We know that we don’t “use” a lot of the genes inside our cells, but our DNA is strung with relics. But what are those relics, and what if they come back to haunt us? Here’s what you’re carrying around, and why it’s not as irrevocably part of the past as you think it is.

Your Immune System Is Still at War With Long-Dead Viruses

The thing that’s stunning about junk DNA is just how much of it we have. Over ninety percent of our DNA is noncoding. It does nothing, as far as we know, but sit in our cells and cause occasional trouble. Why is it there?

Because the rest of our DNA can’t work too hard. One fragile double-helix carries all the information you need to make more you, but it can’t disseminate all that information. In order to do the work involved in building and maintaining a human body, one strand of DNA makes many copies of RNA. One strand of RNA then goes on to make many copies of a necessary protein. That’s not the only possible sequence of actions, though. Sometimes RNA turns around and makes more DNA. And since each DNA can make more than one copy of an RNA sequence, when the RNA turns around and makes DNA, the DNA that gets made then has many copies of the original, single, bit of junk DNA. Eventually most of our current double helix is just copies of copies of copies.

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A lot of those copies aren’t even copies of our own genes. Retroviruses, viruses with RNA instead of DNA, can replicate by using their RNA to insert genes into their host’s DNA. Once that happens, the host cell makes the virus the same way it makes its own cells, until the sequence of DNA gets shut off and becomes noncoding.

It doesn’t always stay noncoding. Once a virus is in our DNA, we ourselves give it chance after chance to come back. Every cell is a chance for the virus’s genes to switch on again. At that point our own bodies reanimates a virus that one of our long-dead ancestors and introduces it into our system. That’s not as big a threat as it seems. If it’s been in our system for the last umpteen generations, our immune system generally can handle it. It’s only a problem if our immune system is compromised. That doesn’t change the fact that right now you could be battling a retrovirus that your great-great-great-great-grandmother caught.

Keeping or Disposing of Junk DNA Isn’t a Simple Matter

We know that humans have a lot of junk DNA, including repetitive elements. How do we stack up to other forms of life? Should we have a lot of extra elements, because we’ve changed a great deal while the fruit fly has remained relatively the same? Or should we have relatively lean and streamlined cells?

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As it turns out, “junk” DNA defies any easy way pattern. Compared to invertebrates, mammals keep our repeated sequences around for a long time. While we, like animals all the way down to the fruit fly, can eventually eliminate the junk, fruit fly junk has a half-life of only twelve million years. That seems like a long time, but it’s nothing compared to mammals, whose junk DNA has a half-life of about 800 million years.

So keeping around junk DNA might be considered a sign of mammalian innovation and complexity—if you don’t factor in hominids. Compared to most mammals, we clear our junk DNA relatively quickly. A rat will let its junk stick around far longer than both a fruit fly and a human.

Sometimes More Junk DNA Is a Life-Saver

The deleterious effects that junk DNA can have first came to the attention of doctors who studied odd, repetitive disorders passed down through families. When doctors analyzed the DNA they got from blood samples, they found that many of them were associated with long strings of repeated gene sequences. These sequences were usually only three or four letters long, but they could be repeated tens, or even hundreds, times.

One of these was myotonic dystrophy. This heartbreaking multi-generational disease gets worse and worse over the generations. The first generation to have the disease often suffers from cataracts or other problems in old age. The second generation tends to have muscle problems, including problems with the muscles of the heart, which start in middle age. The third generation has severe muscular problems from birth.

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When examining the genes of each generation, doctors found that one three sequence repeated gene, which is repeated a few times in nearly every person’s DNA, would, in the sufferers of this disease, be repeated over 50 times in one generation, more in the next, and more in the next. When they examined how the DNA was translated into actual proteins they found that these repeated sequences “used up” the RNA that would translate the code into actual proteins. Nothing else got built. The more sequences are there, the less is done, and so each generation has a more severe form of the disorder than the last.

There are a number of disorders like this in which repeated gene sequences cause the DNA-to-protein manufacturing process to go wrong. And then there’s facioscapulohumeral muscular dystrophy, or FSHD. People without FSHD have a sequence of “junk” DNA that gets repeated between eleven and a hundred times. Those who have the actual disorder have only between one and ten copies of the sequence and also a sequence called “poly A sequence.” No matter what the repeated bits of DNA code for a problematic protein, and are transcribed to RNA to make that protein. Without the poly A sequence, the transcriptions disintegrate without being expressed.

But what about the people who have, say, 50 copies of the sequence and did have the poly A sequence? It turns out that having that many copies of the sequences changes the shape of the chromosome, and the entire sequence isn’t transcribed. It’s only the people who have the poly A sequence, but who don’t have enough junk DNA of this kind who are affected by the disorder. Sometimes having enough junk saves you.

It May Not Entirely Be Junk

In fact, some scientists now think that junk isn’t really junk. They note that what separates rhesus macaques from apes seems to be long sequences of “junk” DNA. The same goes for what separates chimpanzees from humans. These junk sequences could amplify the expression of certain genes, and that expression, not the genes themselves, could have taken us from macaques to humans.

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Alternately, there’s a hypothesis that junk DNA acts as insulation. A lean genome means that if some horrible bit of radiation rips through a chromosome, it is likely to hit something crucial. If over ninety percent of what is in a chromosome is junk, there’s far less need to worry about mutations in the long strings of crap around the few important genes.

So perhaps, sometime soon, we’ll be learning that this entire article was about a fictional concept. Perhaps there is no such thing as junk DNA.

[Source: Junk DNA, by Nessa Carey]

Top Image: National Cancer Institute, DNA Image: Ynse , Mouse Image: Darryl Leja.