-14. PMID 9603938 DOI: 10.1074/jbc.273.23.14309  1
1998 Denu JM, Tanner KG. Specific and reversible inactivation of protein tyrosine phosphatases by hydrogen peroxide: evidence for a sulfenic acid intermediate and implications for redox regulation. Biochemistry. 37: 5633-42. PMID 9548949 DOI: 10.1021/bi973035t  1
1997 Lohse DL, Denu JM, Santoro N, Dixon JE. Roles of aspartic acid-181 and serine-222 in intermediate formation and hydrolysis of the mammalian protein-tyrosine-phosphatase PTP1. Biochemistry. 36: 4568-75. PMID 9109666 DOI: 10.1021/bi963094r  1
1997 Fitzpatrick PF, Kurtz KA, Denu JM, Emanuele JF. Contrasting values of commitment factors measured from viscosity, pH, and kinetic isotope effects: Evidence for slow conformational changes in the D-amino acid oxidase reaction Bioorganic Chemistry. 25: 100-109. DOI: 10.1006/bioo.1997.1057  1
1996 Wiland AM, Denu JM, Mourey RJ, Dixon JE. Purification and kinetic characterization of the mitogen-activated protein kinase phosphatase rVH6. The Journal of Biological Chemistry. 271: 33486-92. PMID 8969212 DOI: 10.1074/jbc.271.52.33486  1
1996 Denu JM, Stuckey JA, Saper MA, Dixon JE. Form and function in protein dephosphorylation. Cell. 87: 361-4. PMID 8898189 DOI: 10.1016/S0092-8674(00)81356-2  1
1996 Hengge AC, Denu JM, Dixon JE. Transition-state structures for the native dual-specific phosphatase VHR and D92N and S131A mutants. Contributions to the driving force for catalysis. Biochemistry. 35: 7084-92. PMID 8679534 DOI: 10.1021/bi960255i  1
1996 Yuvaniyama J, Denu JM, Dixon JE, Saper MA. Crystal structure of the dual specificity protein phosphatase VHR. Science (New York, N.Y.). 272: 1328-31. PMID 8650541  1
1996 Denu JM, Lohse DL, Vijayalakshmi J, Saper MA, Dixon JE. Visualization of intermediate and transition-state structures in protein-tyrosine phosphatase catalysis. Proceedings of the National Academy of Sciences of the United States of America. 93: 2493-8. PMID 8637902  1
1996 Yuvaniyama J, Denu JM, Dixon JE, Saper MA. Crystal structure of VHR, a dual-specificity phosphatase Faseb Journal. 10: A989.  1
1996 Denu JM, Lohse D, Yuvaniyama J, Saper MA, Dixon JE. Structure and function of protein tyrosine phosphatases Faseb Journal. 10: A968.  1
1996 Wishart MJ, Denu JM, Williams JA, Dixon JE. Novel regulatory strategies of protein tyrosine phosphatases Faseb Journal. 10: A989.  1
1995 Lohse DL, Denu JM, Dixon JE. Insights derived from the structures of the Ser/Thr phosphatases calcineurin and protein phosphatase 1. Structure (London, England : 1993). 3: 987-90. PMID 8590008 DOI: 10.1016/S0969-2126(01)00234-9  0.68
1995 Denu JM, Zhou G, Guo Y, Dixon JE. The catalytic role of aspartic acid-92 in a human dual-specific protein-tyrosine-phosphatase. Biochemistry. 34: 3396-403. PMID 7880835  1
1995 Denu JM, Zhou G, Wu L, Zhao R, Yuvaniyama J, Saper MA, Dixon JE. The purification and characterization of a human dual-specific protein tyrosine phosphatase. The Journal of Biological Chemistry. 270: 3796-803. PMID 7876121 DOI: 10.1074/jbc.270.8.3796  1
1995 Zhang ZY, Zhou G, Denu JM, Wu L, Tang X, Mondesert O, Russell P, Butch E, Guan KL. Purification and characterization of the low molecular weight protein tyrosine phosphatase, Stp1, from the fission yeast Schizosaccharomyces pombe. Biochemistry. 34: 10560-8. PMID 7654712  0.32
1995 Denu JM, Dixon JE. A catalytic mechanism for the dual-specific phosphatases. Proceedings of the National Academy of Sciences of the United States of America. 92: 5910-4. PMID 7597052 DOI: 10.1073/pnas.92.13.5910  1
1995 Wishart MJ, Denu JM, Williams JA, Dixon JE. A single mutation converts a novel phosphotyrosine binding domain into a dual-specificity phosphatase. The Journal of Biological Chemistry. 270: 26782-5. PMID 7592916 DOI: 10.1074/jbc.270.45.26782  1
1994 Zhou G, Denu JM, Wu L, Dixon JE. The catalytic role of Cys124 in the dual specificity phosphatase VHR. The Journal of Biological Chemistry. 269: 28084-90. PMID 7961745  1
1994 Denu JM, Fitzpatrick PF. pH and kinetic isotope effects on the oxidative half-reaction of D-amino-acid oxidase. The Journal of Biological Chemistry. 269: 15054-9. PMID 7910822  1
1994 Denu JM, Fitzpatrick PF. Intrinsic primary, secondary, and solvent kinetic isotope effects on the reductive half-reaction of D-amino acid oxidase: evidence against a concerted mechanism. Biochemistry. 33: 4001-7. PMID 7908225  1
1992 Denu JM, Fitzpatrick PF. pH and kinetic isotope effects on the reductive half-reaction of D-amino acid oxidase. Biochemistry. 31: 8207-15. PMID 1356021  1
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