Don't Throw It Out: 'Junk DNA' Essential In Evolution

Aug 18, 2011
Originally published on August 20, 2011 10:55 am

There's a revolution under way in biology. Scientists are coming to understand that genetics isn't just about genes. Just as important are smaller sequences of DNA that control genes.

These so-called regulatory elements tell genes when to turn on and off, and when to stop functioning altogether. A new study suggests that changes in these non-gene sequences of DNA may hold the key to explaining how all species evolved.

To better understand this revolution in biology, we have to go back about a century. At that time, the notion of a gene was fairly simple. A gene was responsible for a particular trait.

"There was a gene for blue eyes, a gene for curly hair, etc.," says Gregory Wray, a geneticist at Duke University. But genes were just a concept in those days. Nobody really knew what a gene looked like. That changed in 1953, when James Watson and Francis Crick showed that genes were made of DNA, and that DNA was the chemical that allowed genes to be passed from parent to child.

"We came to understand a gene as a stretch of DNA that codes for a protein, and the protein is involved in producing that trait, whatever we're interested in — eye color, hair and so forth," says Wray.

Biologists spent the latter half of the 20th century exploring the steps involved in turning genetic instructions inside a stretch of DNA into something the body needs to survive. They wrote tens of thousands of papers explaining how genes make proteins, what proteins do, what piece of DNA codes for a particular protein. "And now we're coming to realize that that's only half the picture," says Wray. Many scientists are now shifting their attention to the other half of the picture.

Regulating Genes

Wray says there are about 20,000 genes in the human genome, but as many as 1 million of these so-called regulatory elements, so scientists have a lot to do.

Early work suggests these elements may play an important role in diseases. Craig Lowe, a genetics researcher at Stanford University, says these regulatory elements are also important in how different species evolved.

"It may not necessarily always be changing in the genes, or gains of genes or losses of genes, that are causing interesting adaptations. But it's how these genes are regulated," says Lowe.

Even a small change in when a gene is switched on as an animal is growing can have a major impact on the animal's size and shape.

Lowe and geneticist David Haussler from the University of California, Santa Cruz, have a paper in Science this week describing how some of these regulatory elements have changed over hundreds of millions of years of evolution.

"There are many genes that have changed remarkably little between a mouse and a human, for example, and yet they behave differently within the cell, and that's largely due to the way they are regulated differently," says Haussler.

Like many revolutions, only a handful of people saw this one coming. David Stern, a geneticist with the Howard Hughes Medical Institute, says as recently as two decades ago, scientists had little interest in the DNA that wasn't part of a gene.

"We used to call this junk DNA, and it's perfectly obvious now what we used to call junk DNA is actually chock-filled with the information that builds out organisms," says Stern.

Geneticists still think a lot of our DNA is junk. Makes you wonder if there are any other undiscovered treasures in all that junk that might spawn the next revolution in biology.

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MELISSA BLOCK, host: The world of biology is undergoing a revolution. Genetics is no longer all about genes. Just as important are smaller sequences of DNA between genes that tell the genes what to do.

NPR's Joe Palca reports on a new study that suggests changes in these non-gene sequences of DNA may hold the key to explaining how all species evolved.

JOE PALCA: To better understand this revolution in biology, we have to go back about a century. At that time, nobody knew exactly what a gene was. The concept was that a gene was responsible for a particular trait.

GREGORY WRAY: There was a gene for blue eyes, a gene for curly hair, etc., etc.

PALCA: Gregory Wray is a geneticist at Duke University. But the notion of what a gene was became more concrete in 1953, when Watson and Crick showed that genes were made of DNA and that DNA was the chemical that allowed genes to be passed from parent to child.

WRAY: We came to understand a gene as a stretch of DNA that codes for a protein and the protein is involved in producing that trait, whatever we're interested in, eye color, hair, so forth.

PALCA: Proteins make up the enzymes and hormones and membranes that make eyes and hair and all the rest of our bits.

Wray says biologists spent the next several decades exploring the steps involved in turning genetic instructions into protein.

WRAY: How do you make a protein? What does that protein do? What's the piece of DNA that codes for that protein?

PALCA: Scientists churned out tens of thousands of scientific papers in the latter half of the 20th century explaining all that.

WRAY: And now, we're really coming to realize that's only half the picture.

PALCA: And this is where the revolution is taking place: understanding this other half of the picture, not about genes, but stretches of DNA that tell genes what to do, regulate them, determine when and where they make proteins.

Wray says humans have about 20,000 genes, but as many as a million of these so-called regulatory elements, so scientists have a lot to do.

Early work suggests these elements hold the key to understanding what goes wrong in many diseases. Craig Lowe at Stanford University says these regulatory elements are also crucial for how different species evolved.

CRAIG LOWE: There may not necessarily always be changes in the genes or gains of genes or losses of genes that are causing interesting adaptations, but it's often how these genes are regulated.

PALCA: Even tiny changes in when genes switch on as an animal is growing can have a major impact on its size or shape.

Lowe and geneticist David Haussler have a paper in Science this week describing how some of these regulatory elements have changed over hundreds of millions of years of evolution. Haussler is at the University of California, Santa Cruz.

DAVID HAUSSLER: There are many genes that have changed remarkable little between a mouse and a human, for example, and yet they behave differently within the cell and that's largely due to the fact that they are regulated differently.

PALCA: Like many revolutions, only a handful of people saw this one coming. David Stern is a geneticist with the Howard Hughes Medical Institute. He says, as recently as two decades ago, scientists had little interest in the DNA that wasn't part of a gene.

DAVID STERN: We used to call this junk DNA and it's perfectly obvious now that what we used to call junk DNA is chock-full of the actual information that builds our organisms.

PALCA: Geneticists still think a lot of our DNA is junk. Makes you wonder if there are any other undiscovered treasures in all that junk that might spawn another revolution in biology.

Joe Palca, NPR News, Washington.

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