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July 3, 2009

Junk DNA? Hardly

The genes in DNA that code for protein production have long been thought to be the only important aspects. The rest was considered “junk.”
DNA is the blueprint for life. Stretches of DNA called genes code for the production of proteins. Proteins are the stuff of life, what cells are built of. Unraveling the steps in the journey from gene to protein to life has kept scientists busy for years and will continue to do so.

Junk DNA really means DNA whose purpose is not understood.

But only about 3% of your DNA is genes. What is the rest of it doing?

Scientists have been so focused on the importance of genes that something strange happened. Around 1970, they invented the term junk DNA. This was based on the idea that DNA that doesn't code for proteins is non-essential material that somehow became attached to the genes and hitched a ride with them through the millenia. It was either genes or junk. This idea even filtered into the public consciousness, possibly during the Human Genome Project.

Junk DNA really means DNA whose purpose is not understood.

When you're looking out of a closed window, you're only using the glass part of the window to see through. But a window is more than a pane of glass. It lets air into a house when it's open and keeps the rain out when it's closed. It couldn't do this without its other parts, like the frame. Similarly, DNA may be much more than a bunch of genes coding for proteins.

There are many possible functions for the non-coding portions of the DNA. They may provide structural integrity. Some could act as spacers; having genes located too closely together might confuse the machinery that actually makes the proteins. And then there's the question of how genes are controlled.

Islet cells in the pancreas produce insulin. Muscle cells in the heart help it beat. A skin cell in your little finger has the exact same DNA as an islet cell or a heart muscle cell does. Yet it doesn't produce insulin or beat. Why not? The genes responsible for this have been turned off. Possibly at sites on the DNA far removed from the genes themselves. Detour-road closed. Just how and where this happens isn't known yet. Non-coding DNA has been giving up its secrets very slowly. But scientists keep finding out more and more uses for pieces of DNA once thought to be junk.

An international team has found how one particular type of non-coding DNA called tandem repeats plays a vital role in yeast, a single-celled organism. They help yeast to rapidly change the activity of their genes in response to changes in their environment. Tandem repeats are repeating palindromes: able was I ere I saw Elba. In DNA language this might be ACTTCA. It loses something in the translation.

Tandem repeats are somewhat unstable. Their exact length changes from generation to generation. The researchers found that the length of a tandem repeat next to a gene influences how active a gene is — how much protein it makes. So by having variation in the length of their tandem repeats, yeast are introducing variation in their progeny — exactly what they need to adapt quickly to the ever changing conditions in their external environment.

When the researchers removed all the tandem repeats near a yeast gene, the progeny showed very little variation in the activity of that gene. In a sense, they stopped evolving. They needed their junk DNA.

Admittedly, this is a rather complicated experiment. But it shows that one function of non-coding DNA is to introduce variability in yeast. Perhaps some parts of the DNA really don't have any use. But as researchers continue to uncover uses for regions of DNA once thought to be junk, it is looking more and more like junk DNA is only a state of mind.

The results of the research were published in the May 29 issue of Science.
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