Regulation of chromatin and gene expression by metabolic enzymes and metabolites

Abstract

Metabolism and gene expression, which are two fundamental biological processes that are essential to all living organisms, reciprocally regulate each other to maintain homeostasis and regulate cell growth, survival and differentiation. Metabolism feeds into the regulation of gene expression via metabolic enzymes and metabolites, which can modulate chromatin directly or indirectly - through regulation of the activity of chromatin trans-acting proteins, including histone-modifying enzymes, chromatin-remodelling complexes and transcription regulators. Deregulation of these metabolic activities has been implicated in human diseases, prominently including cancer.

Fig. 1 |. Chromatin modulation by metabolites.

DNA and histones are modified by different writers and erasers, and the enzymatic activities of these modifiers are regulated by metabolites and metabolic enzymes. Some metabolic enzymes can act as direct modifiers (writers) of the histone code as well. α-KG, α-ketoglutarate; βHB, β-hydroxybutyrate; βhb, β-hydroxybutyrylation; 2-HG, 2-hydroxyglutarate; Ac, acetylation; Ac-CoA, acetyl-CoA; AR, ADP ribosylation; Bu, butyrylation; Bu-CoA, butyryl-CoA; But, butyrate; Ci, citrullination; Cr, crotonylation; Cr-CoA, crotonyl-CoA; DNMT, DNA methyltransferase; Fo, formylation; Fum, fumarate; Glu, glutarylation; GMPS, GMP synthase; HAT, histone acetyltransferase; HDAC, histone deacetylase; Hib, 2-hydroxyisobutyrylation; JMJC, Jumonji C domain-containing demethylase; JMJD6, Jumonji domain-containing 6; KMT, lysine methyltransferase; LSD, lysine-specific histone demethylase; Ma, malonylation; Me, methylation; NAM, nicotinamide; OG, O-GlcNAcylation; OGA, O-GlcNAcase; OGT, O-GlcNAc transferase; OH, hydroxylation; P, phosphorylation; PARP, poly(ADP) ribose polymerase; PKM2, pyruvate kinase M2 isoform; Pr, propionylation; Pr-CoA, propionyl-CoA; PRMT, peptidyl-arginine methyltransferase; SAM, S-adenosylmethionine; SIRT, sirtuin; Su, succinylation; Suc, succinate; Suc-CoA, succinyl-CoA; Sum, sumoylation; TET, ten-eleven translocation (DNA demethylase); Ub, ubiquitylation; UDP-GlcNAc, uridine diphosphate N-acetylglucosamine; USP7, ubiquitin-specific processing protease 7.

Fig. 2 |. Regulation of chromatin methylation by metabolic enzymes and metabolites and their roles in DNA repair.

a | Histone and DNA methylation are regulated by methyltransferases (lysine methyltransferases (KMTs), peptidyl-arginine methyltransferases (PRMTs) or DNA methyltransferases (DNMTs)) and demethylases (lysine-specific demethylase 1A (LSD1) and LSD2, Jumonji C (JMJC) family proteins or ten-eleven translocation (TET) proteins) in a metabolite-dependent manner. Histone and DNA methylation are inhibited when S-adenosylmethionine (SAM) levels are low. Production of phosphatidylcholine (PC) from phosphoethanolamine (PE) consumes SAM, thereby providing a link between chromatin methylation and lipid metabolism. b | Histone methylation allows recruitment of DNA-dependent protein kinase (DNA-PK) to DNA breaks, thereby fuelling DNA repair by nonhomologous end joining (NHEJ). Local generation of fumarate (Fum) at the DNA damage regions by fumarase (FH) promotes DNA repair through inhibition of histone H3 demethylation. In a feedforward mechanism, DNA-PK phosphorylates fumarase and promotes its binding to DNA lesions. Succinate (Suc), Fum and 2-hydroxyglutarate (2-HG) are competitive inhibitors for the α-ketoglutarate (α-KG)-dependent demethylases. DSB, double-strand break; hCys, homocysteine; KDM2B, lysine-specific demethylase 2B; Mal, malate; MAT, methionine adenosyltransferase; Me, methylation; Met, methionine; SAH, S-adenosylhomocysteine; THF, tetrahydrofolate.

Fig. 3 |. Core metabolic functions of metabolic enzymes that also function in epigenetic modifications.

Main metabolic pathways regulated by metabolic enzymes involved in epigenetic modifications are shown. α-KG, α-ketoglutarate; α-KGDH,α-KG dehydrogenase; 1,3-BPG, 1,3-bisphosphoglycerate; 2-HG, 2-hydroxyglutarate; Ac-CoA, acetyl-CoA; Ace, acetate; ACLY, ATP citrate synthase; ACSS2, acetyl-CoA synthetase short-chain family member 2; Cit, citrate; F-1,6 P, fructose 1,6-bisphosphate; F-2,6 P, fructose 2,6-bisphosphate; F-6P, fructose 6-phosphate; FH, fumarase; Fum, fumarate; G3P, glyceraldehyde 3-phosphate; G-6P, glucose 6-phosphate; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GMPS, GMP synthase; hCys, homocysteine; IMP, inosine 5′-monophosphate; IMPDH, IMP dehydrogenase; Lac, lactate; Mal, malate; Mal-CoA, malonyl-CoA; MATII, methionine adenosyltransferase II; Met, methionine; mIDH1, isocitrate dehydrogenase [NADP], cytoplasmic mutant; mIDH2, isocitrate dehydrogenase [NADP], mitochondrial mutant; PDC, pyruvate dehydrogenase complex; PEP, 2-phosphoenolpyruvate; PFKFB4, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4; PKM2, pyruvate kinase M2 isoform; Pyr, pyruvate; R-5P, ribose 5-phosphate; SAH, S-adenosylhomocysteine; SAM, S-adenosylmethionine; SDH, succinate dehydrogenase; Suc, succinate; Suc-CoA, succinyl-CoA; TCA, tricarboxylic acid; XMP, xanthosine monophosphate.

Fig. 4 |. The roles of nuclear PKM2 in gene expression.

The nuclear translocation of pyruvate kinase M2 isoform (PKM2) is regulated by several mechanisms. ERK1 and ERK2 phosphorylate PKM2, which promotes its isomerization (transition from tetramer to monomer) mediated by peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1), resulting in the exposition of nuclear localization signal (NLS) of PKM2 and its interaction with importin α5 (Impα5). Nuclear translocation of PKM2 is also promoted by acetylation (Ac) mediated by histone acetyltransferase p300 and by the interaction of PKM2 with Jumonji domain-containing protein 5 (JMJD5). In the nucleus, PKM2 interacts with β-catenin and binds to β-catenin-regulated promoters, where it phosphorylates histone H3 at T11 and subsequently removes histone deacetylase 3 (HDAC3) to promote histone H3 acetylation and expression of genes regulating the Warburg effect and cell cycle progression. PKM2 also directly increases the transcriptional activity of signal transducer and activator of transcription 3 (STAT3) by phosphorylation (P) of STAT3. PKM2 hydroxylated by prolyl hydroxylase 3 (PHD3) binds to hypoxia-inducible factor 1α (HIF1α) to promote recruitment of HIF1α and p300 to the promoters of HIF1α-regulated genes for expression. CCND1, G1/S-specific cyclin D1; GLUT1, glucose transporter type 1, erythrocyte/brain (also known as SLC2A1); Lac, lactate; LDHA, l-lactate dehydrogenase A chain; LEF, lymphoid enhancer factor; MYC, MYC proto-oncogene protein; OH, hydroxylation; PEP, 2-phosphoenolpyruvate; Pyr, pyruvate; TCF, T cell factor.

Fig. 5 |. Acetylation of histones regulated by metabolic enzymes and metabolites.

a | Histone acetylation (Ac) is mediated by histone acetyltransferases (HATs) and reversed by histone deacetylases (HDACs). Both enzyme groups are metabolically regulated. HDACs are inhibited by β-hydroxybutyrate (βHB) and butyrate (But). Acetyl-CoA (Ac-CoA) synthetase short-chain family member 2 (ACSS2) fuels the activity of HATs by producing Ac-CoA from acetate (Ace) locally. By forming complexes with transcription factor EB (TFEB) (left panel) or cAMP-responsive element-binding protein (CBP) (right panel), ACSS2 regulates the expression of lysosomal and autophagy genes and memory-related neuronal genes, respectively. b | Nuclear ATP citrate (Cit) synthase (ACLY) produces nuclear Ac-CoA to regulate expression of glucose metabolism-related genes (left panel) or DNA repair by homologous recombination (HR) (right panel). In the context of DNA repair, ACLY is regulated by phosphorylation (P) mediated by protein kinase B (AKT), which acts downstream of DNA double-strand break (DSB)-activated ataxia-telangiectasia mutated (ATM) kinase. c | Pyruvate dehydrogenase complex (PDC) together with pyruvate kinase M2 isoform (PKM2) and HAT coordinately acetylates histones and activates expression of genes regulated by aryl hydrocarbon receptor (AhR) as well as genes involved in cell cycle progression. 53BP1, TP53-binding protein; BRCA1, breast cancer type 1 susceptibility protein; PEP, 2-phosphoenolpyruvate; Pyr, pyruvate.

Fig. 6 |. Association of metabolites and metabolic enzymes with cancer development.

a | Nuclear pyruvate kinase M2 isoform (PKM2) promotes gene expression through phosphorylation (P) of histones or regulation of transcription factors, such as hypoxia-inducible factor 1α (HIF1α). HIF1α activity can also be upregulated by fructose-1,6-bisphosphatase 1 (FBP1) deficiency. b | 6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 (PFKFB4) promotes gene expression through phosphorylation of steroid receptor co-activator protein 3 (SRC3) at S857. This phosphorylation increases the interaction between SRC3 and activating transcription factor 4 (ATF4), leading to gene expression. c | In the nucleus, α-ketoglutarate dehydrogenase (α-KGDH) interacts with histone acetyltransferase KAT2A and locally supplies succinyl-CoA (Suc-CoA). This high local concentration of Suc-CoA fuels succinylation (Su) of K79 in histones in the promoter regions of more than 7,000 genes, promoting oncogene expression. d | ATP citrate (Cit) synthase (ACLY) and nuclear acetyl-CoA (Ac-CoA) synthetase short-chain family member 2 (ACSS2) generate local Ac-CoA, which promotes histone acetylation (Ac) by histone acetyltransferases (HATs) and regulates homologous recombination (HR)-dependent DNA repair and the expression of lysosome and autophagy genes under the control of transcription factor EB (TFEB). e | α-KG dioxygenases, including the ten-eleven translocation (TET) and Jumonji C (JMJC) domain-containing demethylases are inhibited by high levels of succinate (Suc) induced by loss-of-function mutations in genes encoding succinate dehydrogenase (SDH^−/−), by high levels of fumarate (Fum), which accumulate in the absence of fumarase (FH) activity in the tricarboxylic acid (TCA) cycle owing to loss-of-function mutations in the fumarase gene (FH^−/−) as well as by aberrant production of 2-hydroxyglutarate (2-HG) induced by mutation of isocitrate dehydrogenases: cytoplasmic (mIDH1) and mitochondrial (mIDH2). This inhibition contributes to the hypermethylation phenotype and aggressiveness of tumours with SDH, FH or IDH1/2 mutations. High levels of Fum also increase the transcriptional activity of nuclear factor erythroid 2-related factor 2 (NRF2) and subsequent antioxidant response by promoting succinylation (Su) and, in turn, inhibition of Kelch-like ECH-associated protein 1 (KEAP1).Wild-type fumarase can be targeted to the nucleus, where it contributes to local production of Fum from malate (Mal) and inhibition of demethylases, which locally increases histone methylation (Me) to support nonhomologous end joining (NHEJ) DNA repair. In addition, wild-type fumarase as a tumour suppressor can be negatively regulated by O-GlcNAcylation (OG) mediated by O-GlcNAc transferase (OGT), which interferes with fumarase phosphorylation and the interaction of fumarase with ATF2, leading to suppression of ATF2-regulated cell growth arrest genes. Ace, acetate; CCND1, G1/S-specific cyclin D1.