Metabolic Regulation of Epigenetics

Overview

Journal Cell Metab

Publisher Cell Press

Specialties Cell Biology
Endocrinology

Date 2012 Jul 10

PMID 22768835

Citations 364

Authors

Chao Lu

Craig B Thompson

Affiliations

Soon will be listed here.

Abstract

How cells sense and respond to environmental cues remains a central question of biological research. Recent evidence suggests that DNA transcription is regulated by chromatin organization. However, the mechanism for relaying the cytoplasmic signaling to chromatin remodeling remains incompletely understood. Although much emphasis has been put on delineating transcriptional output of growth factor/hormonal signaling pathways, accumulated evidence from yeast and mammalian systems suggest that metabolic signals also play critical roles in determining chromatin structure. Here we summarize recent progress in understanding the molecular connection between metabolism and epigenetic modifications of chromatin implicated in a variety of diseases including cancer.

Citing Articles

Lactate and lactylation in cancer.

Chen J, Huang Z, Chen Y, Tian H, Chai P, Shen Y Signal Transduct Target Ther. 2025; 10(1):38.

PMID: 39934144 PMC: 11814237. DOI: 10.1038/s41392-024-02082-x.

The metabolic adaptation in wild vertebrates via omics approaches.

Du X, Hu Y, Huang G, Wei F Life Metab. 2025; 1(3):234-241.

PMID: 39872075 PMC: 11749369. DOI: 10.1093/lifemeta/loac040.

Grapevine cell response to carbon deficiency requires transcriptome and methylome reprogramming.

Berger M, Garcia V, Lacrampe N, Rubio B, Decros G, Petriacq P Hortic Res. 2025; 12(1):uhae277.

PMID: 39845645 PMC: 11750959. DOI: 10.1093/hr/uhae277.

Molecular Regulation of Cardiomyocyte Maturation.

Shewale B, Ebrahim T, Samal A, Dubois N Curr Cardiol Rep. 2025; 27(1):32.

PMID: 39836238 DOI: 10.1007/s11886-024-02189-1.

Metabolism-driven chromatin dynamics: Molecular principles and technological advances.

Sahu V, Lu C Mol Cell. 2025; 85(2):262-275.

PMID: 39824167 PMC: 11750176. DOI: 10.1016/j.molcel.2024.12.012.

References

Baek S . When signaling kinases meet histones and histone modifiers in the nucleus. Mol Cell. 2011; 42(3):274-84. DOI: 10.1016/j.molcel.2011.03.022. View

Loenarz C, Schofield C . Expanding chemical biology of 2-oxoglutarate oxygenases. Nat Chem Biol. 2008; 4(3):152-6. DOI: 10.1038/nchembio0308-152. View

Klose R, Zhang Y . Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol. 2007; 8(4):307-18. DOI: 10.1038/nrm2143. View

Asher G, Gatfield D, Stratmann M, Reinke H, Dibner C, Kreppel F . SIRT1 regulates circadian clock gene expression through PER2 deacetylation. Cell. 2008; 134(2):317-28. DOI: 10.1016/j.cell.2008.06.050. View

Katada S, Imhof A, Sassone-Corsi P . Connecting threads: epigenetics and metabolism. Cell. 2012; 148(1-2):24-8. DOI: 10.1016/j.cell.2012.01.001. View

Nakahata Y, Kaluzova M, Grimaldi B, Sahar S, Hirayama J, Chen D . The NAD+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control. Cell. 2008; 134(2):329-40. PMC: 3526943. DOI: 10.1016/j.cell.2008.07.002. View

Chance B, Estabrook R, Ghosh A . DAMPED SINUSOIDAL OSCILLATIONS OF CYTOPLASMIC REDUCED PYRIDINE NUCLEOTIDE IN YEAST CELLS. Proc Natl Acad Sci U S A. 1964; 51:1244-51. PMC: 300244. DOI: 10.1073/pnas.51.6.1244. View

Tu B, McKnight S . Evidence of carbon monoxide-mediated phase advancement of the yeast metabolic cycle. Proc Natl Acad Sci U S A. 2009; 106(34):14293-6. PMC: 2732868. DOI: 10.1073/pnas.0907786106. View

Bungard D, Fuerth B, Zeng P, Faubert B, Maas N, Viollet B . Signaling kinase AMPK activates stress-promoted transcription via histone H2B phosphorylation. Science. 2010; 329(5996):1201-5. PMC: 3922052. DOI: 10.1126/science.1191241. View

10.

Locasale J, Cantley L . Metabolic flux and the regulation of mammalian cell growth. Cell Metab. 2011; 14(4):443-51. PMC: 3196640. DOI: 10.1016/j.cmet.2011.07.014. View

11.

Metallo C, Gameiro P, Bell E, Mattaini K, Yang J, Hiller K . Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia. Nature. 2011; 481(7381):380-4. PMC: 3710581. DOI: 10.1038/nature10602. View

12.

Um J, Pendergast J, Springer D, Foretz M, Viollet B, Brown A . AMPK regulates circadian rhythms in a tissue- and isoform-specific manner. PLoS One. 2011; 6(3):e18450. PMC: 3069094. DOI: 10.1371/journal.pone.0018450. View

13.

Kim Y . Nutritional epigenetics: impact of folate deficiency on DNA methylation and colon cancer susceptibility. J Nutr. 2005; 135(11):2703-9. DOI: 10.1093/jn/135.11.2703. View

14.

Noushmehr H, Weisenberger D, Diefes K, Phillips H, Pujara K, Berman B . Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010; 17(5):510-22. PMC: 2872684. DOI: 10.1016/j.ccr.2010.03.017. View

15.

Hirota T, Okano T, Kokame K, Shirotani-Ikejima H, Miyata T, Fukada Y . Glucose down-regulates Per1 and Per2 mRNA levels and induces circadian gene expression in cultured Rat-1 fibroblasts. J Biol Chem. 2002; 277(46):44244-51. DOI: 10.1074/jbc.M206233200. View

16.

Shi Y, Lan F, Matson C, Mulligan P, Whetstine J, Cole P . Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell. 2004; 119(7):941-53. DOI: 10.1016/j.cell.2004.12.012. View

17.

He Y, Li B, Li Z, Liu P, Wang Y, Tang Q . Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science. 2011; 333(6047):1303-7. PMC: 3462231. DOI: 10.1126/science.1210944. View

18.

Takahashi H, McCaffery J, Irizarry R, Boeke J . Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Mol Cell. 2006; 23(2):207-17. DOI: 10.1016/j.molcel.2006.05.040. View

19.

Selhub J, Miller J . The pathogenesis of homocysteinemia: interruption of the coordinate regulation by S-adenosylmethionine of the remethylation and transsulfuration of homocysteine. Am J Clin Nutr. 1992; 55(1):131-8. DOI: 10.1093/ajcn/55.1.131. View

20.

Ward P, Patel J, Wise D, Abdel-Wahab O, Bennett B, Coller H . The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. Cancer Cell. 2010; 17(3):225-34. PMC: 2849316. DOI: 10.1016/j.ccr.2010.01.020. View