Advances in Nutritional Epigenetics-A Fresh Perspective for an Old Idea. Lessons Learned, Limitations, and Future Directions

Abstract

Nutritional epigenetics is a rapidly expanding field of research, and the natural modulation of the genome is a non-invasive, sustainable, and personalized alternative to gene-editing for chronic disease management. Genetic differences and epigenetic inflexibility resulting in abnormal gene expression, differential or aberrant methylation patterns account for the vast majority of diseases. The expanding understanding of biological evolution and the environmental influence on epigenetics and natural selection requires relearning of once thought to be well-understood concepts. This research explores the potential for natural modulation by the less understood epigenetic modifications such as ubiquitination, nitrosylation, glycosylation, phosphorylation, and serotonylation concluding that the under-appreciated acetylation and mitochondrial dependant downstream epigenetic post-translational modifications may be the pinnacle of the epigenomic hierarchy, essential for optimal health, including sustainable cellular energy production. With an emphasis on lessons learned, this conceptional exploration provides a fresh perspective on methylation, demonstrating how increases in environmental methane drive an evolutionary down regulation of endogenous methyl groups synthesis and demonstrates how epigenetic mechanisms are cell-specific, making supplementation with methyl cofactors throughout differentiation unpredictable. Interference with the epigenomic hierarchy may result in epigenetic inflexibility, symptom relief and disease concomitantly and may be responsible for the increased incidence of neurological disease such as autism spectrum disorder.

Keywords: 5-methyltetrahydrofolate; DNA; MTHFR; acetylation; autism spectrum disorder; carbon; environment; epigenetics; evolution; folic acid; future directions; gene expression; glycosylation; histone; limitations; methane; methylation; methylenetetrahydrofolate reductase; natural selection; neural tube defects; nitrosylation; nutrition; nutritional epigenetics; one carbon etabolism; phosphorylation; pollution; single nucleotide variant; ubiquitination.

Figure 1.

Heterochromatin and euchromatin. The methyl group (a) bound to the histone tail maintains a positive charge resulting in tight hydrogen bonds and compact genomic structure; heterochromatin (b) Heterochromatin excludes ribonucleic acid polymerase (RNA) (c) from binding the gene and initiating gene transcription. The acetyl group (d) neutralises the methylating positive charge maintaining heterochromatin, loosening the hydrogen bonds and enabling open structural conformation; euchromatin (e) and RNA polymerase to access the genome and initiate gene transcription.

Figure 2.

A cell-specific hypothesis—metabolic effects of bypassing a reduced function MTHFR polymorphism with exogenous methyl. (a) Acetyl-CoA enters the tricarboxylic acid (TCA) (a.1) cycle for adenosine triphosphate (ATP) (a.2) synthesis or is catabolized to an acetyl group for histone and protein acetylation. ATP is used for additional post translational modifications. Acetyl group binds the promoter region of the methylenetetrahydrofolate reductase (MTHFR) (a.4) and initiates transcription for enzymatic reduction of 5,10 methylenetetrahydrofolate from tetrahydrofolate (THF) (a.3). (b) During active one-carbon metabolism, MTHFR carries the one-carbon methyl unit to methionine for ATP dependant methionine adenosyltransferase (MAT) synthesis of S-adenosylmethionine for DNA and histone methylation reactions. Exogenous methane or supplemental methyl groups (5-MTHF) (b.1), supply methyl directly without the need for one-carbon metabolism. Betaine-homocysteine-S-methyltransferase (BMHT) (b.2) has a bound acetyl group and is transcribed to catalyze the conversion of betaine and homocysteine to dimethylglycine and methionine respectively. (c) Deoxyribonucleic acid (DNA) methyltransferase (DNMT) (c.1) utilises exogenous methyl groups, or one-carbon derived S-adenosylmethionine for DNA methylation. A Methyl group is bound to the promoter region cytosine-phosphate guanosine (CpG c.4) of BHMT and MTHFR to depict feedback inhibition of one-carbon metabolism. DNMT initiates DNA methylation through the binding of a methyl group to position 5′ of cytosine bases neighboring guanosine (CpG), generating 5-methyl-cytosine (5-mC). 5-mC is then oxidized to 5-hydroxymethylcytosine (5-hmC). Ten-Eleven translocation di-oxygenase (TET) (c.2) contribute to the removal of the methyl group from cytosine, forming 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Thymine DNA glycosylate (TDG) (c.3) initiates base excision repair of deaminated bases. (d) Unmethylated histone 3-lysine 4 (H3K4) (d.1) allosterically activates DNA methyltransferase 3a (DNMT3a) (d.2) depicting epigenetic cross-talk between DNA and histone methylation. Lysine 9 residue of histone 3 is unphosphorylated and has been methylated by a s-adenosylmethionine dependant histone methyltransferase with bound heterochromatin protein 1, resulting in heterochromatin and the exclusion of RNA polymerase for active gene expression. The metabolic effects of supplemental or environmental methyl group donation are cell-specific. Cell type 1 (e) A build-up of unmetabolized folate, resulting in excess extracellular L-glutamate or polyglutamate activation of glutamate receptors. Cell type 2 (f) Feedback inhibition of one-carbon metabolism, constitutively active gene expression and differential methylation patterns. Cell type 3 (g) Direct methyl group donation, increased DNA or histone methylation.

Figure 3.

Epigenetic cross talk in energy conservation. Pyruvate dehydrogenase (PDH) (a) synthesized acetyl-CoA enters the tricarboxylic acid (TCA) (b) cycle for mixed energy substrate and sustainable adenosine triphosphate (ATP) (c) synthesis. ATP is used for epigenetic methionine synthase, (MAT) (d) ubiquitination, phosphorylation, and chromatin remodeling complexes. Acetyl-CoA catabolized acetyl groups participate in protein and histone acetylation. Oxygen (O₂) (e) intake increases activity jmjC demethylation, reducing methylation and enabling active gene expression and high energy output. Hypoxic reduction of O₂ dependant demethylase and consequent upregulation of methylation marks including activating histone-3-lysine-4 methylation (H3K4me) (f), repressive histone-3-lysine-9 trimethylation (H3K9me) (g) and protein arginine methyltransferase activity (PRMT) (h) and histone-3-arginine-2 dimethylation (H3R2me) (i). Upregulation of PRMT5 and consequent proteolysis of methylated arginine increases asymmetric dimethylarginine (ADMA) (j) resulting in downregulation of endothelial nitric oxide (eNOS) (k). Upregulation of H3K4me results in the induction of hypoxia-inducible factor (HIF) (l) and subsequent upregulation of eNOS, increasing nitric oxide (NO) (m). Upregulated HIF, upregulates pyruvate kinase (PDK) (n), inhibiting PDH, reducing acetyl CoA production and acetylation. Increased HIF induced NO inhibits demethylation, causing persistent methylation, conserving energy and oxygen through switching to glycolysis only metabolism and advancing to respiratory quotient (RQ) (o) = >1. Dihydrofolate reductase (DHFR) (p) promotes eNOS coupling and NO synthesis. Nitrosylation of DHFR stabilises the protein and prevents uncoupling. eNOS is self-regulated by eNOS protein nitrosylation, inhibiting its expression. Hypoxic upregulation of inhibiting H3K9me3 reduces expression of DHFR, resulting in eNOS uncoupling, reduced NO synthesis, superoxide generation, and upregulation of demethylase activity signifying precise epigenetic regulation of energy and O2 conservation in hypoxic conditions.

Figure 4.

Hypothetical cell culture epigenetic manipulation of Janus kinase-2. Folic acid is added to the UKE1 cell line culture media, influencing epigenetic methylation. Upregulation of G9a methyltransferase inhibits Janus kinase-2 (JAK2) (a). Upregulation of histone-lysine N-methyltransferase (SUV39H1) (b) induces trimethylation of histone-3-lysine-9 (H3K9me3 (c) stimulating the binding of heterochromatin protein 1 (HP1) (d) and initiating heterochromatin. Reduced expression of JAK2 is incapable of excluding HP1 and maintaining euchromatin. Excess methylation inhibits one-carbon metabolism (1 Cm) (e) and induces spontaneous deamination of methylated cytosine-phosphate-guanosine (CpG) (f) and loss of CpG resulting in JAK2 constitutive activation or copy number accumulation.