DNA Dark Matter And Genetic Expression
Little is known about dark matter in the universe. We know it’s there, and that it composes around 85 percent of the makeup of the universe.
It doesn’t act like other matter, and we can’t see it. It’s often referred to as a “hypothetical” form of matter. Sometimes it’s hard to believe what you can’t see or don’t yet understand.
Now scientists are discovering more about the “dark matter” in our DNA. These non-coding regions of DNA have largely been considered “junk” or nonfunctional for a long time. But first impressions can be deceiving.
Recent science has shed some light on what non-coding DNA actually does and why we have so much of it.
Spoiler alert: it has to do with genetic expression.
This article will answer these questions:
- What is DNA?
- What is genetic expression?
- What is non-coding DNA?
- What are histones and chromatin?
- What can I do to support the best expression of my own genes?
Review Of DNA And Genetic Expression
Let’s head back to biology class to remember the basics of DNA.
DNA stands for deoxyribonucleic acid and the same DNA is in the nuclei of all our cells (there is some DNA in mitochondria too).
DNA is packaged in chromosomes containing genes that are passed down through generations, with one copy coming from mom and the other from dad. We each have 20 to 25,000 genes distributed over 23 pairs of chromosomes.
DNA is a code, a blueprint. It’s made up of a series of base pairs attached to a ribose (a type of sugar) molecule and a phosphate. All strung together, the DNA forms that twisty double helix structure you are familiar with from depictions of DNA.
The base pairs are the building blocks, and they include:
- Adenine (A)
- Cytosine (C)
- Thymine (T)
- Guanine (G)
A always pairs with T and C with G. The sequence of base pairs codes for amino acids that together build proteins.
Genetic expression refers to turning the DNA code into a physical protein, such as enzymes, hormones, structural proteins and more.
This happens through transcription, which copies the genetic info from the DNA to mRNA (messenger ribonucleic acid), and translation where the RNA copy translates to the building of the protein.
Genetic expression is very tightly regulated, allowing the cell (and ultimately the organism) to respond to the environment around it.
You can think of it like a dial, that turns up or turns down the production of millions of proteins in order for the organism to adapt to its surroundings.
This process is fundamental to life!
Non-Coding DNA – “Dark Matter” In Our Cells
What is described above is the process that happens with coding DNA. The genes code for specific proteins that the cells make.
You might be surprised to learn that only two percent of DNA is coding DNA. The vast majority of DNA, around 98 percent, is non-coding.
This explains why the Human Genome Project, the sequencing of the entire genome, didn’t take as long as expected. It was sort of underwhelming to discover that we don’t have as many genes as predicted and most of the DNA doesn’t actually code for amino acids.
So, what exactly is non-coding DNA? Is it just filler? Is it junk?
It’s definitely not junk and likely plays many roles, but there is still a lot to learn. Here is what we know so far.
Non-coding DNA is found on the chromosomes between genes or within the genes themselves.
Functions of non-coding DNA include:
1. Involvement in genetic expression by turning on and off, or dialing up and down, genetic expression. It also has to do with location and what genes are expressed. Cis-regulatory elements are non-coding regions that regulate transcription of genes next to them.
2. Telomeres are non-coding regions at the end of chromosomes that provide protection for genetic material. Telomere length correlates with biological age.
3. Important for health. Changes in non-coding DNA correlate with diabetes, Alzheimer’s disease, autoimmunity and other diseases. Because changes in non-coding DNA can disrupt or affect transcription, it can lead to changes in gene expression.
Scientists are working to discover variants in non-coding DNA, like we look for variations in the codes for specific genes (like MTHFR, APOE and others), but to understand non-coding DNA we need more information about cell types (because different cells express different genes) and regulators (like histone, discussed below).
A study, published in Cell, worked to map out these non-coding regions, identifying 240 traits and diseases linked to changes in non-coding DNA!
This study fills in gaps of knowledge and provides an important foundation for the next discoveries to come.
Histones, Chromatin and Genetic Expression
When it comes to genetic expression, we discuss methylation a lot and you may be more familiar with this concept. A methyl group is a molecule composed of a carbon plus three hydrogens that can be added to other molecules in a process called methylation.
Methylation at specific DNA locations has the ability to turn on or turn off certain genes.
Balanced methylation is important for health, fertility, cardiovascular function, anti-aging and more.
This concept becomes important when discussing epigenetics, or how the environment affects gene expression. While we can’t change our genetics, our epigenetics is affected by methylation and other factors.
Histones are another factor.
Histones are proteins that play a role in genetic expression and affect non-coding DNA. DNA is coiled around histones, giving it structure. Histone modification plays a major role in epigenetics and is a component of the chromatin structure. Along with methylation, histone modification is one of the major epigenetic controls we have.
Chromatin is a complex of DNA and proteins, including histones, that help to pact the DNA in a compact way inside the nuclei of cells. If the chromatin packages up the DNA differently, it could affect DNA replication and gene expression.
We want our chromatin to be strong and stable, so they provide protection to DNA and allow for appropriate gene expression. When chromatins are altered or weakened, disease ensues.
Understanding the chromatin regions, in different cells and tissues, is key to understanding more about gene regulation and the link between non-coding DNA and disease. The chromatin regions are where the Cell study focused. (You can read the study here.)
How To Optimize Genetic Expression
When we zoom into the microscopic details inside our cells, just as we zoom out to the infinite universe, it can feel overwhelming. Let’s bring it back to what we can see and do in front of us.
What are some concrete ways we can support genetic expression and healthy histones in our everyday lives?
We know that our genes are not our destiny and so much of health has to do with how those genes are expressed. The good news is that a lot of this science ultimately shows support for the simple health practices that we know to produce the optimal conditions for healing and longevity.
Here are some ways to support healthy epigenetics:
1. Eat real food. Food provides information to our genes. What kind of information do you want to give your genetics? Whole, nutrient-dense Paleo foods send a message of health compared to the standard American fare of processed, nutrient-poor food-like products.
2. Meet your protein needs. Did you know that many people don’t meet their daily protein requirements? Not necessarily the amount of protein but the quality of amino acids. Amino acids found in protein foods like eggs, meat and fish become the building blocks in the body for genetic expression. We need protein in the diet to make enzymes, hormones and structural components in every cell in the body.
3. Consider your environment. Nature vs. nurture is the age-old question, but nurture is the clear leader. Our genes respond to our environment so create a life for yourself that is relaxing and low in stress. Some ways to cultivate this are to prioritize sleep, move your body and meditate. It’s incredibly necessary to be educated and diligent about reducing toxin exposure as well. These are all elements of our lifestyle that are within in our control that have immeasurable benefits in terms of prevention and wellness.
4. Listen to your body. Bodies are wise and communicate needs with us all the time. Children are naturally tapped into their intuition, but somewhere along the line we can lose this inner knowing. Being quiet with ourselves to allow the space to listen is a place to start. Consider that symptoms in the body are not there to be squashed, but instead are wise messages from the body directing us to change something.
Just because we can’t see something or fully understand it, doesn’t mean it’s not there.
And waiting for full understanding isn’t required for acting to improve our health. We are learning more each day about gene expression and epigenetics.
The more we learn, the more data we have to underscore the importance of foundational lifestyle behaviors as well as new Functional Medicine tools to support patients in treatment and recovery from disease.
References
- https://www.sciencedaily.com/releases/2021/11/211113072254.htm
- https://medlineplus.gov/genetics/understanding/basics/noncodingdna/
- https://www.cell.com/cell/fulltext/S0092-8674(21)01279-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867421012794%3Fshowall%3Dtrue
- https://pubmed.ncbi.nlm.nih.gov/32590202/
- https://pubmed.ncbi.nlm.nih.gov/33155134/
