Metabolic Regulation of Histone Post-translational Modifications

Overview

Journal ACS Chem Biol

Publisher American Chemical Society

Specialties Biochemistry
Biology

Date 2015 Jan 7

PMID 25562692

Citations 151

Authors

Jing Fan

Kimberly A Krautkramer

Jessica L Feldman

John M Denu

Affiliations

Soon will be listed here.

Abstract

Histone post-translational modifications regulate transcription and other DNA-templated functions. This process is dynamically regulated by specific modifying enzymes whose activities require metabolites that either serve as cosubstrates or act as activators/inhibitors. Therefore, metabolism can influence histone modification by changing local concentrations of key metabolites. Physiologically, the epigenetic response to metabolism is important for nutrient sensing and environment adaption. In pathologic states, the connection between metabolism and histone modification mediates epigenetic abnormality in complex disease. In this review, we summarize recent studies of the molecular mechanisms involved in metabolic regulation of histone modifications and discuss their biological significance.

Citing Articles

Examining the epigenetic transmission of risk for chronic pain associated with paternal post-traumatic stress disorder: a focus on veteran populations.

Freeman J, Salberg S, Noel M, Mychasiuk R Transl Psychiatry. 2025; 15(1):42.

PMID: 39910041 PMC: 11799465. DOI: 10.1038/s41398-025-03267-w.

Mitochondria and its epigenetic dynamics: Insight into synaptic regulation and synaptopathies.

Gupta S, Kishore A, Rishi V, Aggarwal A Funct Integr Genomics. 2025; 25(1):26.

PMID: 39849126 DOI: 10.1007/s10142-025-01530-3.

High-Fat Diet, Epigenetics, and Atherosclerosis: A Narrative Review.

Rai V Nutrients. 2025; 17(1.

PMID: 39796562 PMC: 11722563. DOI: 10.3390/nu17010127.

Bidirectional histone monoaminylation dynamics regulate neural rhythmicity.

Zheng Q, Weekley B, Vinson D, Zhao S, Bastle R, Thompson R Nature. 2025; 637(8047):974-982.

PMID: 39779849 PMC: 11754111. DOI: 10.1038/s41586-024-08371-3.

Mitochondria: the epigenetic regulators of ovarian aging and longevity.

Mani S, Srivastava V, Shandilya C, Kaushik A, Singh K Front Endocrinol (Lausanne). 2024; 15:1424826.

PMID: 39605943 PMC: 11598335. DOI: 10.3389/fendo.2024.1424826.

References

Shimazu T, Hirschey M, Newman J, He W, Shirakawa K, Le Moan N . Suppression of oxidative stress by β-hydroxybutyrate, an endogenous histone deacetylase inhibitor. Science. 2012; 339(6116):211-4. PMC: 3735349. DOI: 10.1126/science.1227166. View

Lee J, Carrer A, Shah S, Snyder N, Wei S, Venneti S . Akt-dependent metabolic reprogramming regulates tumor cell histone acetylation. Cell Metab. 2014; 20(2):306-319. PMC: 4151270. DOI: 10.1016/j.cmet.2014.06.004. View

Luger K, Mader A, Richmond R, Sargent D, Richmond T . Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997; 389(6648):251-60. DOI: 10.1038/38444. View

Preiss J, Handler P . Biosynthesis of diphosphopyridine nucleotide. I. Identification of intermediates. J Biol Chem. 1958; 233(2):488-92. View

Karch K, DeNizio J, Black B, Garcia B . Identification and interrogation of combinatorial histone modifications. Front Genet. 2014; 4:264. PMC: 3868920. DOI: 10.3389/fgene.2013.00264. View

Tan M, Luo H, Lee S, Jin F, Yang J, Montellier E . Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell. 2011; 146(6):1016-28. PMC: 3176443. DOI: 10.1016/j.cell.2011.08.008. View

Fuks F, Hurd P, Wolf D, Nan X, Bird A, Kouzarides T . The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem. 2002; 278(6):4035-40. DOI: 10.1074/jbc.M210256200. View

Xu J, Christian B, Jump D . Regulation of rat hepatic L-pyruvate kinase promoter composition and activity by glucose, n-3 polyunsaturated fatty acids, and peroxisome proliferator-activated receptor-alpha agonist. J Biol Chem. 2006; 281(27):18351-62. PMC: 2766394. DOI: 10.1074/jbc.M601277200. View

Stein L, Imai S . The dynamic regulation of NAD metabolism in mitochondria. Trends Endocrinol Metab. 2012; 23(9):420-8. PMC: 3683958. DOI: 10.1016/j.tem.2012.06.005. View

10.

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

11.

Gardner K, Allis C, Strahl B . Operating on chromatin, a colorful language where context matters. J Mol Biol. 2011; 409(1):36-46. PMC: 3085666. DOI: 10.1016/j.jmb.2011.01.040. View

12.

Sun Z, Allis C . Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature. 2002; 418(6893):104-8. DOI: 10.1038/nature00883. View

13.

Metzger E, Imhof A, Patel D, Kahl P, Hoffmeyer K, Friedrichs N . Phosphorylation of histone H3T6 by PKCbeta(I) controls demethylation at histone H3K4. Nature. 2010; 464(7289):792-6. DOI: 10.1038/nature08839. View

14.

Patnaik D, Chin H, Esteve P, Benner J, Jacobsen S, Pradhan S . Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase. J Biol Chem. 2004; 279(51):53248-58. DOI: 10.1074/jbc.M409604200. View

15.

Feldman J, Baeza J, Denu J . Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. J Biol Chem. 2013; 288(43):31350-6. PMC: 3829447. DOI: 10.1074/jbc.C113.511261. View

16.

Lemons J, Feng X, Bennett B, Legesse-Miller A, Johnson E, Raitman I . Quiescent fibroblasts exhibit high metabolic activity. PLoS Biol. 2010; 8(10):e1000514. PMC: 2958657. DOI: 10.1371/journal.pbio.1000514. View

17.

Del Rizzo P, Trievel R . Molecular basis for substrate recognition by lysine methyltransferases and demethylases. Biochim Biophys Acta. 2014; 1839(12):1404-15. DOI: 10.1016/j.bbagrm.2014.06.008. View

18.

Barbosa M, Soares S, Novak C, Sinclair D, Levine J, Aksoy P . The enzyme CD38 (a NAD glycohydrolase, EC 3.2.2.5) is necessary for the development of diet-induced obesity. FASEB J. 2007; 21(13):3629-39. DOI: 10.1096/fj.07-8290com. View

19.

Olsen J, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P . Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006; 127(3):635-48. DOI: 10.1016/j.cell.2006.09.026. View

20.

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