Publications

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Protein restriction slows the development and progression of pathology in a mouse model of Alzheimer’s disease. Reji Babygirija, Michelle M Sonsalla, Jericha Mill, Isabella James, Jessica H Han, Cara L Green, Mariah F Calubag, Gina Wade, Anna Tobon, John Michael, Michaela M Trautman, Ryan Matoska, Chung-Yang Yeh, Isaac Grunow, Heidi H Pak, Michael J Rigby, Dominique A Baldwin, Natalie M Niemi, John M Denu, Luigi Puglielli, Judith Simcox, Dudley W Lamming. Nature Communications. 2024.

Dot1L is a barrier to histone acetylation during reprogramming to pluripotency. Coral K. Wille, Xiaoya Zhang, Spencer A. Haws, John M. Denu, Rupa Sridharan. Science Advances. 2023

The citrate transporters SLC13A5 and SLC25A1 elicit different metabolic responses and phenotypes in the mouse. Gonzalo Fernandez-Fuente, Katherine A Overmyer, Alexis J Lawton, Ildiko Kasza, Samantha L Shapiro, Patricia Gallego-Muñoz, Joshua J Coon, John M Denu, Caroline M Alexander, Luigi Puglielli. Communications Biology. 2023

Intrinsic catalytic properties of histone H3 lysine-9 methyltransferases preserve monomethylation levels under low S-adenosylmethionine. Spencer A. Haws*, Lillian J. Miller*, Diego Rojas La Luz, Vyacheslav I. Kuznetsov, Raymond C. Trievel, Gheorghe Craciun, and John M. Denu. JBC 2023. *These authors contributed equally.

SIRT3 deficiency decreases oxidative metabolism capacity but increases lifespan in male mice under caloric restriction. Dhillon RS, Qin YA, van Ginkel PR, Fu VX, Vann JM, Lawton AJ, Green CL, Manchado-Gobatto FB, Gobatto CA, Lamming DW, Prolla TA, Denu JM. Aging Cell 2022.

Trimethylamine N-Oxide Reduces Neurite Density and Plaque Intensity in a Murine Model of Alzheimer’s Disease. Zarbock KR, Han JH, Singh AP, Thomas SP, Bendlin BB, Denu JM, Yu JJ, Rey FE, Ulland TK. J Alzheimers Dis 2022.

Histone Acid Extraction and High Throughput Mass Spectrometry to Profile Histone Modifications in Arabidopsis thaliana. Scheid R, Dowell JA, Sanders D, Jiang J, Denu JM, and Zhong X. Current Protocols 2022.

Potent Activation of NAD ⁺-Dependent Deacetylase Sirt7 by Nucleosome Binding. Kuznetsov VI, Liu WH, Klein MA, and Denu JM. ACS Chem Biol. 2022.

Increased expression of SLC25A1/CIC causes an autistic-like phenotype with altered neuron morphology. Rigby MJ, Orefice NS, Lawton AJ, Ma M, Shapiro SL, Yi SY, Dieterich IA, Frelka A, Miles HN, Pearce RA, Yu JPJ, Li L, Denu JM, Puglielli L. Brain 2022.

Discovery and Mechanism of Small Molecule Inhibitors Selective for the Chromatin-Binding Domains of Oncogenic UHRF1. Liu WH, Miner RE, Albaugh BN, Ananiev GE, Wildman SA, Denu JM. Biochemistry 2022.

Sirt6 regulates lifespan in Drosophila melanogaster. Taylor JR, Wood JG, Mizerak E, Hinthorn S, Liu J, Finn M, Gordon S, Zingas L, Chang C, Klein MA, Denu JM, Gorbunova V, Seluanov A, Boeke JD, Sedivy JM, Helfand SL. PNAS 2022.

Metabolomic Analysis of Carbohydrate and Amino Acid Changes Induced by Hypoxia in Naked Mole-Rat Brain and Liver. Cheng H, Qin YA, Dhillon R, Dowell J, Denu JM, Pamenter ME. Metabolites 2022.

SLC13A5/NaCT overexpression causes disrupted white matter integrity and an autistic-like phenotype. Rigby MJ, Orefice NS, Lawton AJ, Ma M, Shapiro SL, Yi WY, Dieterich IA, Frelka A, Miles HN, Pearce RA, Yu JPJ, Denu JM, Puglielli L. Brain Communications 2022.

Short-chain fatty acids activate acetyltransferase p300. Thomas SP and Denu JM. eLife 2021.

Fasting drives the metabolic, molecular and geroprotective effects of a calorie-restricted diet in mice. Pak HH, Haws SA, Green CL, Koller M, Lavarias MT, Richardson NE, Yang SE, Dumas SN, Sonsalla M, Bray L, Johnson M, Barnes S, Darley-Usmar V, Zhang J, Yen CE, Denu JM, Lamming DW. Nat Metab. 2021.

Gut microbiome variation modulates the effects of dietary fiber on host metabolism. Murga-Garrido SM*, Hong Q*, Cross TL*, Hutchison ER, Han J, Thomas SP, Vivas EI, Denu JM, Ceschin DG, Tang ZZ, Rey FE. Microbiome 2021.

Tandem histone methyltransferase upregulation defines a unique aggressive prostate cancer phenotype. Filon M, Gawdzik J, Troung A, Allen G, Huang W, Khemees T, Machhi R, Lewis PW, Yang B, Denu JM, Jarrard D. British Journal of Cancer 2021.

Endoplasmic reticulum acetyltransferases Atase1 and Atase2 differentially regulate reticulophagy, macroautophagy and cellular acetyl-CoA metabolism. Rigby MJ, Lawton AJ, Kaur G, Banduseela VC, Kamm WE, Lakkaraju A, Denu JM, Puglielli L. Commun Biol. 2021.

Benchmarking Quantitative Performance in Label-Free Proteomics. Dowell JA, Wright LJ, Armstrong EA and Denu JM. ACS Omega 2021.

Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway. Dieterich IA, Cui Y, Braun MM, Lawton AJ, Robinson NH, Peotter JL, Yu Q, Casler JC, Glick BS, Audhya A, Denu JM, Li L, Puglielli L. Scientific Reports 2021.

Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity. Latorre-Murro P, Baeza J, Hurtado-Guerrero R, Hicks T, Delso I, Hernández-Ruiz C, Velázquez-Campoy A, Lawton AJ, Angulo J, Denu JM, Carrodeguas JA. JBC 2021.

Catalysis by protein acetyltransferase Gcn5. Albaugh BN and Denu JM. Biochim Biophys Acta Gene Regul Mech. 2021.

Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6. Liu WH, Zheng J, Feldman JL, Klein MA, Kuznetsov VI, Peterson CL, Griffin PR, Denu JM.  Nat Commun 2020.

Mechanism of Activation for the Sirtuin 6 Protein Deacylase. Klein MA, Lie C, Kuznetsov VI, Feltenberger JB, Tang W, Denu JM. J Biol Chem 2020.

Methyl-Metabolite Depletion Elicits Adaptive Responses to Support Heterochromatin Stability and Epigenetic Persistence. Haws SA, Yu D, Ye C, Wille CK, Nguyen LC, Krautkramer KA, Tomasiewicz JL, Yang SE, Miller BR, Liu WH, Igarashi K, Sridharan R, Tu BP, Cryns VL, Lamming DW, Denu JM. Mol Cell 2020.

Revealing Dynamic Protein Acetylation across Subcellular Compartments. Baeza J, Lawton AJ, Fan J, Smallegan MJ, Lienert I, Gandhi T, Bernhardt OM, Reiter L, Denu JM. J Proteome Res 2020.

Metabolism and the Epigenome: A Dynamic Relationship. Haws SA, Leech CM and Denu JM. Trends Biochem Sci. 2020.

Biological and Catalytic Functions of Sirtuin 6 as Targets for Small-Molecule Modulators. Klein MA and Denu JM. J Biol Chem. 2020.

A practical guide for analysis of histone post-translational modification by mass spectrometry: Best practices and pitfalls. Thomas SP, Haws SA, Borth LE and Denu JM. Methods 2019.

Acetyl-CoA flux regulates the proteome and acetyl-proteome to maintain intracellular metabolic crosstalk. Dieterich IA, Lawton AJ, Peng Y, Yu Q, Rhoads, TW, Overmyer, KA, Cui Y, Armstrong EA,  Howell PR, Burhans MS, Li L, Denu JM, Anderson RM, Puglielli L. Nat Commun 2019.

Histone Acetyltransferase 1 Links Metabolism and Transcription to Cell-Cycle Progression. Denu JM. Mol Cell 2019.

Bacterial Analogs of Plant Tetrahydropyridine Alkaloids Mediate Microbial Interactions in Rhizosphere Model System. Lozano GL, Bravo JI, Armstrong EA, Denu JM, Stabb EV, Broderick NA, Crawford JM, Handelsman. Applied and Environmental Microbiology 2019.

Site-Specific Lysine Acetylation Stoichiometry Across Subcellular Compartments. Lindahl AJ, Lawton AJ, Baeza J, Dowell JA and Denu JM. Methods Mol Biol. 2019.

Obesity-dependent CDK1 signaling stimulates mitochondrial respiration at complex I in pancreatic β-cells. Gregg T, Sdao SM, Dhillon RS, Rensvold JW, Lewandowski SL, Pagliarini DJ, Denu JM, Merrins MJ. JBC 2019. 

PGC-1a Integrates a Metabolism and Growth Network Linked to Caloric Restriction. Miller KN, Clark JP, Martin SA, Howell PR, Burhans MS, Haws SA, Johnson NB, Rhoads TW, Pavelec DM, Eliceiri KW, Roopra AS, Ntambi JM, Denu JM, Parks BW, Anderson RM. Aging Cell 2019.

Histone Acetyltransferase 1 Links Metabolism and Transcription to Cell-Cycle Progression. Denu JM. Mol Cell 2019.

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model. Kasahara K, Krautkramer KA, Org E, Romano KA, Kerby RL, Vivas EI, Mehrabian M, Denu JM, Bäckhed F, Lusis AJ, Rey FE. Nature Microbiology 2018.

General method for rapid purification of native chromatin fragments. Kuznetsov VI, Haws SH, Fox CA, Denu JM. J Biol Chem 2018.

An Inactivating Mutation in the Histone Deacetylase SIRT6 Causes Human Perinatal Lethality. Ferrer CM, Alders M, Postma AV, Park S, Klein MA, Cetinbas M, Pajkrt E, Glas A, van Koningsbruggen S, Christoffels VM, Mannens MMAM, Knegt L, Etchegaray JP, Sadreyev RI, Denu JM, Mostoslavsky G, van Maarle MC, Mostoslavsky R. Genes Dev. 2018.

Dynamic Acetylation of Phosphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions. Latorre-Muro P, Baeza J, Armstrong EA, Hurtado-Guerrero R, Corzana F, Wu LE, Sinclair DA, López-Buesa P, Carrodeguas JA, Denu JM. Mol Cell 2018.

EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. 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. Nat Genet 2018.

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. 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, Ruiz VE, Livanos A, van ‘t Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. eLife 2018.

Dual recognition of H3K4me3 and H3K26me3 by a plant histone reader SHL. Qian S, Lv X, Scheid RN, Lu L, Yang Z, Chen W, Liu R, Boersma MD, Denu JM, Zhong X, Du J. Nature Communications 2018.

Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys. Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, Stark JL, McIlwain SJ, Eghbalnia HR, Pavelec DM, Ong IM, Denu JM, Markley JL, Coon JJ, Colman RJ, Anderson RM. Cell Metabolism 2018.

Dysregulation of Sirtuin 2 (SIRT2) and histone H3K18 acetylation pathways associates with adverse prostate cancer outcomes. Damodaran S, Damaschke N, Gawdzik J, Yang B, Shi C, Allen GO, Huang W, Denu J, Jarrard D. BMC Cancer 2017. 

Identifying Dysregulated Epigenetic Enzyme Activity in Castrate-Resistant Prostate Cancer Development. Lee JH, Yang B, Lindahl AJ, Damaschke N, Boersma MD, Huang W, Corey E, Jarrard DF, Denu JM. ACS Chem Biol. 2017.

Chemical Signaling Between Git Microbiota and Host Chromatin: What is You Gut Really Saying? Krautkramer KA, Rey FE, Denu JM. J Biol Chem 2017.

Metabolic Programming of the Epigenome: Host and Git Microbial Metabolite Interactions with Host Chromatin. Krautkramer KA, Dhillon RS, Denu JM, Carey HV. Transl Res. 2017.

Identification of a Tissue-Restricted Isoform of SIRT1 Defines a Regulatory Domain that Encodes Specificity. Deota S, Chattopadhyay T, Ramachandran D, Armstrong E, Camacho B, Maniyadath B, Fulzele A, Gonzalez-de-Peredo A, Denu JM, Kolthur-Seetharam U. Cell Rep 2017. 

Histone Lysine-to-Methionine Mutations Reduce Histone Methylation and Cause Developmental Pleiotropy. Sanders D, Qian S, Fieweger R, Lu L, Dowell JA, Denu JM, Zhong X. Plant Physiol. 2017. 

Using comparative biology to understand how aging affects mitochondrial metabolism. Dhillon RS, Denu JM. Molecular and Cellular Endocrinology 2017.