Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling

Environmental epigenetics and epigenetic inheritance in domestic farm animals

(2020) Ryan P. Thompson et al.   ANIMAL REPRODUCTION SCIENCE

BCAT2-mediated BCAA catabolism is critical for development of pancreatic ductal adenocarcinoma

(2020) Jin-Tao Li et al.   NATURE CELL BIOLOGY

Advances in understanding molecular regulation of innate immune memory

(2020) Jorge Domínguez-Andrés et al.   CURRENT OPINION IN CELL BIOLOGY

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

(2020) Spencer A. Haws et al.   MOLECULAR CELL

Common biochemical properties of metabolic genes recurrently dysregulated in tumors

(2020) Krishnadev Oruganty et al.   Cancer & Metabolism

Targeting Chromatin Remodeling for Cancer Therapy

(2019) Jasmine Kaur et al.   Current Molecular Pharmacology

Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation

(2019) Sergi Aranda et al.   Science Advances

Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells

(2019) Won Dong Lee et al.   Nature Communications

Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation

(2019) Bogi Karbech Hansen et al.   Nature Communications

MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation

(2019) Sara Sdelci et al.   NATURE GENETICS

The conditions under which consolidation of serial-order conditioned fear requires de novo protein synthesis in the basolateral amygdala complex

(2019) Matthew J. Williams-Spooner et al.   JOURNAL OF NEUROSCIENCE

Human adipose tissue H3K4me3 histone mark in adipogenic, lipid metabolism and inflammatory genes is positively associated with BMI and HOMA-IR

(2019) Daniel Castellano-Castillo et al.   PLoS One

Molecular mechanisms of epigenetic inheritance: Possible evolutionary implications

(2019) Peter Sarkies   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

Should we consider subcellular compartmentalization of metabolites, and if so, how do we measure them?

(2019) Kathryn E. Wellen et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

High-resolution 13C metabolic flux analysis

(2019) Christopher P. Long et al.   Nature Protocols

Alcohol metabolism contributes to brain histone acetylation

(2019) P. Mews et al.   NATURE

Metabolic regulation of gene expression by histone lactylation

(2019) Di Zhang et al.   NATURE

Diet-Induced Modification of the Sperm Epigenome Programs Metabolism and Behavior

(2019) Carina Bodden et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Subcellular metabolic pathway kinetics are revealed by correcting for artifactual post harvest metabolism

(2019) Sophie Trefely et al.   Molecular Metabolism

Impaired brain energy gain upon a glucose load in obesity

(2018) Ewelina K. Wardzinski et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

Spatiotemporal Control of Acetyl-CoA Metabolism in Chromatin Regulation

(2018) Sharanya Sivanand et al.   TRENDS IN BIOCHEMICAL SCIENCES

Intergenerational and transgenerational epigenetic inheritance in animals

(2018) Marcos Francisco Perez et al.   NATURE CELL BIOLOGY

Nuclear Acetyl-CoA Production by ACLY Promotes Homologous Recombination

(2017) Sharanya Sivanand et al.   MOLECULAR CELL

The impact of cellular metabolism on chromatin dynamics and epigenetics

(2017) Michael A. Reid et al.   NATURE CELL BIOLOGY

Nutritional psychiatry: the present state of the evidence

(2017) Wolfgang Marx et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

The mechanisms mediating the antiepileptic effects of the ketogenic diet, and potential opportunities for improvement with metabolism-altering drugs

(2017) Neil A. Youngson et al.   SEIZURE-EUROPEAN JOURNAL OF EPILEPSY

The Various Metabolic Sources of Histone Acetylation

(2017) Carlos Sebastián et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

The evolutionary implications of epigenetic inheritance

(2017) Eva Jablonka   Interface Focus

Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

(2017) Sriram Chandrasekaran et al.   Cell Reports

Acetate Recapturing by Nuclear Acetyl-CoA Synthetase 2 Prevents Loss of Histone Acetylation during Oxygen and Serum Limitation

(2017) Vinay Bulusu et al.   Cell Reports

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

(2017) Aarash Bordbar et al.   Scientific Reports

Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance

(2016) Sunjae Lee et al.   Cell Metabolism

AMPK/α-Ketoglutarate Axis Dynamically Mediates DNA Demethylation in the Prdm16 Promoter and Brown Adipogenesis

(2016) Qiyuan Yang et al.   Cell Metabolism

Metabolic control of methylation and acetylation

(2016) Xiaoyang Su et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Diverse Activities of Histone Acylations Connect Metabolism to Chromatin Function

(2016) Arnob Dutta et al.   MOLECULAR CELL

Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia

(2016) Xue Gao et al.   Nature Communications

Lipids Reprogram Metabolism to Become a Major Carbon Source for Histone Acetylation

(2016) Eoin McDonnell et al.   Cell Reports

O-GlcNAc signaling in cancer metabolism and epigenetics

(2015) Jay Prakash Singh et al.   CANCER LETTERS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Histone Methylation Dynamics and Gene Regulation Occur through the Sensing of One-Carbon Metabolism

(2015) Samantha J. Mentch et al.   Cell Metabolism

Glycolysis-Mediated Changes in Acetyl-CoA and Histone Acetylation Control the Early Differentiation of Embryonic Stem Cells

(2015) Arieh Moussaieff et al.   Cell Metabolism

Direct Lineage Reprogramming: Strategies, Mechanisms, and Applications

(2015) Jun Xu et al.   Cell Stem Cell

Sirtuins and the Metabolic Hurdles in Cancer

(2015) Natalie J. German et al.   CURRENT BIOLOGY

A roadmap for interpreting 13 C metabolite labeling patterns from cells

(2015) Joerg M Buescher et al.   CURRENT OPINION IN BIOTECHNOLOGY

Synthetic histone code

(2015) Wolfgang Fischle et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Aggression is associated with aerobic glycolysis in the honey bee brain1

(2015) S. Chandrasekaran et al.   GENES BRAIN AND BEHAVIOR

Modeling cancer metabolism on a genome scale

(2015) K. Yizhak et al.   Molecular Systems Biology

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

(2015) Henrik Sperber et al.   NATURE CELL BIOLOGY

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Stratification of Hepatocellular Carcinoma Patients Based on Acetate Utilization

(2015) Elias Björnson et al.   Cell Reports

A Nuclear Pyruvate Dehydrogenase Complex Is Important for the Generation of Acetyl-CoA and Histone Acetylation

(2014) Gopinath Sutendra et al.   CELL

Acetate Dependence of Tumors

(2014) Sarah A. Comerford et al.   CELL

Methionine Metabolism Regulates Maintenance and Differentiation of Human Pluripotent Stem Cells

(2014) Nobuaki Shiraki et al.   Cell Metabolism

Akt-Dependent Metabolic Reprogramming Regulates Tumor Cell Histone Acetylation

(2014) Joyce V. Lee et al.   Cell Metabolism

Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders

(2014) Katrina J. Falkenberg et al.   NATURE REVIEWS DRUG DISCOVERY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Influence of Metabolism on Epigenetics and Disease

(2013) William G. Kaelin et al.   CELL

Quantitative Dynamics of the Link between Cellular Metabolism and Histone Acetylation

(2013) Adam G. Evertts et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Ten-Eleven Translocation-2 (TET2) gene in hematopoiesis and hematopoietic diseases

(2013) E Solary et al.   LEUKEMIA

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink

(2013) Olesya A Ulanovskaya et al.   Nature Chemical Biology

The Histone Deacetylase SIRT6 Is a Tumor Suppressor that Controls Cancer Metabolism

(2012) Carlos Sebastián et al.   CELL

Histone Acetylation Regulates Intracellular pH

(2012) Matthew A. McBrian et al.   MOLECULAR CELL

A two-way street: reciprocal regulation of metabolism and signalling

(2012) Kathryn E. Wellen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HEMD: An Integrated Tool of Human Epigenetic Enzymes and Chemical Modulators for Therapeutics

(2012) Zhimin Huang et al.   PLoS One

Influence of Threonine Metabolism on S-Adenosylmethionine and Histone Methylation

(2012) N. Shyh-Chang et al.   SCIENCE

FAD-dependent lysine-specific demethylase-1 regulates cellular energy expenditure

(2012) Shinjiro Hino et al.   Nature Communications

Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes

(2011) Ling Cai et al.   MOLECULAR CELL

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Cell-Type Independent MYC Target Genes Reveal a Primordial Signature Involved in Biomass Accumulation

(2011) Hongkai Ji et al.   PLoS One

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

SIRT3 Is a Mitochondria-Localized Tumor Suppressor Required for Maintenance of Mitochondrial Integrity and Metabolism during Stress

(2010) Hyun-Seok Kim et al.   CANCER CELL

The Language of Histone Crosstalk

(2010) Jung-Shin Lee et al.   CELL

Myc-dependent Mitochondrial Generation of Acetyl-CoA Contributes to Fatty Acid Biosynthesis and Histone Acetylation during Cell Cycle Entry

(2010) Fionnuala Morrish et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Chromatin structure and the inheritance of epigenetic information

(2010) Raphaël Margueron et al.   NATURE REVIEWS GENETICS

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signaling Kinase AMPK Activates Stress-Promoted Transcription via Histone H2B Phosphorylation

(2010) D. Bungard et al.   SCIENCE

ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation

(2009) K. E. Wellen et al.   SCIENCE

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY