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Impact of toxins and heavy metals on methylation

Impact of toxins and heavy metals on methylation

Impact of toxins and heavy metals on methylation


Many toxins and metals can adversely affect your health, and many are damaging to DNA methylation, particularly if you have a MTHFR mutation. 

Growing evidence shows that environmental metal exposure involves changes in epigenetic marks, which may lead to a possible link between heritable changes in gene expression and disease susceptibility and development.

Protection from and elimination of toxins, along with living a well-balanced life with good nutrition, stress management, sleep and exercise and provide you with what you need avoid chronic disease and live life optimally.  Balancing methylation and understanding your MTHFR gene and other associated pathways are key in ensuring optimal health and that your detoxification pathways are working efficiently.

What is methylation?

“Methylation is a biological mechanism for the removal of toxic metal(loid)s (e.g., Mercury {Hg} ) by converting them to methyl derivatives that are subsequently removed by volatilization [86].”

Methylation happens all over the body, all the time. Methylation is a key biochemical process that is essential for the proper function of almost all of your body’s systems. 

A methyl group is one carbon and three hydrogens.

When a methyl group attaches to a molecule, or is passed from one molecule to another, it acts like a green traffic light causing the molecule to start doing its work.

CpG islands (CGIs) are regions of the genome that contain a large number of CpG dinucleotide repeats. They are important because they represent areas of the genome that have for some reason been protected from the mutating properties of methylation through evolutionary time.

When methylation is going well, the process helps repair your DNA, regulates hormones, produces energy, protects against cancer, supports detoxification, keeps your immune system healthy, supports the protective coating along your nerves, strengthens the nervous system and on and on ad on.

Methylation is upstream of many biochemical pathways in the body, including the Cystathionine-β-synthase (CBS) pathway.  The CBS pathway is the first step of the transsulfuration pathway responsible for detoxification and production of the body’s master antioxidant, Glutathione.

What happens when methylation isn’t going well?

A breakdown in methylation puts you at higher risk for conditions like osteoporosis, diabetes, cervical dysplasia and cancer, colon cancer, lung cancer, depression, paediatric cognitive dysfunction (mood and other behavioural disorders), dementia, stroke, miscarriages and cardiovascular disease.

Factors that affect your methylation process

There are a number of factors, including toxicity in the body, that affect the methylation process. These include:

  • Genetics – 20 percent of us are genetically predisposed to high homocysteine
  • Poor diet – you need to get adequate levels of vitamins B6 and B12, betaine and folate. 
  • Smoking – the carbon monoxide from cigarette smoke inactivates vitamin B6
  • Malabsorption – conditions like digestive diseases, food allergies and even aging can reduce absorption of nutrients
  • Decreased stomach acid – aging and other conditions can reduce stomach acid — and therefore absorption of vitamin B12
  • Medications – drugs like acid blockers, methotrexate (for cancer and arthritis and other autoimmune diseases), oral contraceptives, HCTZ (for high blood pressure), and Dilantin (for seizures) can all affect levels of B vitamins
  • Other conditions – these include hypothyroidism, kidney failure or having only one kidney, cancer, and pregnancy
  • Toxic exposures – some toxins can interfere with vitamin production 

Let’s look in detail at toxic exposure.

How do toxins affect methylation?

Although slight amounts of some heavy metals, such as iron (Fe), zinc (Zn) and copper (Cu), are essential for enzymatic activities, other metals like lead (Pb), arsenic (As), cadmium (Cd), and mercury (Hg), are toxic for humans. These metals are able to pass through the blood brain barrier (BBB), disturb the central nervous system, affect ion channels, compete with enzyme cofactors, and finally cause oxidative stresses in the body.

Exposure to toxins and certain metals, especially if you have an MTHFR genetic mutation, can affect your methylation process. 

Toxins and heavy metals stress our bodies and one of the ways they stress our bodies is by blocking methylation.

Methylation is the process by which our bodies turn B-vitamins (folate or B9 and B12, in particular) into SAMe (S-adenosylmethionine) and glutathione, two substances that are essential to our well-being. 

SAMe and glutathione play a role in creating energy, protecting our cells, and maintaining our mood, focus and daily functioning. They also help the liver to detoxify substances that enter our blood stream, including toxins, medications and estrogens.

If you have an MTHFR mutation, your body will have a harder time making SAMe and glutathione. 

When your body experiences stress, including when it is exposed to toxins and/or heavy metals and your body needs extra help getting rid of those substances, your liver is already struggling to keep up, leaving you vulnerable to the negative effects of these toxic substances.

Another function of methylation is to protect our genes. Methyl groups help keep our DNA wound up in bundles, called histones, protected from the harmful effects of stress. However, when toxins and metals enter the body, they prevent methylation of our DNA, making our genes vulnerable to damage. A gene that was previously “turned off” could be “turned on”. In other words, a latent genetic predisposition can get “switched on” when exposed to toxins and metals.

The activation of the potential problems the gene can cause can trigger a tendency toward autoimmunity, dementia or cancer. This is referred to as “epigenetic modification” and means toxins and heavy metals can influence our genes beyond our inherent predispositions.

Damaging toxins and metals that affect methylation

Environmental toxicants such as toxic metals can alter epigenetic regulatory features such as DNA methylation, histone modification, and non-coding RNA expression. Heavy metals influence gene expression by epigenetic mechanisms and by directly binding to various metal response elements in the target gene promoters.

Lead, mercury, cadmium and other metals, as well as toxins such as glyphosate, parabens, and phthalates, slow down the enzymatic steps in the methylation pathway. So, even when you have plenty of B-vitamins, including methylfolate (the form of folate that is important for addressing MTHFR), metals and toxins bring things to a standstill.

Each of the following metals and toxins slows down the methylation process and activates dormant genes. In addition, metals often impair the immune system and trigger neurological conditions.


Glyphosate is weed killer that is used on many crops including corn, soy and wheat. Plants are genetically modified to withstand treatment with glyphosate. It has a negative impact on methylation and causes oxidative stress and neurotoxicity and is a potential carcinogen.


Parabens are a preservative, frequently used to prevent bacteria from growing in personal care products like toothpaste, shampoo, soaps, skin lotion and lipstick. They negatively impact methylation by mimicking estrogen in the body. Parabens can be stored in the body, so the amount in your body accumulates with time and use. Once in the body, they are hard to get rid of, especially if your liver is already overworked.


Lead is found in some paints, dishes with lead paint in the glaze, air, water, and soil due to industrial processes/sites that release it. Symptoms of toxicity include abdominal pain, nausea, headache, joint and muscle pain, decreased memory and sleep disturbances.


Mercury is found in mercury thermometers, amalgam dental fillings and large sea fish like tuna and swordfish. Mercury poisoning can lead to irritability, fatigue, memory loss, tremors, and sleep disturbances.


The main exposure to cadmium is from cigarette smoke, although it is also in some industrial fumes. Symptoms of toxicity include lung inflammation, shortness of breath, cough, headache, dizziness and chest pain.

Testing for exposure to toxins and metals

It is possible to test for both toxins and metals in urine, including levels of glyphosate, parabens, phthalates, and many other toxins, including benzene and perchlorates.

Metal levels are also often checked with a hair analysis, oligioscan and other specific GPL Tox testing.  We offer all of these testing methods at Advanced Functional Medicine.

Treatments for the removal of toxins and metals

For the removal of heavy metals, it is important to work with an experienced practitioner with relevant training. It is important to follow a protocol that includes nutrient and antioxidant support for the liver to detoxify metals, and individualized dosing of a chelating agent based on your unique body weight, genetic profile and sensitivities.  

Tips for avoiding toxins and metals

  • Go to a holistic dentist if you need to have amalgam fillings replaced. 
  • Decrease your intake of swordfish to no more than once per month.
  • Check your home environment for lead paint and dishes. 
  • Switch to non-plastic containers (plastic water bottles are a big source of exposure not just to phthalates but other harmful chemicals).
  • Switch to paraben-free and fragrance-free personal care products. 
  • Use a reverse-osmosis water filter to filter out metals and toxins.

Diet advice to reduce toxicity

Specialist Nutrition
  • Eat more dark, leafy greens – eat at least one cup a day of vegetables like bok choy, escarole, Swiss chard, kale, watercress, spinach, or dandelion, mustard, collard or beet greens. These are among the most abundant sources of the nutrients needed for optimal methylation 
  • Get more Bs in your diet – good food sources include sunflower seeds and wheat germ (vitamin B6); fish and eggs (vitamin B6 and B12); cheese (B12); beans and walnuts (vitamin B6 and folate); leafy dark green vegetables; asparagus, almonds, and whole grains (folate); and liver (all three)  
  • Minimize animal protein, sugar, and saturated fat – certain compounds can raise levels of homocysteine and deplete the B vitamins. These include excess animal protein, sugar, saturated fat, coffee, and alcohol. Irradiation of food depletes nutrients, so foods treated this way may also be lower in B vitamins
  • Avoid processed foods and canned foods – these are depleted in vitamins
  • Avoid caffeine – excess amounts can deplete your B vitamin levels
  • Limit alcohol to three drinks a week – more than this can deplete your B vitamin levels
  • Don’t smoke – smoking inactivates vitamin B6
  • Avoid medications that interfere with methylation
  • Keep the bacteria in your gut healthy – take targeted probiotic supplements and use other measures to make sure the bacteria in your gut are healthy so you can properly absorb the vitamins you do get
  • Improve stomach acid – use herbal digestives (bitters) or taking supplemental HCl
  • Take supplements that prevent damage from homocysteine – antioxidants protect you from homocysteine damage. Also make sure you support methylation with supplements like magnesium and zinc 
  • Supplement with folate, vitamin B6, vitamin B12 and betaine to help support proper homocysteine metabolism

How we can help eliminate toxins and metals from your body

Current evidence supports the notion that environmental exposures are associated with DNA-methylation and expression changes that can impact human health.  

To help eliminate toxins and metals from your body, a key objection is to maximize the methylation process and assist with chelation of metals. That means avoiding the things that cause your methylation process to break down, testing to find out how well your methylation is working and what toxins and metals are present.

Working to return to proper methylation and optimal health with dietary, supplement and lifestyle advice is our approach.

Contact us to find out more

The above information is intended to be general, educational advice only, on topics which are of interest to us. It is not intended to represent specific or individual health or medical advice and is not specific to your situation. The below information is educative and is not intended to advertise any service.

Before making any decisions in relation to your health, you should always discuss your individual situation with your own health practitioners to ensure that any advice you have read is right for you.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

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