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DNA image: Drew Berry, The Walter and Eliza Hall Institute of Medical Research
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If it's not in our genes, maybe it's in our junk. So-called "junk DNA" may turn out to be just as important as our much sought-after genes. As this ScienCentral News video reports, a new study of junk DNA could open up new areas of medical research.
Trash Becomes Treasure
There are so many scientists working to understand human disease genes, and mapping the genomes of different species, it might be surprising to learn that our genes only make up a small portion of our DNA.
"Only a tiny fraction of [DNA] actually makes up what are conventionally thought of as genes— little stretches of DNA that make protein," says David Haussler, director of the Center for Biomolecular Science and Engineering at the University of California at Santa Cruz. "Probably the fraction of the DNA that actually is genes in the traditional sense of making proteins is as little as 1.2 percent. The rest of the DNA is what people used to call "junk."
All DNA gets passed down from parent to offspring, a process that's been going on for billions of years. "About four to five hundred million years ago, the common ancestor of fish, birds and mammals was a creature that lived in the ocean," explains Haussler, "and that creature passed on DNA to its offspring and they passed on the DNA to their offspring, and through the millions of years different species have evolved from a common ancestor."
When Haussler and his colleague Gill Bejerano used computers to compare the human genome with the mouse and the rat genomes, they assumed that because humans, mice, and rats look so different, there would be differences in the genome. They did see the expected differences in the shared genes from the common ancestor, but they were surprised to find long stretches of shared "junk" DNA that were exactly the same in humans and rodents. "There were about five hundred stretches of DNA in the human genome that hadn't changed at all in the millions and millions of years that separated the human from the mouse and the rat," says Haussler. "I about fell off my chair. It's very unusual to have such an amount of conservation continually over such a long stretch of DNA."
Long stretches of "junk" DNA are exactly the same in humans and rodents.
Many of these stretches of DNA, called "ultra-conserved" regions, don't appear to code for protein, so they might have been dismissed as junk if they hadn't shown up in so many different species. And if nature has gone to so much trouble to preserve these ultra-conserved regions over all these years, Haussler reasons, then they must be more important than just "junk." "From what we know about the rate at which DNA changes from generation to generation, the chance of finding even one stretch of DNA in the human genome that is unchanged between humans and mice and rats over these hundred million years is less than one divided by ten followed by 22 zeros. It's a tiny, tiny fraction. It's virtually impossible that this would happen by chance."
Long stretches of "junk" DNA are exactly the same in humans and rodents.
Many of these stretches of DNA, called "ultra-conserved" regions, don't appear to code for protein, so they might have been dismissed as junk if they hadn't shown up in so many different species. And if nature has gone to so much trouble to preserve these ultra-conserved regions over all these years, Haussler reasons, then they must be more important than just "junk." "From what we know about the rate at which DNA changes from generation to generation, the chance of finding even one stretch of DNA in the human genome that is unchanged between humans and mice and rats over these hundred million years is less than one divided by ten followed by 22 zeros. It's a tiny, tiny fraction. It's virtually impossible that this would happen by chance."
This discovery suggests that the genome must be doing something other than coding for proteins, but the purpose of these ultra-conserved regions remains a mystery. Solving it might unlock the secrets of diseases like autism and epilepsy. "There are many cases that are unexplained by any changes in the genes," says Haussler. "This is a new area to look. Doctors who have patients where they have collected DNA samples can look for something common in all of those DNA samples that might explain what is going wrong with their patients— how does the DNA from their patients differ from the DNA of other people who don't have the disease? You look for the consistent difference. These places are a great place to look for some of the diseases that we are still mystified about."
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