Publications

John Denu

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.

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.

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.

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, Coon JJ. Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome. Mol Cell. 2013 Jan 10;49(1):186-99. doi: 10.1016/j.molcel.2012.10.024. Epub 2012 Nov 29. (PubMed 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. The Deacetylase Sirt6 Activates the Acetyltransferase GCN5 and Suppresses Hepatic Gluconeogenesis. Mol Cell. 2012 Dec 28;48(6):900-13. doi: 10.1016/j.molcel.2012.09.030. Epub 2012 Nov 8. (PubMed PMID: 23142079; PubMed Central PMCID: PMC3534905).

Feldman JL, Dittenhafer-Reed KE, Denu JM. Sirtuin catalysis and regulation. JBiol Chem. 2012 Dec 14;287(51):42419-27. doi: 10.1074/jbc.R112.378877. Epub 2012 Oct 18. (PubMed PMID: 23086947; PubMed Central PMCID: PMC3522242).

Denu JM, 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. (PubMed PMID: 23086946; PubMed Central PMCID: PMC3522241).

Wagner EK, Nath N, Flemming R, Feltenberger JB, Denu JM. Identification and Characterization of Small Molecule Inhibitors of a Plant Homeodomain Finger. Biochemistry. 2012 Oct 2. [Epub ahead of print] (PubMed PMID: 22994852).

Wagner EK, Albaugh BN, Denu JM. High-throughput strategy to identify inhibitors of histone-binding domains. Methods Enzymol. 2012;512:161-85. doi: 10.1016/B978-0-12-391940-3.00008-1. (PubMed PMID: 22910207).

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 Aug 21;51(33):6534-44. doi: 10.1021/bi3006972. Epub 2012 Aug 8. (PubMed PMID: 22834704; PubMed Central PMCID: PMC3518043).

Denu JM. Fortifying the link between SIRT1, resveratrol, and mitochondrial function. Cell Metab. 2012 May 2;15(5):566-7. doi: 10.1016/j.cmet.2012.04.016. (PubMed PMID: 22560207; PubMed Central PMCID: PMC3491563).

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. J Inherit Metab Dis. 2010 Jun;33(3):195-210. doi: 10.1007/s10545-010-9100-z. Epub 2010 May 13. (PubMed PMID: 20464498; PubMed Central PMCID: PMC287731z).

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. J Comp Neurol. 2010 Aug 1;518(15):2952-77. doi: 10.1002/cne.22373. (PubMed PMID: 20533355; PubMed Central PMCID: PMC3047483).

Albaugh BN, Kolonko EM, Denu JM. Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex. Biochemistry. 2010 Aug 3;49(30):6375-85. doi: 10.1021/bi100381y. (PubMed PMID: 20560668; PubMed Central PMCID: PMC2917178).

Smith BC, Settles B, Hallows WC, Craven MW, Denu JM. SIRT3 substrate specificity determined by peptide arrays and machine learning. ACS Chem Biol. 2011 Feb 18;6(2):146-57. doi: 10.1021/cb100218d. Epub 2010 Nov 1. (PubMed PMID: 20945913; PubMed Central PMCID: PMC3042044).

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. Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20275-80. doi: 10.1073/pnas.1009860107. Epub 2010 Nov 5. (PubMed PMID: 21057107; PubMed Central PMCID: PMC2996700).

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 Nov 24;143(5):802-12. doi: 10.1016/j.cell.2010.10.002. (PubMed PMID: 21094524; PubMed Central PMCID: PMC3018849).

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 Metab. 2010 Dec 1;12(6):654-61. doi: 10.1016/j.cmet.2010.11.003. (PubMed PMID: 21109197; PubMed Central PMCID: PMC3310379).

Arnold KM, Lee S, Denu JM. Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex. Biochemistry. 2011 Feb 8;50(5):727-37. doi: 10.1021/bi101355a. Epub 2011 Jan 12. (PubMed PMID: 21182309; PubMed Central PMCID: PMC3038686).

Dittenhafer-Reed KE, Feldman JL, Denu JM. Catalysis and mechanistic insights into sirtuin activation. Chembiochem. 2011 Jan 24;12(2):281-9. doi: 10.1002/cbic.201000434. Epub 2010 Nov 9. Review. (PubMed PMID: 21243715; PubMed Central PMCID: PMC3327882).

Albaugh BN, Arnold KM, Denu JM. KAT(ching) metabolism by the tail: insight into the links between lysine acetyltransferases and metabolism. Chembiochem. 2011 Jan 24;12(2):290-8. doi: 10.1002/cbic.201000438. Epub 2010 Nov 24. Review. (PubMed PMID: 21243716; PubMed Central PMCID: PMC3327878).

Oliver SS, Denu JM. Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a “histone language”. Chembiochem. 2011 Jan 24;12(2):299-307. doi: 10.1002/cbic.201000474. Epub 2010 Oct 29. Review. (PubMed PMID: 21243717; PubMed Central PMCID: PMC3073147).

Hallows WC, Yu W, Smith BC, Devries 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. Mol Cell. 2011 Jan 21;41(2):139-49. doi: 10.1016/j.molcel.2011.01.002. Erratum in: Mol Cell. 2011 Feb 18;41(4):493. Devires, Mark K [corrected to Devries, Mark K]. (PubMed PMID: 21255725; PubMed Central PMCID: PMC3101115).

Garske AL, Oliver SS, Wagner EK, Musselman CA, LeRoy G, Garcia BA, Kutateladze TG, and Denu JM. Combinatorial profiling of chromatin-binding modules reveals multi-site discrimination. Nature Chemical Biology 2010 Apr;6(4):283-90. (PMCID: PMC2922993, Publ.ID: NCHEMB-A090503857).

Someya S, Yu W, Hallows WC, Xu J, Vann JM, Leeuwenburgh, C, Tanokura M, *Denu JM and *Prolla TA. Mitochondrial Sirt3 Mediates Reduction of Oxidative Damage and Prevention of Age-related Hearing Loss in Response to Caloric Restriction. Cell, 143, 802-812. 2010. (*corresponding authors)

Kolonko EM, Albaugh BN, Lindner SE, Chen Y, Satyshur KA, Arnold KM, Kaufman PD, Keck JL, and Denu JM. Catalytic Activation of Histone Acetyltransferase Rtt109 by a Histone Chaperone. Proc Natl Acad Sci USA. 2010, 07(47):20275-80. PMCID: PMC2996700

Smith BC, Settles B, Hallows WC, Craven MW, Denu JM. SIRT3 Substrate Specificity Determined by Peptide Arrays and Machine Learning. ACS Chem Biol. 2011 Feb 18;6(2):146-57. PMCID: PMC3042044

Hallows, WC, Wei , Y, Smith, BC, Devries, MK, Ellinger, JJ, Someya, S, Shortreed, MR, Prolla, T, Markley, JL, Smith, LM, Zhao, S, Guan, K-L, Denu, JM. Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction. Molecular Cell, 41, 139-149, 2011. PMCID: PMC3101115

Pan PW, Feldman JL, Devries MK, Dong A, Edwards AM, Denu JM. Structure and Biochemical Functions of SIRT6. J Biol Chem. 2011 Mar 1. PMCID: PMC3077655

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 macro domain proteins as novel O-acetyl-ADP-ribose deacetylases. J Biol Chem. 2011 Jan 21. (*corresponding authors). PMCID: PMC3075673

Smith BC, Hallows WC, Denu JM. A continuous microplate assay for sirtuins and nicotinamide-producing enzymes. Anal Biochem. 2009 Nov 1;394(1):101-9. PMCID: PMC2752052.

Tong, L, Lee, S, and Denu, JM. Hydrolase regulates NAD metabolites and modulates cellular REDOX. J Biol Chem. 2009, Apr 24;284(17):11256-66. PMCID: PMC2670130.

Smith, BC, Hallows, WC, Denu, JM. Mechanisms and Molecular Probes of Sirtuins. Chemistry and Biology, 2008 Oct 20;15(10):1002-13. PMCID: PMC2626554.

Lee, S. Tong, L. and Denu, JM. Quantification of endogenous sirtuin metabolite O-acetyl-ADP-ribose. Anal Biochem. 2008 Dec 15;383(2):174-9. PMCID: PMC2586145.

Berndsen, CE, Tsubota, T, Lindner, SE, Lee, S, Holton, JM, Kaufman, PD, Keck, JL, and Denu, JM. Molecular functions of the histone acetyltransferase•chaperone complex Rtt109•Vps75. Nature Structural and Molecular Biology, 2008 Sep;15(9):948-56. PMCID: PMC2678805.

Kowieski TM, Lee S, Denu JM. Acetylation-dependent ADP-ribosylation by trypanosoma brucei sir2. J Biol Chem. Feb 2008 283(9):5317-26.

Smith, BC and Denu, JM. Mechanism-Based Inhibition of Sir2 Deacetylases by Thioacetyl-Lysine Peptide. Biochemistry. 2007, 46(50):14478-86.

Smith, BC and Denu, JM. Acetyl-lysine analog peptides as mechanistic probes of protein deacetylases. J Biol Chem. 2007, 282(51):37256-65.

Comstock, LR and Denu JM. Synthesis and biochemical evaluation of O-acetyl-ADP-ribose and N-acetyl analogs, Org. Biomol. Chem., 2007, 5(19):3087-91.

Smith, BC and Denu, JM. Sir2 Deacetylases Exhibit Nucleophilic Participation of Acetyl-lysine in NAD+ Cleavage. J Am Chem Soc. 2007 May 9;129(18):5802-3.

Denu, JM. Vitamins and Aging: Pathways to NAD+ Synthesis. Cell. 2007 May 4;129:453-454.

Grubisha, O, Rafty, LA, Takanishi, CL, Xu, X, Tong, L, Perraud, AL, Scharenberg, AM, Denu, JM. Metabolite of SIR2 reaction modulates TRPM2 ion channel. J Biol Chem. 281(20):14057-15065 (2006).

Smith, BC and Denu, JM. Sir2 Protein Deacetylases: Evidence for Chemical Intermediates and Functions of a Conserved Histidine.Biochemistry, 45(1):272-82 (2006).

Hallows, WC, Lee, S, Denu, JM. Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases. Proc Natl Acad Sci USA. 103(27):10230-5 (2006).

Rupa Sridharan

Tran, K.A., Jackson, S.A., Olufs, Z.P.G., Zaidan, N.Z., Leng, N., Kendziorski, C., Roy, S., and Sridharan, R. (2014) Collaborative rewiring of the pluripotency network by chromatin and signaling modulating pathways. In press Nature Communications

Jackson, S.A. and Sridharan, R.  (2013) The nexus of Tet1 and the pluripotency network. Cell Stem Cell, 12, 387-88.

Jackson, S.A. and Sridharan, R.  (2013) Peering into the black box of reprogramming to the pluripotent state. Curr Pathobiol Rep, 1,129-136.

Sridharan, R., Gonzales-Cope, M., Chronis, C.,Bonora, G., McKee, R., Patel,S.,Lopez,D., Mishra, N.,Pellegrini, M., Carey, M., Garcia, B.A. and Plath, K. (2013) Proteomic and genomic approaches reveal critical functions of H3K9 methylation and Heterochromatin Protein-1γ in reprogramming to pluripotency. Nat Cell Bio  doi10.1038/ncb2768.

Sridharan, R *., Tchieu, J *., Mason, M.J. *,Yachechko, R., Kuoy, E., Horvath, S., Zhou, Q. and Plath, K. (2009). Role of the murine reprogramming factors in the induction of pluripotency. * equal contribution. Cell, 136(2):364-77.

Maherali, N.*, Sridharan, R.*, Xie, W., Utikal, J., Eminli, S., Arnold, K., Stadtfeld, M., Yachechko, R., Tchieu. J., Jaenisch, R., Plath, K.#, and Hochedlinger, K.# (2007). Global epigenetic remodeling in directly reprogrammed fibroblasts.* equal contribution; # co-corresponding authors. Cell Stem Cell, 1(1): 55-70.

Lowry, W. E., Richter, L.,Yachechko, R., Pyle, A. D., Tchieu, J., Sridharan, R., Clark, A. T. and Plath, K.(2008). Generation of human induced pluripotent cells from dermal fibroblasts, PNAS, 105(8): 2883-88.

Sridharan, R., and Plath, K. (2008). Illuminating the black box of reprogramming. Cell Stem Cell, 2(4): 295-97.

Gaspar-Maia, A., Alajem, A., Polesso, F., Sridharan, R., Mason, M.J., Heidersbach, A., Ramalho-Santos, J., McManus, M.T., Plath, K., Meshorer, E. and Ramalho-Santos, M. (2009). Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature, 460(7257):863-8

Xie, W., Song, C., Sperling, A., Xu, F., Sridharan, R., Conway, A., Plath, K., Clark, A.T. and Grunstein, M. (2009). Histone H3 K56 acetylation marks canonical histone genes and the core transcriptional network for pluripotency in human embryonic stem cells. Mol Cell, 33(4):417-27

Sridharan, R. and Plath, K. (2011) Small RNAs loom large during reprogramming. Cell Stem Cell, 8, 599-601.

Lin, J.J., Lehmann, L.W., Bonora, G., Sridharan, R., Vashisht, A.A., Tran, N., Plath, K., Wohlschlegel, J.A., Carey, M. (2011) Mediator coordinates PIC assembly with recruitment of CHD1. Genes Dev 25, 2198-209.

Papathanasiou, P., Perkins, A. C., Cobb, B. S., Ferrini, R., Sridharan, R., Hoyne, G. F., Nelms, K. A., Smale, S.T., and Goodnow,C.C. (2003). Widespread failure of hematolymphoid differentiation caused by a recessive niche-filling allele of the Ikaros transcription factor. Immunity 19(1):131-44.

Su, R. C., Sridharan, R., and Smale, S.T. (2005). Assembly of silent chromatin during thymocyte development. Semin Immunol 17(2):129-40

Ramirez-Carrozzi, V. R., Nazarian, A. A., Li, C. C., Gore, S.L., Sridharan, R., Imbalzano, A. N., and Smale, S. T. (2006). Selective and antagonistic functions of SWI/SNF and Mi-2beta nucleosome remodeling complexes during an inflammatory response. Genes Dev 20(3):282-96.

Sridharan, R., and Smale, S.T. (2007). Predominant interaction of both Ikaros and Helios with the NuRD complex in immature thymocytes. J Biol Chem, 282(41): 20227-38.