The Many Roles of Methylation
If you have ever learned anything about methylation, you might have received the impression that methylation governs just about everything in the body. And certainly methylation is massively important and is involved in many processes.
But it's also important to understand how methylation gets affected by even more foundational processes. So in this post I will attempt to provide additional clarity about what methylation is and does, and how it interacts with other processes in the body.
As a quick reminder, methylation is simply the addition of a small molecule called a "methyl group" to any other molecule. Methyl groups consist of one carbon atom and 3 hydrogen atoms.
The addition of methyl groups changes how molecules function. It can change a molecule with certain functions into a different molecule with different functions.
The body uses methylation in thousands of processes like detoxification, regulating neurotransmitters, and DNA expression.
Methylation is also involved in producing molecules that enable your cell membranes, nerves, brain, muscles, liver, etc to function (e.g. phosphatidylcholine and creatine)
And methylation is involved in eliminating excess neurotransmitters or hormones like estrogen.
Methylation is even used to regulate the expression of DNA, turning genes off when the expression of those genes is not needed.
Obviously, methylation is hugely important.
HOWEVER, when it comes to dealing with health issues that involve problems with methylation, focusing too much on the methylation issue can be the wrong strategy.
Why Focusing Too Much on Methylation Can Be the Wrong Strategy
The reason that focusing too much on methylation can be the wrong strategy is that methylation does not exist in a vaccum, and problems with methylation are often driven by many other factors like toxins, oxidative stress, inflammation, and the phenomenon known as the "Cell Danger Response" (CDR).
The CDR is a cascade of metabolic changes in response to a threat like an infection. toxic exposure, physical trauma, or psychological trauma. And when the body's response is not effective, the CDR can become chronic. In his research on the CDR, Robert Naviaux, Ph.D. found that one of the changes brought on by the CDR is a reduction in methylation.
So whether or not a person has genes or nutritional deficiencies or excesses that would tend to cause undermethylation or overmethylation, it's important to look at everything going on in the body that affects methylation.
That's why one of the tools I use in my evaluation of a person's situation is a genetic analysis tool that arranges genes into a pyramid structure.
The "Pyramid" Approach to Understanding Methylation and Other Genes
The pyramid chart shown below is designed to examine genes, enzymes, and the interactions between them. It map how oxidative stress, inflammation, detoxification, gut function, nutrient utilization, etc influence one another.

Methylation is at the top of the pyramid because methylation is being influenced by everything below it on the pyramid. Resolving problems with methylation usually involves resolving problems in pathways appearing beneath it on the pyramid.
In other words, methylation is kind of like the tail on a dog. And it's probably fair to say that at least in chronic illness, the dog (the entire body and its many processes that affect methylation) wags the tail (methylation). The tail does not usually wag the dog.
In other words, methylation does not drive all of the other factors (inflammation, oxidative stress, etc). Instead, methylation is typically getting messed up by those other factors. And when those factors are resolved, methylation can normalize.
Then again, methylation drives and regulates many processes, so it's far more significant and influential than the tail on a dog. And it does kind of wag the dog in certain ways. So this dog and tail thing is not a perfect metaphor. In any case, even as important as methylation is, health issues that involve problems with methylation are generally not all about methylation.
In fact, there may even be a constructive reason that the body reduces methylation in the Cell Danger Response. So it might even be counterproductive to push methylation in somebody that is undermethylating due to the Cell Danger Response.
These are just some things to keep in mind when you see or hear methylation discussed in the functional medicine and nutrition world because things can go wrong when methylation is taken out of context and treated in an overly simplistic manner like giving people megadoses of methylfolate and methylcobalamine (methylated B12). Doing this in the wrong people can have disastrous results.
This is why I use tools like the pyramid chart shown earlier in this post as part of the Bio-Individual Blueprint system.
To learn more about how the system works to help you overcome wellness challenges, maximize your energy, and even become biologically younger, download the Bio-Individual Blueprint Roadmap and watch the walkthrough video by going here.
Then if appropriate, you can book a time to ...
- Go over your situation
- Review what you've done so far
- Identify some potential next steps for you to take
- Discuss whether the Bio-Individual Blueprint might be a fit for you
