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DNA methylation is different from the nutrient methylation process

TruDiagnostic Admin


The topic of methylation is attracting a lot of buzz recently. No topic has grabbed the attention of integrative health practitioners quite like methylation has. Methylation is characterized as the transfer of the four atom molecule, CH3, from one substance to another. CH3 is also referred to as a methyl group, the addition of a methyl group to a preexisting chemical structure is the specific process of methylation.

Before DNA methylation became well known, most would correlate the methylation process to the methylation cycle that happens in the body regarding the MTHRF, SAMe, and methylated B vitamins. However, this type of methylation is viewed differently clinically than the natural, predictable methylation that occurs as a result of the aging process.  

It is important to differentiate these two processes of methylation because of the clinical implication of both processes. 

The Methylation Cycle

The methylation cycle is a series of chemical changes that occur in the body. The cycle’s primary purpose is to regulate neurotransmitters, regulate genetic repair and expression, and generate energy-rich molecules such as ATP. Many additional and equally important biological cyclical processes intersect with the methylation cycle as well [3]. 

The methylation cycle begins in the blood vessels with the vitamin folate, which is obtained from the diet. Dietary folate enters the folate cycle and rotates through several enzymatic modifications. This generates one-carbon units required for the synthesis of DNA/RNA and the methyl groups required to regenerate methionine from homocysteine [9].

When methylenetetrahydrofolate reductase (MTHFR) acts on folate it picks up a methyl group and transforms into methyltetrahydrofolate (MTHF). MTHF can methylate the amino acid homocysteine. Homocysteine is not obtained from the diet, but it is biosynthesized from methionine via MTHF methylation. 

The “methionine cycle” provides the methyl groups required for all genomic and non-genomic methylation reactions in the form of S-adenosyl methionine (SAM). SAM serves as a methyl donor for multiple chemicals in the body, including DNA and RNA. The donation of SAM’s methyl group reduces it to SAMe, which reforms homocysteine, and the cycle begins all over again. (Figure 1).


Figure 1: The interlinked folate and methionine cycles. Dietary folate enters the folate cycle and rotates through several enzymatic modifications that generate the one-carbon units required for the synthesis of DNA/RNA and the methyl groups required to regenerate methionine from homocysteine. The methionine cycle provides the methyl groups required for all genomic and non-genomic methylation reactions in the form of S-adenosyl methionine (SAM). 

Poor methylation can negatively impact the body’s ability to produce and regulate glutathione, produce high-energy molecules, regulate neurotransmitters, repair DNA, and convert serotonin to melatonin. Various B vitamins act as cofactors for methylation, including B2 and B12. If methylation is not working properly due to various B vitamin deficiencies, disease-states, genetic mishaps, or higher levels of homocysteine may result. Homocysteine is the de-methylated derivative of the amino acid methionine and is an independent risk factor for various morbidities. 

Methylation Cycle’s Essential Functions

What can happen if you have a methylation imbalance? The folate and methionine cycles involved in methylation are highly dependent on an adequate supply of nutrients that act as cofactors and substrates. Without an adequate amount of these nutrients, including folate, serine, choline and vitamins B2, B6, and B12 methylation imbalances occur. 

There are many reasons this imbalance can happen which include inadequate dietary intake of nutrients, malabsorption of the nutrients, single nucleotide polymorphism, and lifestyle factors such as smoking, stress, and environmental toxicity. Methylation imbalances result in the build-up of homocysteine and inadequate production of methionine and SAMe, which can translate into accumulating certain diseases and conditions [3]. 

Homocysteine is an inflammatory marker that may increase the risk of thrombosis and endothelial dysfunction, cause errors in vascular smooth muscle proliferation and skeletal muscle metabolism, contribute to schizophrenia, birth defects, osteoporosis, cancer, and heart disease [1]. 


There are many types of supplements meant to support healthy methylation for cardiovascular, cognitive, and bone health. The main supplement you probably will hear about the most when it comes to methylation support is folate, also known as vitamin B9. Before folic acid is added to the folate cycle, it undergoes an enzymatic modification at several key steps and is ultimately transformed into 5-MTHF, the active form of folate. 

Supplemental folate is available in three main forms: folic acid, folinic acid, and 5-MTHF. 5-MTHF is the newest supplemental form of folate, and research shows it is more effective than folic acid [6]. Research confirms that 5-MTHF and folinic acid supplementation increases serum folate levels, improves folate status, and reduces homocysteine levels [11]. Individuals with methylation defects are most likely to benefit from 5-MTHF or folinic acid supplementation over folic acid, where these active forms of folate can be incorporated directly into the methylation pathways.

Other nutrients, in addition to folate, that can support healthy methylation and each step in the interconnected folate and methionine cycles are B2, B6, B12, choline, and serine which act as methyl donors or cofactors [3]. 

Uncovering the methylation cycle’s function and purpose can help us better understand the differences in the different types of biological methylation. Knowing the difference between genomic and non-genomic methylation will allow a deeper understanding of the significance of these types of methylation and ways we can implement these understandings into health and lifestyle regimens. 

DNA methylation

Most methylation research has been redirected toward one specific type of biological methylation, known as DNA methylation. DNA methylation is a part of the overall cycle, but before the field of epigenetics became a giant in modern research, most methylation research was focused on the overall cycle. 

DNA methylation is the addition of methyl groups to sites on the DNA. These sites are either adenine or cytosine nucleotide bases. Most DNA methylation occurs at CpG islands (Figure 2) which is where a cytosine is immediately followed by guanine and is connected by a phosphate bond, hence the abbreviated name CpG. 


Figure 2: Methyl markers attaching to Cytosine-phosphate-guanine (CpG) sites in the DNA. DNA methyltransferases (Dnmts) catalyzes the transfer of a methyl group from S-adenyl methionine (SAM) to the fifth carbon of cytosine residue to form 5-methylcytosine (5mC).

The transfer of a methyl group onto a cytosine forms 5-methylcytosine. This epigenetic modification regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA [Moore].  DNA methylation doesn’t alter genetic sequencing, which is the coding of our DNA. The code remains the same across all cell types from the moment you are born to the moment you die. Whereas DNA methylation changes the expression of your DNA without having an effect on your genomic sequence [9].

DNA methylation occurs as a result of several factors including aging, lifestyle, and the environment [2]. An example of lifestyle factors that can methylate your DNA is your diet, activity level, smoking, and alcohol consumption (Figure 3). Uncovering the various contributions to DNA methylation have led researchers to uncover that our DNA is changeable and that we can regulate the expression of our genes [4]. 


Figure 3: The environment, lifestyle, and individual characteristics’ epigenetic role

DNA methylation plays an extensive role in our overall health and longevity. About 45% of mammal’s genomes consist of transposable elements that are silenced by bulk methylation. DNA methylation is essential for silencing retroviral elements, regulating tissue-specific gene expression, genomic imprinting, and X chromosome inactivation. Importantly, DNA methylation in different genomic regions may exert different influences on gene activities based on the underlying genetic sequence [9].

Modifications caused by DNA methylation are associated with a growing number of human diseases [10]. The list of diseases DNA methylation has a role in are:

  • Various types of cancer

  • Cardiovascular disease

  • Dementia

  • Various neurological disorders such as schizophrenia and autism

  • Metabolic disorders like diabetes and hyperlipidemia [7]. 

The study of these diseases has provided key insights toward the functions that DNA methylation has toward the morbidity and mortality of people all over the world. 

One fascinating and relevant discovery in the field of DNA methylation that makes this type of methylation stand out from others is its ability to predict biological age. Aging is the leading cause of chronic disease globally, and chronological age (measuring one’s age in terms of years) has been the longstanding mode for measuring one’s age. Finding a reliable biological marker for age has been the goal of medical research for decades. In 2013, the anticipated discovery of using a biological marker for aging occurred. Researchers discovered the use of DNA methylation-based biomarkers to apply all sources of DNA to the entire age spectrum. The use of DNA methylation-based biomarkers have concluded that using epigenetics to create an objective biological clock is the most accurate and promising method for indicating one's age [5]. The use of an accurate biological age estimator is valuable for assessing and treating various aging-related diseases. 

Methylation Beyond DNA

In conclusion, methylation is a biochemical process where the addition of a methyl group is added to a substrate such as DNA, RNA, hormones, immune cells, and neurotransmitters. Biological implications for these methyl groups’ ability to complete various functions in the body include DNA synthesis and repair, immune function, and metabolism. Methylation occurs billions of times every second across multiple types of locations in the body and involves several different pathways. Non-genomic methylation involves several pathways including the folate and methionine cycles. Genomic methylation (DNA methylation) is characterized by the addition of a methyl group to a CpG site, which causes changes to the phenotype of an individual.

Uncovering the differences across genomic and non-genomic methylation will help further our understanding of how these various types of methylation play a significant role in human’s overall health, disease risk, and mortality risk.


  1. 5-methyltetrahydrofolate monograph. Altern Med Rev 2006;11(4):330-337. http://www.altmedrev.com/archive/publications/11/4/330.pdf 

  2. Alegría-Torres, J. A., Baccarelli, A., & Bollati, V. (2011). Epigenetics and lifestyle. Epigenomics, 3(3), 267–277. https://doi.org/10.2217/epi.11.22 

  3. Boyd, A. (2017, January 2). What is Methylation? [Web log review]. Retrieved from https://www.fxmedicine.com.au/blog-post/what-methylation 

  4. Gensous, N., Garagnani, P., Santoro, A., Giuliani, C., Ostan, R., Fabbri, C., Milazzo, M., Gentilini, D., di Blasio, A. M., Pietruszka, B., Madej, D., Bialecka-Debek, A., Brzozowska, A., Franceschi, C., & Bacalini, M. G. (2020). One-year Mediterranean diet promotes epigenetic rejuvenation with country- and sex-specific effects: a pilot study from the NU-AGE project. GeroScience, 42(2), 687–701. https://doi.org/10.1007/s11357-019-00149-0 

  5. Horvath, S., & Raj, K. (2018). DNA methylation-based biomarkers and the epigenetic clock theory of ageing. In Nature Reviews Genetics (Vol. 19, Issue 6, pp. 371–384). Nature Publishing Group. https://doi.org/10.1038/s41576-018-0004-3 

  6. Houghton LA, Sherwood KL, Pawlosky R, et al. [6S]-5-Methyltetrahydrofolate is at least as effective as folic acid in preventing a decline in blood folate concentrations during lactation. Am J Clin Nutr 2006, from https://doi.org/10.1093/ajcn/83.4.842  

  7. Jin, Z., & Liu, Y. (2018). DNA methylation in human diseases. Genes & Diseases, 5(1), 1–8. https://doi.org/https://doi.org/10.1016/j.gendis.2018.01.002 

  8. Kennedy D. O. (2016). B Vitamins and the Brain: Mechanisms, Dose and Efficacy--A Review. Nutrients, 8(2), 68. https://doi.org/10.3390/nu8020068 

  9. Moore, L. D., Le, T., & Fan, G. (2013). DNA methylation and its basic function. Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology, 38(1), 23–38. https://doi.org/10.1038/npp.2012.112 

  10. Robertson, K. D. (2005). DNA methylation and human disease. Nature Reviews Genetics, 6(8), 597–610. https://doi.org/10.1038/nrg1655 

  11. Scaglione, F., & Panzavolta, G. (2014). Folate, folic acid and 5-methyltetrahydrofolate are not the same thing. Xenobiotica; the fate of foreign compounds in biological systems, 44(5), 480–488. https://doi.org/10.3109/00498254.2013.845705 


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