J. Denu

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Sirt3 Substrate Specificity Determined by Peptide Arrays and Machine Learning

Mark W. Craven, Brian C. Smith, B. Settles, 2022 .

J. Denu, M. Borra, 2006 .

Mechanistic Basis for Catalytic Activation of Mitogen-activated Protein Kinase Phosphatase 3 by Extracellular Signal-regulated Kinase*

J. Denu, C. Fjeld, A. Rice, 2000, The Journal of Biological Chemistry.

THE PLANT HOMEODOMAIN ( PHD ) FINGERS OF CHD 4 ARE HISTONE H 3-BINDING MODULES WITH PREFERENCE FOR UNMODIFIED H 3 K 4 AND METHYLATED H 3 K 9

J. Denu, J. Mackay, C. Musselman, 2011 .

Identification of Macrodomain Proteins as Novel O-Acetyl-ADP-ribose Deacetylases*

John M Denu, Frank von Delft, Opher Gileadi, 2011, The Journal of Biological Chemistry.

Gut microbiome variation modulates the effects of dietary fiber on host metabolism

J. Denu, Zheng-Zheng Tang, F. Rey, 2020, Microbiome.

Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose.

R. Sternglanz, J. Denu, J. Landry, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Protein tyrosine phosphatases: mechanisms of catalysis and regulation.

J. Dixon, J. Denu, J. Dixon, 1998, Current opinion in chemical biology.

Metabolic regulation of histone post-translational modifications.

J. Denu, Jing Fan, Kimberly A Krautkramer, 2015, ACS chemical biology.

Dynamic Interplay between Histone H3 Modifications and Protein Interpreters: Emerging Evidence for a “Histone Language”

J. Denu, S. Oliver, Samuel S. Oliver, 2011, Chembiochem : a European journal of chemical biology.

Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases

W. C. Hallows, J. Denu, John M. Denu, 2006, Proceedings of the National Academy of Sciences.

Sirtuin 1 inhibition delays cyst formation in autosomal-dominant polycystic kidney disease.

E. Avner, J. Denu, W. Sweeney, 2013, The Journal of clinical investigation.

Circadian Control of Fatty Acid Elongation by SIRT1 Protein-mediated Deacetylation of Acetyl-coenzyme A Synthetase 1*

P. Baldi, W. C. Hallows, J. Denu, 2014, The Journal of Biological Chemistry.

of Acetyl-coenzyme A Synthetase 1 by SIRT 1 Protein-mediated Deacetylation Circadian Control of Fatty Acid Elongation Gene Regulation :

P. Baldi, W. C. Hallows, J. Denu, 2014 .

Peek Metabolism in Mice Cycle Drives Mitochondrial Oxidative + Circadian Clock NAD

Milan Mrksich, Navdeep S. Chandel, Wei Yu, 2013 .

Binding of the Fkh1 Forkhead Associated Domain to a Phosphopeptide within the Mph1 DNA Helicase Regulates Mating-Type Switching in Budding Yeast

J. Denu, C. Fox, Xiaolan Zhao, 2016, PLoS genetics.

Molecular reactions of protein phosphatases--insights from structure and chemistry.

J. Denu, M. Jackson, Michael D. Jackson, 2001, Chemical reviews.

Ure(k)a! Sirtuins Regulate Mitochondria

Brian C. Smith, W. C. Hallows, J. Denu, 2009, Cell.

Fasting drives the metabolic, molecular, and geroprotective effects of a calorie restricted diet in mice

Shany E. Yang, Dudley Lamming, J. Denu, 2021, Nature Metabolism.

Mechanisms and Dynamics of Protein Acetylation in

J. Denu, Michael J. Smallegan, Michael J Smallegan, 2016 .

Kinetic and Structural Basis for Acyl-Group Selectivity and NAD(+) Dependence in Sirtuin-Catalyzed Deacylation.

Minoru Yoshida, John M Denu, J. Denu, 2015, Biochemistry.

Identification of a Tissue-Restricted Isoform of SIRT1 Defines a Regulatory Domain that Encodes Specificity.

J. Denu, Tandrika Chattopadhyay, Deepti Ramachandran, 2017, Cell reports.

Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys.

Paul D Hutchins, Jaime L. Stark, R. Colman, 2018, Cell metabolism.

The Near Eastern Origin of Cat Domestication

B. Hyman, E. Masliah, J. Denu, 2007 .

Analysis of O-Acetyl-ADP-ribose as a Target for Nudix ADP-ribose Hydrolases*

A. Perraud, A. Scharenberg, J. Denu, 2002, The Journal of Biological Chemistry.

Identification and characterization of small molecule inhibitors of a plant homeodomain finger.

N. Nath, J. Denu, John B Feltenberger, 2012, Biochemistry.

Protein-mediated Deacetylation Phosphoglycerate Mutase-1 by Sirt 1 Regulation of Glycolytic Enzyme Metabolism :

W. C. Hallows, J. Denu, Wei Yu, 2012 .

Metabolite of SIR2 Reaction Modulates TRPM2 Ion Channel*

A. Perraud, A. Scharenberg, J. Denu, 2006, Journal of Biological Chemistry.

Where in the cell is SIRT3?--functional localization of an NAD+-dependent protein deacetylase.

W. C. Hallows, J. Denu, Brittany N Albaugh, 2008, The Biochemical journal.

General method for rapid purification of native chromatin fragments

J. Denu, C. Fox, Spencer A. Haws, 2018, The Journal of Biological Chemistry.

Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes.

C. Peterson, L. Boyer, J. Denu, 2002, Molecular cell.

Acetylation-dependent ADP-ribosylation by Trypanosoma brucei Sir2*

J. Denu, Susan Lee, Terri M Kowieski, 2008, Journal of Biological Chemistry.

Molecular Reactions of Protein PhosphatasesInsights from Structure and Chemistry

J. Denu, Michael D. Jackson and, 2001 .

Site-Specific Lysine Acetylation Stoichiometry Across Subcellular Compartments.

J. Denu, J. Dowell, J. Baeza, 2019, Methods in molecular biology.

Form and Function in Protein Dephosphorylation

J. Dixon, J. Denu, J. Stuckey, 1996, Cell.

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

Wei Chen, J. Denu, Xuehua Zhong, 2018, Nature Communications.

The deacetylase Sirt6 activates the acetyltransferase GCN5 and suppresses hepatic gluconeogenesis.

P. Puigserver, S. Gygi, G. Shulman, 2012, Molecular cell.

EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis

Lloyd M. Smith, M. Scalf, J. Denu, 2018, Nature Genetics.

Revealing dynamic protein acetylation across subcellular compartments.

Oliver M. Bernhardt, Tejas Gandhi, L. Reiter, 2020, Journal of proteome research.

Fortifying the link between SIRT1, resveratrol, and mitochondrial function.

J. Denu, 2012, Cell metabolism.

SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production.

F. Alt, Lan Hua, J. Bunkenborg, 2010, Cell metabolism.

Structural and Kinetic Isotope Effect Studies of Nicotinamidase (Pnc1) from S. cerevisiae †

Brian C. Smith, J. Denu, J. Keck, 2012 .

High-throughput strategy to identify inhibitors of histone-binding domains.

J. Denu, Elise K. Wagner, Brittany N Albaugh, 2012, Methods in enzymology.

Sirt3 Mediates Reduction of Oxidative Damage and Prevention of Age-Related Hearing Loss under Caloric Restriction

Wei Yu, Tomas A. Prolla, Masaru Tanokura, 2010, Cell.

SIRT3 deficiency decreases oxidative-metabolism capacity but increases lifespan under caloric restriction

Dudley Lamming, T. Prolla, J. Denu, 2022, bioRxiv.

SIRT1 top 40 hits: use of one-bead, one-compound acetyl-peptide libraries and quantum dots to probe deacetylase specificity.

J. Denu, A. Garske, 2006, Biochemistry.

Catalysis by protein acetyltransferase Gcn5.

J. Denu, Brittany N Albaugh, 2020, Biochimica et biophysica acta. Gene regulatory mechanisms.

Histone Acetyltransferase 1 Links Metabolism and Transcription to Cell-Cycle Progression.

J. Denu, 2019, Molecular cell.

Intramolecular dephosphorylation of ERK by MKP3.

J. Denu, A. Rice, Youngjo Kim, 2003, Biochemistry.

Intrinsic primary, secondary, and solvent kinetic isotope effects on the reductive half-reaction of D-amino acid oxidase: evidence against a concerted mechanism.

J. Denu, P. Fitzpatrick, 1994, Biochemistry.

pH and kinetic isotope effects on the reductive half-reaction of D-amino acid oxidase.

J. Denu, P. Fitzpatrick, 1992, Biochemistry.

Dynamic acetylation of cytosolic phosphoenolpyruvate carboxykinase toggles enzyme activity between gluconeogenic and anaplerotic reactions

D. Sinclair, J. Denu, José, 2018 .

Dysregulation of Sirtuin 2 (SIRT2) and histone H3K18 acetylation pathways associates with adverse prostate cancer outcomes

J. Denu, Wei Huang, G. Allen, 2017, BMC Cancer.

Visualization of intermediate and transition-state structures in protein-tyrosine phosphatase catalysis.

J. Dixon, J. Denu, J. Dixon, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Histone Lysine-to-Methionine Mutations Reduce Histone Methylation and Cause Developmental Pleiotropy1[OPEN]

J. Denu, Xuehua Zhong, Shuiming Qian, 2017, Plant Physiology.

NAD+ deficiency in age-related mitochondrial dysfunction.

T. Prolla, J. Denu, 2014, Cell metabolism.

Mutational Analysis of Conserved Residues in the GCN5 Family of Histone Acetyltransferases*

J. Denu, K. G. Tanner, M. R. Langer, 2001, The Journal of Biological Chemistry.

Nucleosome recognition by the Piccolo NuA4 histone acetyltransferase complex.

Christopher E. Berndsen, J. Denu, Song Tan, 2007, Biochemistry.

Insights derived from the structures of the Ser/Thr phosphatases calcineurin and protein phosphatase 1.

J. Dixon, J. Denu, J. Dixon, 1995, Structure.

Discovery and Mechanism of Small Molecule Inhibitors Selective for the Chromatin-Binding Domains of Oncogenic UHRF1.

J. Denu, G. Ananiev, S. Wildman, 2022, Biochemistry.

SLC13A5/sodium-citrate co-transporter overexpression causes disrupted white matter integrity and an autistic-like phenotype.

John-Paul J. Yu, R. Pearce, J. Denu, 2022, Brain communications.

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway

J. Denu, A. Audhya, L. Puglielli, 2021, Scientific Reports.

Acetyl-CoA flux regulates the proteome and acetyl-proteome to maintain intracellular metabolic crosstalk

J. Coon, J. Denu, L. Puglielli, 2019, Nature Communications.

Multivalent recognition of histone tails by the PHD fingers of CHD5.

J. Denu, J. Svaren, C. Musselman, 2012, Biochemistry.

Transition state analysis and requirement of Asp-262 general acid/base catalyst for full activation of dual-specificity phosphatase MKP3 by extracellular regulated kinase.

J. Denu, A. Rice, A. Hengge, 2001, Biochemistry.

Histone Acid Extraction and High Throughput Mass Spectrometry to Profile Histone Modifications in Arabidopsis thaliana

J. Denu, Xuehua Zhong, J. Dowell, 2022, Current protocols.

Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications.

J. Denu, J. Mackay, C. Musselman, 2009, The Biochemical journal.

Purification and characterization of the low molecular weight protein tyrosine phosphatase, Stp1, from the fission yeast Schizosaccharomyces pombe.

P. Russell, G. Zhou, J. Denu, 1995, Biochemistry.

Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System

Gabriel L. Lozano, Nichole A. Broderick, J. Handelsman, 2019, Applied and Environmental Microbiology.

Bacterial analogs of plant piperidine alkaloids mediate microbial interactions in a rhizosphere model system

Gabriel L. Lozano, Nichole A. Broderick, J. Handelsman, 2018 .

Trimethylamine N-oxide reduces neurite density and plaque intensity in a murine model of Alzheimer’s disease

John-Paul J. Yu, B. Bendlin, J. Denu, 2022, bioRxiv.

Metabolomic Analysis of Carbohydrate and Amino Acid Changes Induced by Hypoxia in Naked Mole-Rat Brain and Liver

J. Denu, R. Dhillon, Yiming Qin, 2022, Metabolites.

Intrinsic catalytic properties of histone H3 lysine-9 methyltransferases preserve monomethylation levels under low S-adenosylmethionine

G. Craciun, J. Denu, Spencer A. Haws, 2022, bioRxiv.

Antagonistic H3K79me-H3K9ac crosstalk determines elongation at housekeeping genes to promote pluripotency

J. Denu, R. Sridharan, Spencer A. Haws, 2022, bioRxiv.

Kinetic mechanism of human histone acetyltransferase P/CAF.

J. Denu, K. G. Tanner, M. R. Langer, 2000, Biochemistry.

Sirtuins caught in the act.

Brian C. Smith, J. Denu, 2006, Structure.

Vitamin B3 and sirtuin function.

J. Denu, 2005, Trends in biochemical sciences.

Extracellular Regulated Kinases (ERK) 1 and ERK2 Are Authentic Substrates for the Dual-specificity Protein-tyrosine Phosphatase VHR

J. Denu, K. G. Tanner, Jacob L. Todd, 1999, The Journal of Biological Chemistry.

Potent activation of NAD+-dependent deacetylase Sirt7 by nucleosome binding

J. Denu, Mark A. Klein, Wallace H. Liu, 2022, bioRxiv.

SIRT3 deficiency decreases oxidative metabolism capacity but increases lifespan in male mice under caloric restriction

Dudley Lamming, T. Prolla, J. Denu, 2022, Aging cell.

Quantification of endogenous sirtuin metabolite O-acetyl-ADP-ribose.

J. Denu, Susan Lee, Lei Tong, 2008, Analytical biochemistry.

Mechanism-based inhibition of Sir2 deacetylases by thioacetyl-lysine peptide.

Brian C. Smith, John M Denu, J. Denu, 2007, Biochemistry.

Vitamins and Aging: Pathways to NAD+ Synthesis

J. Denu, 2007, Cell.

Circadian Clock NAD+ Cycle Drives Mitochondrial Oxidative Metabolism in Mice

J. Denu, N. Chandel, O. Ilkayeva, 2013, Science.

Chemical mechanisms of histone lysine and arginine modifications.

Brian C. Smith, J. Denu, John M. Denu, 2009, Biochimica et biophysica acta.

Trimethylamine N-oxide reduces neurite density and plaque intensity in a murine model of Alzheimer’s disease

John-Paul J. Yu, B. Bendlin, J. Denu, 2022, bioRxiv.

Hydrolysis of O-Acetyl-ADP-ribose Isomers by ADP-ribosylhydrolase 3*

Brian C. Smith, J. Denu, J. Moss, 2011, The Journal of Biological Chemistry.

Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin

J. Denu, Kimberly A Krautkramer, R. Dhillon, 2017, Translational research : the journal of laboratory and clinical medicine.

Chemical signaling between gut microbiota and host chromatin: What is your gut really saying?

J. Denu, F. Rey, Kimberly A Krautkramer, 2017, The Journal of Biological Chemistry.

Synthesis and biochemical evaluation of O-acetyl-ADP-ribose and N-acetyl analogs.

J. Denu, Lindsay R. Comstock, 2007, Organic & biomolecular chemistry.

Structural Identification of 2′- and 3′-O-Acetyl-ADP-ribose as Novel Metabolites Derived from the Sir2 Family of β-NAD+-dependent Histone/Protein Deacetylases* 210

J. Denu, M. Jackson, 2002, The Journal of Biological Chemistry.

A continuous, nonradioactive assay for histone acetyltransferases.

J. Denu, Y. Kim, K. G. Tanner, 2000, Analytical biochemistry.

Coenzyme Specificity of Sir2 Protein Deacetylases

Brian C. Smith, J. Denu, Manning T Schmidt, 2004, Journal of Biological Chemistry.

Kinetic Mechanism of the Histone Acetyltransferase GCN5 from Yeast*

J. Denu, K. G. Tanner, Y Kim, 2000, The Journal of Biological Chemistry.

Structural basis for the recognition of a bisphosphorylated MAP kinase peptide by human VHR protein Phosphatase.

J. Denu, M. Schumacher, A. Rice, 2002, Biochemistry.

Mechanism of Human SIRT1 Activation by Resveratrol*

Brian C. Smith, John M Denu, J. Denu, 2005, Journal of Biological Chemistry.

Calcium-mediated inactivation of the MAP kinase pathway in sea urchin eggs at fertilization.

D. J. Carroll, J. Denu, M. Kumano, 2001, Developmental biology.

Short-chain fatty acids activate acetyltransferase p300

J. Denu, Sydney P. Thomas, 2021, bioRxiv.

Hydrolase Regulates NAD+ Metabolites and Modulates Cellular Redox

J. Denu, Susan Lee, Lei Tong, 2009, Journal of Biological Chemistry.

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues.

John M Denu, A. Attie, J. Denu, 2016, Molecular cell.

Substrate specificity and kinetic mechanism of the Sir2 family of NAD+-dependent histone/protein deacetylases.

J. Denu, M. Borra, J. Slama, 2004, Biochemistry.

Histone acetyltransferases.

C. Allis, J. Denu, S. Roth, 2001, Annual review of biochemistry.

Kinetic mechanism of adenine phosphoribosyltransferase from Leishmania donovani.

C. Bashor, J. Denu, R. Brennan, 2002, Biochemistry.

Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome.

Wei Yu, Sushmita Roy, Derek J. Bailey, 2013, Molecular cell.

The Acetyltransferase Activity of CBP Is Required for wingless Activation and H4 Acetylation in Drosophila melanogaster

J. Denu, R. Goodman, S. Smolik, 2002, Molecular and Cellular Biology.

Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation.

C. Allis, J. Denu, P. Sassone-Corsi, 2000, Molecular cell.

Function and metabolism of sirtuin metabolite O-acetyl-ADP-ribose.

J. Denu, Lei Tong, 2010, Biochimica et biophysica acta.

Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes.

Michael A. Freitas, Christopher E. Berndsen, J. Denu, 2007, Molecular cell.

Plant Homeodomain (PHD) Fingers of CHD4 Are Histone H3-binding Modules with Preference for Unmodified H3K4 and Methylated H3K9*

J. Denu, J. Mackay, C. Musselman, 2011, The Journal of Biological Chemistry.

Kinetic mechanism of histone acetyltransferase and chaperone complex, Rtt109-Vps75 †

J. Denu, Brittany N Albaugh, Erin M. Kolonko, 2011 .

Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex.

J. Denu, Brittany N Albaugh, Erin M. Kolonko, 2010, Biochemistry.

Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence

Deyang Yu, Shany E. Yang, Dudley Lamming, 2019, bioRxiv.

An inactivating mutation in the histone deacetylase SIRT6 causes human perinatal lethality

R. Sadreyev, J. Denu, R. Mostoslavsky, 2018, Genes & development.

Iron Deprivation Induces Transcriptional Regulation of Mitochondrial Biogenesis*

J. Denu, D. Pagliarini, Kimberly A. Krautkramer, 2016, The Journal of Biological Chemistry.

Linking chromatin function with metabolic networks: Sir2 family of NAD(+)-dependent deacetylases.

J. Denu, 2003, Trends in biochemical sciences.

Conserved Enzymatic Production and Biological Effect of O-Acetyl-ADP-ribose by Silent Information Regulator 2-like NAD+-dependent Deacetylases*

J. Denu, E. Verdin, M. Borra, 2002, The Journal of Biological Chemistry.

Metabolism in the Midwest: research from the Midwest Aging Consortium at the 49th Annual Meeting of the American Aging Association

Dudley Lamming, J. Denu, Hua Bai, 2021, GeroScience.

PGC‐1a integrates a metabolism and growth network linked to caloric restriction

J. Ntambi, J. Denu, A. Roopra, 2019, Aging cell.

Mechanisms and Dynamics of Protein Acetylation in Mitochondria.

John M Denu, J. Denu, Josue Baeza, 2016, Trends in biochemical sciences.

Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction.

Lloyd M. Smith, Brian C. Smith, James J. Ellinger, 2011, Molecular cell.

The human Sir2 ortholog, SIRT2, is an NAD+-dependent tubulin deacetylase.

J. Denu, E. Verdin, M. Borra, 2003, Molecular cell.

Biological and catalytic functions of sirtuin 6 as targets for small-molecule modulators

J. Denu, Mark A. Klein, 2020, The Journal of Biological Chemistry.

NUP98-PHF23 is a chromatin-modifying oncoprotein that causes a wide array of leukemias sensitive to inhibition of PHD histone reader function.

P. Meltzer, S. Bilke, Y. Ning, 2014, Cancer discovery.

Reader Function a Wide Array of Leukemias Sensitive to Inhibition of PHD Histone PHF23 Is a Chromatin-Modifying Oncoprotein That Causes

P. Meltzer, S. Bilke, Y. Ning, 2014 .

Sirt6 regulates lifespan in Drosophila melanogaster

J. Boeke, S. Helfand, J. Denu, 2022, Proceedings of the National Academy of Sciences.

Specific and reversible inactivation of protein tyrosine phosphatases by hydrogen peroxide: evidence for a sulfenic acid intermediate and implications for redox regulation.

J. Denu, K. G. Tanner, 1998, Biochemistry.

Catalysis and Mechanistic Insights into Sirtuin Activation

J. Denu, Jessica L. Feldman, Jessica L Feldman, 2011, Chembiochem : a European journal of chemical biology.

Collagen Matrix Density Drives the Metabolic Shift in Breast Cancer Cells

J. Castracane, J. Denu, J. Condeelis, 2016, EBioMedicine.

SIRT3 mediates multi-tissue coupling for metabolic fuel switching.

Jing Fan, Sushmita Roy, John M Denu, 2015, Cell metabolism.

Site-Specific Reactivity of Nonenzymatic Lysine Acetylation

J. Denu, Josue Baeza, Michael J. Smallegan, 2015, ACS chemical biology.

The Purification and Characterization of a Human Dual-specific Protein Tyrosine Phosphatase (*)

J. Dixon, J. Denu, Gaochao Zhou, 1995, The Journal of Biological Chemistry.

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

Richard Bonneau, Dan Knights, Gabriel A Al-Ghalith, 2018, eLife.

Identifying Dysregulated Epigenetic Enzyme Activity in Castrate-Resistant Prostate Cancer Development.

J. Denu, E. Corey, Wei Huang, 2017, ACS chemical biology.

New Frontiers in Epigenetic Modifications

J. Denu, A. Garske, 2009 .

1 New Frontiers in Epigenetic Modifications

J. Denu, A. Garske, 2009 .

Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75

Christopher E. Berndsen, J. Holton, J. Denu, 2008, Nature Structural &Molecular Biology.

The Sir 2 family of protein deacetylases.

J. Denu, 2005, Current opinion in chemical biology.

Sir2 protein deacetylases: evidence for chemical intermediates and functions of a conserved histidine.

Brian C. Smith, J. Denu, 2006, Biochemistry.

Mechanism of Nicotinamide Inhibition and Transglycosidation by Sir2 Histone/Protein Deacetylases*

N. Oppenheimer, J. Denu, Manning T Schmidt, 2003, Journal of Biological Chemistry.

Metabolism and the Epigenome: A Dynamic Relationship.

J. Denu, Spencer A. Haws, Cassandra M Leech, 2020, Trends in biochemical sciences.

Activation of the Protein Deacetylase SIRT6 by Long-chain Fatty Acids and Widespread Deacylation by Mammalian Sirtuins* ♦

John M Denu, J. Denu, Jessica L. Feldman, 2013, The Journal of Biological Chemistry.

A catalytic mechanism for the dual-specific phosphatases.

J. Dixon, J. Denu, J. Dixon, 1995, Proceedings of the National Academy of Sciences of the United States of America.

Combinatorial profiling of chromatin-binding modules reveals multi-site discrimination

Benjamin A. Garcia, Gary LeRoy, Tatiana G. Kutateladze, 2009, Nature chemical biology.

Kinetic Analysis of Human Serine/Threonine Protein Phosphatase 2Cα*

J. Denu, C. Fjeld, Clark C. Fjeld, 1999, The Journal of Biological Chemistry.

Increased expression of SLC25A1/CIC causes an autistic-like phenotype with altered neuron morphology.

John-Paul J. Yu, R. Pearce, J. Denu, 2022, Brain : a journal of neurology.

Acetyl-lysine Analog Peptides as Mechanistic Probes of Protein Deacetylases*

Brian C. Smith, J. Denu, 2007, Journal of Biological Chemistry.

Modulating Acetyl-CoA Binding in the GCN5 Family of Histone Acetyltransferases*

John M Denu, C. Peterson, J. Denu, 2002, The Journal of Biological Chemistry.

Benchmarking Quantitative Performance in Label-Free Proteomics

J. Denu, E. Armstrong, J. Dowell, 2021, ACS omega.

Regulation of Glycolytic Enzyme Phosphoglycerate Mutase-1 by Sirt1 Protein-mediated Deacetylation♦

J. Denu, Wei Yu, William C Hallows, 2011, The Journal of Biological Chemistry.

Structure and Biochemical Functions of SIRT6*

P. Pan, J. Denu, A. Dong, 2011, The Journal of Biological Chemistry.

Reading the Combinatorial Histone Language.

J. Denu, Zhangli Su, 2016, ACS chemical biology.

ChIP-less analysis of chromatin states

B. Garcia, J. Denu, Shichong Liu, 2014, Epigenetics & Chromatin.

Catalysis and substrate selection by histone/protein lysine acetyltransferases.

Christopher E. Berndsen, John M Denu, J. Denu, 2008, Current opinion in structural biology.

Sirtuin Catalysis and Regulation*

J. Denu, Jessica L. Feldman, Jessica L Feldman, 2012, The Journal of Biological Chemistry.

Mechanisms and molecular probes of sirtuins.

Brian C. Smith, J. Denu, William C Hallows, 2008, Chemistry & biology.

Loss of SIRT3 Provides Growth Advantage for B Cell Malignancies*

J. Denu, Wei Yu, P. Hematti, 2015, The Journal of Biological Chemistry.

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model

F. Bäckhed, A. Lusis, J. Denu, 2018, Nature Microbiology.

Dynamic Acetylation of Phosphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions.

D. Sinclair, J. Carrodeguas, J. Denu, 2018, Molecular cell.

Environmental Impact on Epigenetic Histone Language

J. Denu, 2013 .

A practical guide for analysis of histone post-translational modifications by mass spectrometry: best practices and pitfalls.

Sydney P Thomas, Spencer A Haws, Laura E Borth, 2019, Methods.

Dynamic Acetylation of Ph osphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions Graphical Abstract Highlights

D. Sinclair, J. Carrodeguas, J. Denu, 2018 .

Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone

J. Denu, K. Satyshur, J. Keck, 2010, Proceedings of the National Academy of Sciences.

Roles of aspartic acid-181 and serine-222 in intermediate formation and hydrolysis of the mammalian protein-tyrosine-phosphatase PTP1.

J. Dixon, J. Denu, J. Dixon, 1997, Biochemistry.

The catalytic role of Cys124 in the dual specificity phosphatase VHR.

G. Zhou, J. Dixon, J. Denu, 1994, The Journal of biological chemistry.

Using comparative biology to understand how aging affects mitochondrial metabolism

J. Denu, R. Dhillon, 2017, Molecular and Cellular Endocrinology.

Endoplasmic reticulum acetyltransferases Atase1 and Atase2 differentially regulate reticulophagy, macroautophagy and cellular acetyl-CoA metabolism

J. Denu, L. Puglielli, Gulpreet Kaur, 2021, Communications Biology.

Increased expression of AT-1/SLC33A1 causes an autistic-like phenotype in mice by affecting dendritic branching and spine formation

Heather A. Mitchell, J. Denu, L. Puglielli, 2016, The Journal of experimental medicine.

Autoacetylation of the Histone Acetyltransferase Rtt109*

J. Denu, Susan Lee, Brittany N Albaugh, 2011, The Journal of Biological Chemistry.

A Single Mutation Converts a Novel Phosphotyrosine Binding Domain into a Dual-specificity Phosphatase (*)

J. Denu, J. Dixon, John A. Williams, 1995, The Journal of Biological Chemistry.

Pancreatic β-Cells From Mice Offset Age-Associated Mitochondrial Deficiency With Reduced KATP Channel Activity

Emma L. Baar, Dudley Lamming, J. Denu, 2016, Diabetes.

Obesity-dependent CDK1 signaling stimulates mitochondrial respiration at complex I in pancreatic β-cells

J. Denu, D. Pagliarini, R. Dhillon, 2019, The Journal of Biological Chemistry.

Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase

J. Denu, B. Volkman, I. Ahel, 2011, The Journal of Biological Chemistry.

Redox regulation of protein tyrosine phosphatases by hydrogen peroxide: detecting sulfenic acid intermediates and examining reversible inactivation.

J. Denu, K. G. Tanner, 2002, Methods in enzymology.

Disrupting the reader of histone language.

John M Denu, J. Denu, Samuel S. Oliver, 2011, Angewandte Chemie.

Crystal Structure of the Dual Specificity Protein Phosphatase VHR

Jack E. Dixon, J. Dixon, J. Denu, 1996, Science.

Small molecule regulation of Sir2 protein deacetylases

Brian C. Smith, John M Denu, J. Denu, 2005, The FEBS journal.

Methyl magic and HAT tricks

J. Denu, R. Dutnall, 2002, Nature Structural Biology.

The Sirtuin family: therapeutic targets to treat diseases of aging.

J. Denu, J. Milne, 2008, Current opinion in chemical biology.

Stoichiometry of Site-specific Lysine Acetylation in an Entire Proteome*♦

Daniel Amador-Noguez, J. Denu, D. Amador-Noguez, 2014, The Journal of Biological Chemistry.

Purification and Kinetic Characterization of the Mitogen-activated Protein Kinase Phosphatase rVH6*

J. Denu, J. Dixon, R. Mourey, 1996, The Journal of Biological Chemistry.

Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression

Joel P Mackay, John M Denu, J. Denu, 2012, Proceedings of the National Academy of Sciences.

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

Wei Chen, J. Denu, Xuehua Zhong, 2018, Nature Communications.

Reader domain specificity and lysine demethylase-4 family function

Ekaterina Voronina, Mitchell D. Miller, John M Denu, 2016, Nature Communications.

Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex.

J. Denu, Susan Lee, Kevin M. Arnold, 2011, Biochemistry.

Revealing dynamic protein acetylation across subcellular compartments.

Oliver M. Bernhardt, Tejas Gandhi, L. Reiter, 2018, Journal of proteome research.

Quantifying dynamic protein acetylation using quantitative stoichiometry

Oliver M. Bernhardt, Tejas Gandhi, L. Reiter, 2018, bioRxiv.

SIRT3 Protein Deacetylates Isocitrate Dehydrogenase 2 (IDH2) and Regulates Mitochondrial Redox Status*♦

J. Denu, Wei Yu, Kristin E. Dittenhafer-Reed, 2012, The Journal of Biological Chemistry.

A continuous microplate assay for sirtuins and nicotinamide-producing enzymes.

Brian C. Smith, J. Denu, William C Hallows, 2009, Analytical biochemistry.

A combinatorial H4 tail library for exploring the histone code.

G. Craciun, J. Denu, A. Garske, 2008, Biochemistry.

Dysregulation of Sirtuin 2 (SIRT2) and histone H3K18 acetylation pathways associates with adverse prostate cancer outcomes

J. Denu, Wei Huang, G. Allen, 2017, BMC Cancer.

KAT(ching) Metabolism by the Tail: Insight into the Links between Lysine Acetyltransferases and Metabolism

J. Denu, Brittany N. Albaugh , Kevin M. Arnold , 2011, Chembiochem : a European journal of chemical biology.

Quantification of Mitochondrial Acetylation Dynamics Highlights Prominent Sites of Metabolic Regulation*

M. Westphall, A. Attie, J. Coon, 2013, The Journal of Biological Chemistry.

Acss2 Deletion Reveals Functional Versatility via Tissue-Specific Roles in Transcriptional Regulation

J. Moffett, P. Arun, A. Namboodiri, 2023, International journal of molecular sciences.

Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6

P. Griffin, C. Peterson, J. Denu, 2020, Nature Communications.

Mechanism of activation for the sirtuin 6 protein deacylase

J. Denu, Weiping Tang, Mark A. Klein, 2019, The Journal of Biological Chemistry.

RNA Molecules That Bind to and Inhibit the Active Site of a Tyrosine Phosphatase*

A. Ellington, J. Denu, J. Dixon, 1998, The Journal of Biological Chemistry.

CHAPTER 109 – Protein Tyrosine Phosphatase Structure and Mechanisms

J. Denu, Youngjo Kim, 2003 .

The catalytic role of aspartic acid-92 in a human dual-specific protein-tyrosine-phosphatase.

G. Zhou, J. Dixon, J. Denu, 1995, Biochemistry.

Transition-state structures for the native dual-specific phosphatase VHR and D92N and S131A mutants. Contributions to the driving force for catalysis.

J. Dixon, J. Denu, A. Hengge, 1996, Biochemistry.

Assays for mechanistic investigations of protein/histone acetyltransferases.

Christopher E. Berndsen, J. Denu, 2005, Methods.

Quantitative assays for characterization of the Sir2 family of NAD(+)-dependent deacetylases.

J. Denu, M. Borra, 2004, Methods in enzymology.

Catalytic mechanism of a MYST family histone acetyltransferase.

Song Tan, Christopher E. Berndsen, John M Denu, 2007, Biochemistry.

Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity

A. Velázquez‐Campoy, J. Carrodeguas, J. Denu, 2020, The Journal of biological chemistry.

Tandem histone methyltransferase upregulation defines a unique aggressive prostate cancer phenotype

J. Denu, G. Allen, D. Jarrard, 2021, British Journal of Cancer.

Gut microbiome variation modulates the effects of dietary fiber on host metabolism

J. Denu, Zheng-Zheng Tang, F. Rey, 2021, Microbiome.

Intrinsic catalytic properties of histone H3 lysine-9 methyltransferases preserve monomethylation levels under low S-adenosylmethionine

G. Craciun, J. Denu, R. Trievel, 2023, bioRxiv.

Nuclear‐cytoplasmic localization of acetyl coenzyme a synthetase‐1 in the rat brain

D. Jacobowitz, J. Moffett, P. Arun, 2010, The Journal of comparative neurology.

Linking SIRT2 to Parkinson's disease.

Brian C. Smith, J. Denu, A. Garske, 2007, ACS chemical biology.

Crystal structure of VHR, a dual-specificity phosphatase

J. Dixon, J. Denu, J. Yuvaniyama, 1996 .

Dual-specificity protein tyrosine phosphatase VHR down-regulates c-Jun N-terminal kinase (JNK)

J. Denu, L. Rafty, J. Rigas, 2002, Oncogene.

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

J. Denu, P. Fitzpatrick, Kevin A. Kurtz, 1997 .

Metabolic acetate therapy improves phenotype in the tremor rat model of Canavan disease

J. Moffett, P. Arun, C. N. Madhavarao, 2010, Journal of Inherited Metabolic Disease.

Regulation of Histone Methylation via Methionine Metabolism

J. Denu, Spencer A. Haws, 2017 .

Author response: Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

Benjamin M Hillmann, Robin R. Shields-Cutler, Richard Bonneau, 2018 .

Catalytic Mechanism and Function of Invariant Glutamic Acid 173 from the Histone Acetyltransferase GCN5 Transcriptional Coactivator*

S. Berger, C. Allis, J. Denu, 1999, The Journal of Biological Chemistry.

Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry.

Lukas Reiter, John M Denu, L. Reiter, 2015, Journal of proteome research.

The C-Terminus of Human Nucleotide Receptor P2X7 Is Critical for Receptor Oligomerization and N-Linked Glycosylation

J. Denu, P. Bertics, L. Denlinger, 2013, PloS one.

Identification of and Molecular Basis for SIRT6 Loss-of-Function Point Mutations in Cancer.

G. Getz, C. Mermel, J. Denu, 2015, Cell Reports.

MARCC (Matrix‐Assisted Reader Chromatin Capture): An Antibody‐Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications

J. Denu, Zhangli Su, John M. Denu, 2015, Current protocols in molecular biology.

A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics*

B. Garcia, J. Denu, K. Karch, 2016, Molecular & Cellular Proteomics.

Acetylation in an Entire Proteome Stoichiometry of Site-specific Lysine Genomics and Proteomics :

J. Denu, D. Amador-Noguez, Jing Fan, 2014 .

Structural and kinetic isotope effect studies of nicotinamidase (Pnc1) from Saccharomyces cerevisiae.

Brian C. Smith, J. Denu, W. Cleland, 2012, Biochemistry.

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model

F. Bäckhed, A. Lusis, J. Denu, 2018, Nature Microbiology.

Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in a Rhizosphere Model System

Gabriel L. Lozano, J. Handelsman, J. Crawford, 2019, Applied and Environmental Microbiology.

Structure of Arabidopsis thaliana At1g77540 protein, a minimal acetyltransferase from the COG2388 family.

Christopher E. Berndsen, G. Phillips, J. Markley, 2006, Biochemistry.

Development of a multiplex assay to assess activated p300/CBP in circulating prostate tumor cells

J. Lang, J. Denu, D. Jarrard, 2023, Oncotarget.

1 STRUCTURE AND BIOCHEMICAL FUNCTIONS OF SIRT 6

P. Pan, J. Denu, A. Dong, 2011 .

1 AUTOACETYLATION OF THE HISTONE ACETYLTRANSFERASE RTT 109 *

J. Denu, Susan Lee, Brittany N Albaugh, 2011 .

Quantification of Mitochondrial Acetylation Dynamics Highlights Prominent Sites of Metabolic Regulation*

M. Westphall, A. Attie, J. Coon, 2013, Journal of Biological Chemistry.

Protein restriction slows the development and progression of Alzheimer’s disease in mice

Dudley Lamming, J. Denu, R. Babygirija, 2023, Research square.

Catalysis and Mechanistic Insights into Sirtuin Activation

J. Denu, Jessica L Feldman, Kristin E. Dittenhafer-Reed, 2011, Chembiochem : a European journal of chemical biology.

Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome.

Derek J. Bailey, T. Prolla, M. Westphall, 2013, Molecular cell.

Fortifying the link between SIRT1, resveratrol, and mitochondrial function.

J. Denu, 2012, Cell metabolism.

Using comparative biology to understand how aging affects mitochondrial metabolism

J. Denu, R. Dhillon, 2017, Molecular and Cellular Endocrinology.

SIRT3 substrate specificity determined by peptide arrays and machine learning.

J. Denu, Burr Settles, William C Hallows, 2011, ACS chemical biology.

Sirt3 promotes the urea cycle and fatty acid oxidation during dietary restriction.

Lloyd M. Smith, Brian C. Smith, James J. Ellinger, 2011, Molecular cell.

Sirt3 Substrate Specificity Determined by Peptide Arrays and Machine Learning Sirt3 Also Physically Interacts with at Least One of the Known

J. Denu, Burr Settles, William C Hallows, 2022 .

Revealing dynamic protein acetylation across subcellular compartments.

Oliver M. Bernhardt, Tejas Gandhi, L. Reiter, 2020, Journal of proteome research.

Probing the Function of Conserved Residues in the Serine/Threonine Phosphatase PP2Cα†

J. Denu, Clark C. Fjeld, M. Jackson, 2003 .

Probing the function of conserved residues in the serine/threonine phosphatase PP2Calpha.

J. Denu, Clark C. Fjeld, M. Jackson, 2003, Biochemistry.

The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse

J. Denu, Ildikó Kasza, K. Overmyer, 2023, Communications biology.

DOT1L is a barrier to histone acetylation during reprogramming to pluripotency

J. Denu, Spencer A. Haws, C. Wille, 2023, Science advances.

Identification of and Molecular Basis for SIRT6 Loss-of-Function Point Mutations in Cancer.

G. Getz, C. Mermel, J. Denu, 2015, Cell reports.

Dietary restriction of individual amino acids stimulates unique molecular responses in mouse liver

Dudley Lamming, J. Denu, R. Babygirija, 2023, bioRxiv.

Orphan Macrodomain Protein (Human C6orf130) Is an O-Acyl-ADP-ribose Deacylase

J. Denu, B. Volkman, F. Peterson, 2011, The Journal of Biological Chemistry.

Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex.

J. Denu, Susan Lee, Kevin M. Arnold, 2011, Biochemistry.

Nuclear‐cytoplasmic localization of acetyl coenzyme a synthetase‐1 in the rat brain

D. Jacobowitz, J. Moffett, C. N. Madhavarao, 2010, The Journal of comparative neurology.

Protein restriction slows the development and progression of pathology in a mouse model of Alzheimer’s disease

Dudley Lamming, J. Denu, Natalie M. Niemi, 2024, Nature communications.