Methylation: What It Is, Why You Should Care About It + What To Do If It Isn’t Working

Methylation

You are alive because of brilliant biochemistry. In my telehealth functional medicine clinic I spend every day looking at people’s health cases and lab work and seeing how true this statement really is.

As we go through our daily lives barely giving it a second thought, every system inside the body is working diligently alongside each other to help us live, breathe, and perform all of our daily functions as optimally as possible.

There’s no greater example of this than methylation, a biochemical process most people have never heard of, but one that affects nearly every function in the body.

So let’s take a look at why we need to put more weight on this important process, what happens when it’s not working properly, and how to support methylation with food, lifestyle, testing, and targeted supplements.

What Is Methylation?

Methylation is a biochemical process that your body relies on to keep you healthy and thriving. The process involves transferring a methyl group (one carbon atom and three hydrogen atoms) onto another molecule. This happens close to 1 billion times every second and controls your ability to detox and in turn, lower inflammation, produce neurotransmitters, and protect your DNA.

Every cell in your body depends on methylation. It affects everything from mental health to cardiovascular disease risk to hormone balance, and plays a role in how your body synthesizes melatonin for sleep, glutathione for antioxidant defence, and creatine for muscle performance.

So, understandably, if this process isn’t working properly, your body’s ability to function and repair itself takes a hit.

What Happens With Poor Methylation?

Poor methylation has been linked to a wide range of health problems, including:

Some of the most compelling recent research on methylation has looked into the important role this process plays in cognitive function, and specifically forming and retrieving long-term memories. (6) Researchers have linked impaired DNA methylation with neurodegeneration, including Alzheimer’s Disease. (4)

A recent systematic review also highlighted that many individuals with type 2 diabetes have genetic variations related to methylation. (5)

These are just a few examples. I don’t think it’s an overstatement to say that methylation could be linked to just about every chronic health condition you can think of, given its crucial role in immune system function, inflammation, brain health, gut health, thyroid health, and hormonal health.

Genetics and What Can Go Wrong With Methylation

There are many reasons why methylation could be hindered, one major one being MTHFR gene mutations. The MTHFR enzyme is responsible for converting folic acid into its usable form, 5-MTHF (5-methyltetrahydrofolate), which fuels the methylation cycle.

It is estimated (7) that those with MTHFR gene mutations make 70% less methyl-folate than those without a mutation.

There are two main MTHFR gene variants: A1298C and C677T, and they’re both linked to different health challenges.

Mutations of A1298C are associated with neurotransmitter imbalances, including dopamine and serotonin, which can lead to mood disorders. C677T is linked to higher levels of homocysteine, which is connected with an increased risk of heart disease and autoimmune conditions.

Mutations in the MTR and MTRR genes can also contribute to methylation problems. These genes are both needed to produce vitamin B12, which is a critical methyl donor. Those with this MTR or MTRR gene variants typically use B12 quicker than their body can produce it, and often require supplemental B12 (especially in its activated form, methylcobalamin) to support the methylation process and the body’s needs.

Close to 40% of the world’s population has an MTHFR genetic mutation, but most don’t even know it. (8) Genetic testing is important to determine if you have any of these mutations that are hindering the methylation process.

But remember that your genes are not your destiny! Environmental factors play an essential role in determining how your genetics are expressed. That’s what we’re going to explore further down.

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How To Test Your Methylation Capacity

I highly recommend testing your methylation capacity (including genetic factors) in order to arm yourself with knowledge about how to support this process within your body.

This is an empowering, proactive step you can take in order to uncover potential methylation blocks before they turn into chronic symptoms (or help your body heal if you’re currently experiencing health problems).

Some of the tests I run to assess methylation include:

  1. DNA Methylation Pathway Profile

This test looks at around 30 different methylation-related SNPs (single nucleotide polymorphisms) to assess your unique genetic profile as it relates to methylation. It offers a comprehensive view of how well your methylation cycle may be functioning.

  1. Homocysteine

Homocysteine is recycled down by the methylation process, so elevated homocysteine is a red flag that methylation is impaired (and that risk of cardiovascular disease is elevated). Homocysteine levels can be measured with a simple blood test that can be run by any healthcare provider. I look for an optimal range under 7.

  1. Microbiome Labs

Gut imbalances, like candida overgrowth and dysbiosis, can further perpetuate methylation problems by increasing inflammation and impairing nutrient absorption. Gut testing helps us get a more complete picture of what’s going on.

  1. Hair Mineral Analysis 

We look at lithium levels in particular, which play a subtle but important role in transporting vitamin B12 into cells (and impaired intracellular B12 activity further compromises methylation).

How To Support Methylation

Even if you have a genetic mutation, that doesn’t mean you are “doomed” to suffer the health consequences. The study of epigenetics shows us that genes are not our destiny. Our environment, lifestyle, and nutrient status, along with other factors, shape how our genes express themselves. Understanding our genetic abnormalities allows us to work with them to support our health.

And thankfully, there are many natural ways to support methylation and detox pathways throughout your body. Here are a few strategies I recommend:

  1. Incorporate methylation-supportive superfoods

Green leafy vegetables like spinach, kale, and Swiss chard are loaded with folate. Grass-fed organ meats provide methionine, vitamin B12, and choline. All of these micronutrients are key methyl donors. These foods can help support your methylation pathways and promote healthy gene expression. (9)

  1. Eat sulfur-rich cruciferous vegetables

Foods high in sulfur like cabbage, cauliflower, broccoli, onions, garlic, and mushrooms also help to support methylation, as sulfur supports glutathione production and phase II liver detoxification.  These foods may help to maintain antioxidant status and support DNA repair. (10)

  1. Support detoxification pathways

Certain herbs and spices, including cilantro, parsley, turmeric, dandelion root, and milk thistle, have powerful detoxification properties. These herbs may support liver methylation capacity, especially when the body is overloaded by environmental toxins, heavy metals, or estrogen dominance.

  1. Switch to clean products

Your methylation pathways have to deal with the toxins you come into contact with daily, so the more toxins you’re exposed to, the harder your detox pathways have to work. Reducing exposure can help to maintain healthy methylation processes. (11) You can decrease your burden by switching your cleaning, beauty, and other everyday products over to clean, non-toxic versions as much as possible.

  1. De-stress

If you needed another reason to manage your stress levels, did you know that stress can actually change the methylation of your DNA and alter the activity of certain genes? (12) Try changing your relationship with stress by incorporating a daily ritual of mindfulness, meditation, or breathwork to help you stay calm throughout your day. These practices help regulate cortisol and calm the nervous system, reducing inflammation and supporting neurotransmitter balance.

  1. Use targeted supplementation: 

Activated B vitamins are often necessary in order to bypass genetic roadblocks. These may include:

  • 5-MTHF (methylfolate) for those with MTHFR variants
  • Methylcobalamin (B12) and P5P (vitamin B6) to support neurotransmitter synthesis (dopamine, serotonin, norepinephrine)
  • Choline and betaine (TMG) as additional methyl donors
  • Magnesium, which supports over 300 enzymatic reactions, including methylation

Since B vitamins act as fuel for your methylation pathways, they are often needed to wake them up and give them that much-needed boost. However, not all supplements are created equally. In fact, folic acid in particular can be problematic for anyone with an MTHFR mutation. Instead, natural folate and activated forms of B vitamins are your best bet.

As someone with an MTHFR gene mutation myself, I saw the need for this next-level supplement but I wasn’t finding one on the market. That’s why I personally curated The Methylator’s comprehensive formula with the highest quality B vitamins including:

  • Folate (5-Methyltetrahydrofolate)
  • B6 (Pyridoxal 5′-phosphate)
  • B12 (methylcobalamin)
  • B2 (Riboflavin 5′ phosphate)
  • Anhydrous betaine (trimethylglycine)

Together these five nutrients work synergistically to support methylation and restore you to a state of thriving health and well-being.

Next Steps: Personalized Methylation Support 

While these methylation tips are an important starting point, most people with methylation issues benefit from expert guidance and a more personalized dietary, supplement, and lifestyle strategy.

We work with clients globally via webcam to explore methylation genetics, underlying depleters of methyl donors, and other individual factors– and then create customized healing protocols that support real healing. If you’re interested in working with us, you can get started right here.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.

FAQ

There are several different kinds of tests you can take to assess your body’s methylation capacity. These include genetic testing for variants in the MTHFR and other genes that affect methylation pathways, as well as blood testing for homocysteine levels.

Yes, poor methylation can lead to weight gain or weight loss resistance, due to its impact on metabolic and hormonal function.

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FUNCTIONAL MEDICINE CONSULTATIONS FOR PEOPLE AROUND THE WORLD

  1. Wierzbicki, Anthony S. “Homocysteine and cardiovascular disease: a review of the evidence.” Diabetes & vascular disease research vol. 4,2 (2007): 143-50. doi:10.3132/dvdr.2007.033
  2. Simon Gilbody, Sarah Lewis, Tracy Lightfoot, Methylenetetrahydrofolate Reductase (MTHFR) Genetic Polymorphisms and Psychiatric Disorders: A HuGE Review, American Journal of Epidemiology, Volume 165, Issue 1, 1 January 2007, Pages 1–13, https://doi.org/10.1093/aje/kwj347
  3. Richardson, Bruce. “DNA methylation and autoimmune disease.” Clinical immunology (Orlando, Fla.) vol. 109,1 (2003): 72-9. doi:10.1016/s1521-6616(03)00206-7
  4. Weymouth, L., Smith, A. R., & Lunnon, K. (2024). DNA Methylation in Alzheimer’s Disease.
  5. Nadiger, N., Veed, J. K., Chinya Nataraj, P., & Mukhopadhyay, A. (2024). DNA methylation and type 2 diabetes: a systematic review. Clinical epigenetics, 16(1), 67.
  6. Chen, X., Peng, Y., & Liu, X. S. (2025). DNA Methylation in Long-term Memory. Physiology.
  7. Sibani, S et al. “Characterization of six novel mutations in the methylenetetrahydrofolate reductase (MTHFR) gene in patients with homocystinuria.” Human mutation vol. 15,3 (2000): 280-7. doi:10.1002/(SICI)1098-1004(200003)15:3<280::AID-HUMU9>3.0.CO;2-I
  8. Traci Stein Ph.D., MPH A Genetic Mutation That Can Affect Mental & Physical Health Psychology 2014. https://www.psychologytoday.com/us/blog/the-integrationist/201409/genetic-mutation-can-affect-mental-physical-health
  9. Stidley, C. A., Picchi, M. A., Leng, S., Willink, R., Crowell, R. E., Flores, K. G., ... & Belinsky, S. A. (2010). Multivitamins, folate, and green vegetables protect against gene promoter methylation in the aerodigestive tract of smokers. Cancer research, 70(2), 568-574.
  10. Royston, K. J., & Tollefsbol, T. O. (2015). The epigenetic impact of cruciferous vegetables on cancer prevention. Current pharmacology reports, 1, 46-51.
  11. Ruiz-Hernandez, A., Kuo, C. C., Rentero-Garrido, P., Tang, W. Y., Redon, J., Ordovas, J. M., ... & Tellez-Plaza, M. (2015). Environmental chemicals and DNA methylation in adults: a systematic review of the epidemiologic evidence. Clinical epigenetics, 7, 1-24.
  12. Unternaehrer, E., Luers, P., Mill, J. et al. Dynamic changes in DNA methylation of stress-associated genes (OXTR, BDNF ) after acute psychosocial stress. Transl Psychiatry 2, e150 (2012). https://doi.org/10.1038/tp.2012.77

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BY DR. WILL COLE

Evidence-based reviewed article

Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is also the host of the popular The Art of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, Gut Feelings, and The Inflammation Spectrum.

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