John M Denu

Affiliations

Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.

Publications (40)

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

Communications biology

Avec: Michael J Rigby , Alexis J Lawton , Gulpreet Kaur , Varuna C Banduseela , William E Kamm , Aparna Lakkaraju , John M Denu , Luigi Puglielli

Benchmarking Quantitative Performance in Label-Free Proteomics.

ACS omega

Avec: James A Dowell , Logan J Wright , Eric A Armstrong , John M Denu

Site-Specific Lysine Acetylation Stoichiometry Across Subcellular Compartments.

Methods in molecular biology (Clifton, N.J.)

Avec: Anastasia J Lindahl , Alexis J Lawton , Josue Baeza , James A Dowell , John M Denu

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

Molecular cell

Avec: Spencer A Haws , Deyang Yu , Cunqi Ye , Coral K Wille , Long C Nguyen , Kimberly A Krautkramer , Jay L Tomasiewicz , Shany E Yang , Blake R Miller , Wallace H Liu , Kazuhiko Igarashi , Rupa Sridharan , Benjamin P Tu , Vincent L Cryns , Dudley W Lamming , John M Denu

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

Current protocols

Avec: Ray Scheid , James A Dowell , Dean Sanders , Jianjun Jiang , John M Denu , Xuehua Zhong

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7.

Angewandte Chemie (International ed. in English)

Avec: Julie E Bolding , Alexander L Nielsen , Iben Jensen , Tobias N Hansen , Line A Ryberg , Samuel T Jameson , Pernille Harris , Günther H J Peters , John M Denu , Joseph M Rogers , Christian A Olsen

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

Research square

Avec: Reji Babygirija , Michelle M Sonsalla , Jessica H Han , Isabella James , Cara L Green , Mariah F Calubag , Jericha Mill , Gina Wade , Anna Tobon , John Michael , Michaela M Trautman , Ryan Matoska , Chung-Yang Yeh , Isaac Grunow , Heidi H Pak , Michael J Rigby , John M Denu , Luigi Puglielli , Judith Simcox , Dudley W Lamming

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

bioRxiv : the preprint server for biology

Avec: Spencer A Haws , Yang Liu , Cara L Green , Reji Babygirija , Eric A Armstrong , Anusha T Mehendale , Dudley W Lamming , John M Denu

Catalysis by protein acetyltransferase Gcn5.

Biochimica et biophysica acta. Gene regulatory mechanisms

Avec: Brittany N Albaugh , John M Denu

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

The Journal of biological chemistry

Avec: Mark A Klein , John M Denu

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

The Journal of biological chemistry

Avec: Trillian Gregg , Sophia M Sdao , Rashpal S Dhillon , Jarred W Rensvold , Sophie L Lewandowski , David J Pagliarini , John M Denu , Matthew J Merrins

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

Scientific reports

Avec: Inca A Dieterich , Yusi Cui , Megan M Braun , Alexis J Lawton , Nicklaus H Robinson , Jennifer L Peotter , Qing Yu , Jason C Casler , Benjamin S Glick , Anjon Audhya , John M Denu , Lingjun Li , Luigi Puglielli

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

Nature metabolism

Avec: Heidi H Pak , Spencer A Haws , Cara L Green , Mikaela Koller , Mitchell T Lavarias , Nicole E Richardson , Shany E Yang , Sabrina N Dumas , Michelle Sonsalla , Lindsey Bray , Michelle Johnson , Stephen Barnes , Victor Darley-Usmar , Jianhua Zhang , Chi-Liang Eric Yen , John M Denu , Dudley W Lamming

Sirt6 regulates lifespan in

Proceedings of the National Academy of Sciences of the United States of America

Avec: Jackson R Taylor , Jason G Wood , Evan Mizerak , Samuel Hinthorn , Julianna Liu , Matthew Finn , Sarah Gordon , Louis Zingas , Chengyi Chang , Mark A Klein , John M Denu , Vera Gorbunova , Andrei Seluanov , Jef D Boeke , John M Sedivy , Stephen L Helfand

Trimethylamine N-Oxide Reduces Neurite Density and Plaque Intensity in a Murine Model of Alzheimer's Disease.

Journal of Alzheimer's disease : JAD

Avec: Katie R Zarbock , Jessica H Han , Ajay P Singh , Sydney P Thomas , Barbara B Bendlin , John M Denu , John-Paul J Yu , Federico E Rey , Tyler K Ulland

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

Communications biology

Avec: 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

Fasting is required for many of the benefits of calorie restriction in the 3xTg mouse model of Alzheimer's disease.

bioRxiv : the preprint server for biology

Avec: Reji Babygirija , Jessica H Han , Michelle M Sonsalla , Ryan Matoska , Mariah F Calubag , Cara L Green , Anna Tobon , Chung-Yang Yeh , Diana Vertein , Sophia Schlorf , Julia Illiano , Yang Liu , Isaac Grunow , Michael J Rigby , Luigi Puglielli , David A Harris , John M Denu , Dudley W Lamming

Mechanism of activation for the sirtuin 6 protein deacylase.

The Journal of biological chemistry

Avec: Mark A Klein , Can Liu , Vyacheslav I Kuznetsov , John B Feltenberger , Weiping Tang , John M Denu

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

Applied and environmental microbiology

Avec: Gabriel L Lozano , Hyun Bong Park , Juan I Bravo , Eric A Armstrong , John M Denu , Eric V Stabb , Nichole A Broderick , Jason M Crawford , Jo Handelsman

Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6.

Nature communications

Avec: Wallace H Liu , Jie Zheng , Jessica L Feldman , Mark A Klein , Vyacheslav I Kuznetsov , Craig L Peterson , Patrick R Griffin , John M Denu

Potent Activation of NAD

ACS chemical biology

Avec: Vyacheslav I Kuznetsov , Wallace H Liu , Mark A Klein , John M Denu

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

International journal of molecular sciences

Avec: Narayanan Puthillathu Vasudevan , Dharmendra K Soni , John R Moffett , Jishnu K S Krishnan , Abhilash P Appu , Sarani Ghoshal , Peethambaran Arun , John M Denu , Thomas P Flagg , Roopa Biswas , Aryan M Namboodiri

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

Nature communications

Avec: 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

Revealing Dynamic Protein Acetylation across Subcellular Compartments.

Journal of proteome research

Avec: Josue Baeza , Alexis J Lawton , Jing Fan , Michael J Smallegan , Ian Lienert , Tejas Gandhi , Oliver M Bernhardt , Lukas Reiter , John M Denu

Metabolism and the Epigenome: A Dynamic Relationship.

Trends in biochemical sciences

Avec: Spencer A Haws , Cassandra M Leech , John M Denu

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

Nature communications

Avec: Inca A Dieterich , Alexis J Lawton , Yajing Peng , Qing Yu , Timothy W Rhoads , Katherine A Overmyer , Yusi Cui , Eric A Armstrong , Porsha R Howell , Maggie S Burhans , Lingjun Li , John M Denu , Joshua J Coon , Rozalyn M Anderson , Luigi Puglielli

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

Metabolites

Avec: Hang Cheng , Yiming Amy Qin , Rashpal Dhillon , James Dowell , John M Denu , Matthew E Pamenter

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

Brain communications

Avec: Michael J Rigby , Nicola Salvatore Orefice , Alexis J Lawton , Min Ma , Samantha L Shapiro , Sue Y Yi , Inca A Dieterich , Alyssa Frelka , Hannah N Miles , Robert A Pearce , John Paul J Yu , Lingjun Li , John M Denu , Luigi Puglielli

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

Biochemistry

Avec: Wallace H Liu , Robert E Miner , Brittany N Albaugh , Gene E Ananiev , Scott A Wildman , John M Denu

Nucleic acid sequence contributes to remodeler-mediated targeting of histone H2A.Z.

bioRxiv : the preprint server for biology

Avec: Cynthia Converso , Leonidas Pierrakeas , Lirong Chan , Shalvi Chowdhury , Vyacheslav I Kuznetsov , John M Denu , Ed Luk

The role of ATP citrate lyase in myelin formation and maintenance.

Glia

Avec: Andrew Schneider , Seongsik Won , Eric A Armstrong , Aaron J Cooper , Amulya Suresh , Rachell Rivera , Gregory Barrett-Wilt , John M Denu , Judith A Simcox , John Svaren

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

Molecular cell

Avec: John M Denu

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

Aging cell

Avec: Karl N Miller , Josef P Clark , Stephen A Martin , Porsha R Howell , Maggie S Burhans , Spencer A Haws , Nathan B Johnson , Timothy W Rhoads , Derek M Pavelec , Kevin W Eliceiri , Avtar S Roopra , James M Ntambi , John M Denu , Brian W Parks , Rozalyn M Anderson

Short-chain fatty acids activate acetyltransferase p300.

eLife

Avec: Sydney P Thomas , John M Denu

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

Methods (San Diego, Calif.)

Avec: Sydney P Thomas , Spencer A Haws , Laura E Borth , John M Denu

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

The Journal of biological chemistry

Avec: Pedro Latorre-Muro , Josue Baeza , Ramon Hurtado-Guerrero , Thomas Hicks , Ignacio Delso , Cristina Hernández-Ruiz , Adrian Velázquez-Campoy , Alexis J Lawton , Jesús Angulo , John M Denu , José A Carrodeguas

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

Brain : a journal of neurology

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

Aging cell

Avec: Rashpal S Dhillon , Yiming Amy Qin , Paul R van Ginkel , Vivian X Fu , James M Vann , Alexis J Lawton , Cara L Green , Fúlvia B Manchado-Gobatto , Claudio A Gobatto , Dudley W Lamming , Tomas A Prolla , John M Denu

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

The Journal of biological chemistry

Avec: Spencer A Haws , Lillian J Miller , Diego Rojas La Luz , Vyacheslav I Kuznetsov , Raymond C Trievel , Gheorghe Craciun , John M Denu

DOT1L is a barrier to histone acetylation during reprogramming to pluripotency.

Science advances

Avec: Coral K Wille , Xiaoya Zhang , Spencer A Haws , John M Denu , Rupa Sridharan

Réseau de co-auteurs

Alexis J Lawton 10 collaborations

Luigi Puglielli 9 collaborations

Spencer A Haws 8 collaborations

Dudley W Lamming 7 collaborations

Michael J Rigby 6 collaborations

Cara L Green 6 collaborations

Eric A Armstrong 5 collaborations

Mark A Klein 5 collaborations

Vyacheslav I Kuznetsov 5 collaborations

Wallace H Liu 4 collaborations

Reji Babygirija 4 collaborations

Jessica H Han 4 collaborations

Inca A Dieterich 4 collaborations

Lingjun Li 4 collaborations

James A Dowell 3 collaborations

Josue Baeza 3 collaborations

Michelle M Sonsalla 3 collaborations

Mariah F Calubag 3 collaborations

Anna Tobon 3 collaborations

Ryan Matoska 3 collaborations

Chung-Yang Yeh 3 collaborations

Isaac Grunow 3 collaborations

Heidi H Pak 3 collaborations

Sydney P Thomas 3 collaborations

Samantha L Shapiro 3 collaborations

Coral K Wille 2 collaborations

Shany E Yang 2 collaborations

Rupa Sridharan 2 collaborations

Isabella James 2 collaborations

Jericha Mill 2 collaborations

Gina Wade 2 collaborations

John Michael 2 collaborations

Michaela M Trautman 2 collaborations

Judith Simcox 2 collaborations

Yang Liu 2 collaborations

Brittany N Albaugh 2 collaborations

Rashpal S Dhillon 2 collaborations

Yusi Cui 2 collaborations

Qing Yu 2 collaborations

Katherine A Overmyer 2 collaborations

Joshua J Coon 2 collaborations

Timothy W Rhoads 2 collaborations

Porsha R Howell 2 collaborations

Maggie S Burhans 2 collaborations

Rozalyn M Anderson 2 collaborations

Yiming Amy Qin 2 collaborations

Nicola Salvatore Orefice 2 collaborations

Min Ma 2 collaborations

Sue Y Yi 2 collaborations

Alyssa Frelka 2 collaborations

Hannah N Miles 2 collaborations

Robert A Pearce 2 collaborations

John Paul J Yu 2 collaborations

Gulpreet Kaur 1 collaboration

Varuna C Banduseela 1 collaboration

William E Kamm 1 collaboration

Aparna Lakkaraju 1 collaboration

Logan J Wright 1 collaboration

Anastasia J Lindahl 1 collaboration

Deyang Yu 1 collaboration

Cunqi Ye 1 collaboration

Long C Nguyen 1 collaboration

Kimberly A Krautkramer 1 collaboration

Jay L Tomasiewicz 1 collaboration

Blake R Miller 1 collaboration

Kazuhiko Igarashi 1 collaboration

Benjamin P Tu 1 collaboration

Vincent L Cryns 1 collaboration

Ray Scheid 1 collaboration

Dean Sanders 1 collaboration

Jianjun Jiang 1 collaboration

Xuehua Zhong 1 collaboration

Julie E Bolding 1 collaboration

Alexander L Nielsen 1 collaboration

Iben Jensen 1 collaboration

Tobias N Hansen 1 collaboration

Line A Ryberg 1 collaboration

Samuel T Jameson 1 collaboration

Pernille Harris 1 collaboration

Günther H J Peters 1 collaboration

Joseph M Rogers 1 collaboration

Christian A Olsen 1 collaboration

Anusha T Mehendale 1 collaboration

Trillian Gregg 1 collaboration

Sophia M Sdao 1 collaboration

Jarred W Rensvold 1 collaboration

Sophie L Lewandowski 1 collaboration

David J Pagliarini 1 collaboration

Matthew J Merrins 1 collaboration

Megan M Braun 1 collaboration

Nicklaus H Robinson 1 collaboration

Jennifer L Peotter 1 collaboration

Jason C Casler 1 collaboration

Benjamin S Glick 1 collaboration

Anjon Audhya 1 collaboration

Mikaela Koller 1 collaboration

Mitchell T Lavarias 1 collaboration

Nicole E Richardson 1 collaboration

Sabrina N Dumas 1 collaboration

Michelle Sonsalla 1 collaboration

Lindsey Bray 1 collaboration

Michelle Johnson 1 collaboration

Stephen Barnes 1 collaboration

Victor Darley-Usmar 1 collaboration

Jianhua Zhang 1 collaboration

Chi-Liang Eric Yen 1 collaboration

Jackson R Taylor 1 collaboration

Jason G Wood 1 collaboration

Evan Mizerak 1 collaboration

Samuel Hinthorn 1 collaboration

Julianna Liu 1 collaboration

Matthew Finn 1 collaboration

Sarah Gordon 1 collaboration

Louis Zingas 1 collaboration

Chengyi Chang 1 collaboration

Vera Gorbunova 1 collaboration

Andrei Seluanov 1 collaboration

Jef D Boeke 1 collaboration

John M Sedivy 1 collaboration

Stephen L Helfand 1 collaboration

Katie R Zarbock 1 collaboration

Ajay P Singh 1 collaboration

Barbara B Bendlin 1 collaboration

John-Paul J Yu 1 collaboration

Federico E Rey 1 collaboration

Tyler K Ulland 1 collaboration

Gonzalo Fernandez-Fuente 1 collaboration

Ildiko Kasza 1 collaboration

Patricia Gallego-Muñoz 1 collaboration

Caroline M Alexander 1 collaboration

Diana Vertein 1 collaboration

Sophia Schlorf 1 collaboration

Julia Illiano 1 collaboration

David A Harris 1 collaboration

Can Liu 1 collaboration

John B Feltenberger 1 collaboration

Weiping Tang 1 collaboration

Gabriel L Lozano 1 collaboration

Hyun Bong Park 1 collaboration

Juan I Bravo 1 collaboration

Eric V Stabb 1 collaboration

Nichole A Broderick 1 collaboration

Jason M Crawford 1 collaboration

Jo Handelsman 1 collaboration

Jie Zheng 1 collaboration

Jessica L Feldman 1 collaboration

Craig L Peterson 1 collaboration

Patrick R Griffin 1 collaboration

Narayanan Puthillathu Vasudevan 1 collaboration

Dharmendra K Soni 1 collaboration

John R Moffett 1 collaboration

Jishnu K S Krishnan 1 collaboration

Abhilash P Appu 1 collaboration

Sarani Ghoshal 1 collaboration

Peethambaran Arun 1 collaboration

Thomas P Flagg 1 collaboration

Roopa Biswas 1 collaboration

Aryan M Namboodiri 1 collaboration

Dominique A Baldwin 1 collaboration

Natalie M Niemi 1 collaboration

Jing Fan 1 collaboration

Michael J Smallegan 1 collaboration

Ian Lienert 1 collaboration

Tejas Gandhi 1 collaboration

Oliver M Bernhardt 1 collaboration

Lukas Reiter 1 collaboration

Cassandra M Leech 1 collaboration

Yajing Peng 1 collaboration

Hang Cheng 1 collaboration

Rashpal Dhillon 1 collaboration

James Dowell 1 collaboration

Matthew E Pamenter 1 collaboration

Robert E Miner 1 collaboration

Gene E Ananiev 1 collaboration

Scott A Wildman 1 collaboration

Cynthia Converso 1 collaboration

Leonidas Pierrakeas 1 collaboration

Lirong Chan 1 collaboration

Shalvi Chowdhury 1 collaboration

Ed Luk 1 collaboration

Andrew Schneider 1 collaboration

Seongsik Won 1 collaboration

Aaron J Cooper 1 collaboration

Amulya Suresh 1 collaboration

Rachell Rivera 1 collaboration

Gregory Barrett-Wilt 1 collaboration

Judith A Simcox 1 collaboration

John Svaren 1 collaboration

Karl N Miller 1 collaboration

Josef P Clark 1 collaboration

Stephen A Martin 1 collaboration

Nathan B Johnson 1 collaboration

Derek M Pavelec 1 collaboration

Kevin W Eliceiri 1 collaboration

Avtar S Roopra 1 collaboration

James M Ntambi 1 collaboration

Brian W Parks 1 collaboration

Laura E Borth 1 collaboration

Pedro Latorre-Muro 1 collaboration

Ramon Hurtado-Guerrero 1 collaboration

Thomas Hicks 1 collaboration

Ignacio Delso 1 collaboration

Cristina Hernández-Ruiz 1 collaboration

Adrian Velázquez-Campoy 1 collaboration

Jesús Angulo 1 collaboration

José A Carrodeguas 1 collaboration

Paul R van Ginkel 1 collaboration

Vivian X Fu 1 collaboration

James M Vann 1 collaboration

Fúlvia B Manchado-Gobatto 1 collaboration

Claudio A Gobatto 1 collaboration

Tomas A Prolla 1 collaboration

Lillian J Miller 1 collaboration

Diego Rojas La Luz 1 collaboration

Raymond C Trievel 1 collaboration

Gheorghe Craciun 1 collaboration

Xiaoya Zhang 1 collaboration