Professor at Oklahoma State University studies so-called junk DNA

OSU Research Matters is a bi-weekly look at the work of Oklahoma State University’s faculty, staff and students.

Much of the study of our genome focuses on the genes that make proteins, but these only make up about one percent of our DNA. What about the other 99% that is considered non-coding – what used to be called junk DNA? It might not be junk.

Up to 80% of the genome has some biochemical function, but we remain confused about its role.

In this episode, Meghan Robinson talks to Dr. Darren Hagen, who, together with his students, studies a variety of species to identify genome features and decode the role of the unknown 99%.


HAGEN: Our DNA is the same DNA you inherited from your parents and you started out as a single cell. After that, your cells replicated millions or trillions of times, and that got you where you are today. And each of those cells, especially cell types, different cell types, will need very unique gene patterns. And we say “on” or “is expressed,” and that means the DNA is transcribed into RNA and can be transcribed or translated into proteins.

When these proteins are found in cells or how abundantly they are present in the cells, this determines the cell type and ultimately the composition.

ROBINSON: In high school biology, we study high school biology, we learn that the genome makes proteins that are involved in our cells. However, that is only 1% of our DNA. What makes up the rest? That’s a question asked by assistant professor of animal genomics, Dr. Darren Hagen tries to answer through his research.

HAGEN: My lab and my students, what we’re doing is commonly called functional annotation of the genome. So what we’re trying to do is look at the many parts of the animal genome and assign functions to all the different elements. My lab is trying to assign a function to that other 99%. We refer to it as non-coding DNA because it doesn’t make proteins. Historically we called it junk DNA, so we didn’t even really look. That was part of the problem.

Now that we’re looking — and we’ve been looking for 20-25 years, I think the other part of the problem is that the genome hasn’t been sequenced, so we just weren’t there technologically. Now that we have all the information, it turns out that these parts are really unique to different species, and our proteins are therefore conserved across species. The difference between us and cows isn’t that big in the protein coat genes, but if we look at the other places in the genome, that makes us human and cows cows. And they are very different. It’s really challenging because we have to go to each species and look at them independently and try to figure out which of the elements is important, which of the things would turn a gene on or off in different species.

ROBINSON: dr Hagen is also learning how we are influenced by the genes inherited from our parents.

HAGEN: Some of the DNA that you get from your mother is switched off in you. Because you are a woman, if you have children, it will be turned off for them as well. you are a copy But my mother had a switched off DNA, which I inherited from her as switched off. While my dad’s is on and because I’m male, mine is remodeled as male and so my kids will inherit all of those genetics when it’s on. And it will be interesting and challenging because the DNA that you inherited from your mother is not shown in me. Or you know, what I inherited from my mother won’t show up in me, but it will show up in my kids because they got it from their father.

And that makes disease transmission pretty interesting, and again, livestock traits or whatever really interesting. Because how that DNA, the three-dimensional structure, changes, or how the modifications we have to our DNA, how they behave, based on the parent they came from is different. And again, it’s based on the gender of the parent.

So I still have DNA in me that I got from my mother, but you won’t see that trait. But because I’m a male, if I pass that on to my kids, you can see that trait, and if that trait is a disease, you can see how it could be skipping generations, and we’re just not aware that we’re doing that have in our genetics.


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