Junk DNA: Alive and Well

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What’s the story on the flotsam and jetsam within our genetic code?

The media have been abuzz with more reports proclaiming the death of what’s known as “junk DNA.” This usually happens every time an infinitesimally small chunk of DNA thought to be “junk” is determined to actually do something. Those with an agenda or little knowledge of the subject pile on and proclaim junk DNA to be a failed idea of the past. The biggest offenders are usually creationist and pseudo-science websites that feel that humans are just too damn special to be full of useless genetic flotsam; yes, every little flick of God’s work must have a purpose. But the mainstream media often get it just as wrong, either because they want a sensational headline or because the reporter simply doesn’t understand the topic. This time around, however, some of the researchers, along with their publicity departments, are to blame for this erroneous reporting, and it has caused quite an uproar in the scientific community.

We’ve had the human genome sequenced for more than a decade, but (as expected) figuring out what all the snippets of DNA do and how everything interacts is much more difficult and time-consuming. Of our DNA’s many functions, two are primary. The first is to code for the proteins that are constructed by ribosomes inside our cells. These are called genes, and humans have about 20,000 of them. The second function of DNA is to provide control sequence data describing when and where genes get turned on and off. The gene/regulatory ideas started in the 1960s and the original work was done with bacteria, which have a compact and organized genome, with 85 percent of it coding for proteins and the rest for gene regulation. When researchers turned to vertebrates, however, they got quite a shock. Vertebrate genes turned out to be broken up and scattered, interrupted by huge stretches of DNA, called introns, which didn’t code for anything or apparently do much besides take up space. Some of these introns were the size of an entire bacterium genome. Today, we know that parts of some introns can have a function or contain another gene, but most of the time the splicing mechanism constructing RNA simply has to waste energy skipping past these large stretches of junk while picking up the fragmented bits of gene data along the way. Saying that introns aren’t junk because there are useful bits here and there is akin to finding that stick-shift knob you’ve been looking for at the local junkyard and then proclaiming that the whole lot should now be enshrined.

There are many other types of junk DNA. A favorite example is the LINE sequence, or Long INterspersed Elements. LINEs are genetic parasites that blindly make copies of themselves that are re-inserted back into the genome. LINEs have no known function in vertebrates, yet in humans take up 21 percent of the entire genome. Evolutionary biologist Dr. PZ Myers described them this way: “LINEs are like the asshole in the office who sits on the copier making photocopies of his butt. Almost a quarter of your genome is used up by this guy.” (You can follow Myers’ blog at freethoughtblogs.com/pharyngula.)

LINEs are viral relics from the ancient past and have been part of the vertebrate genome for possibly 100 million years. Like all good viruses, they simply use the cell’s machinery to construct copies of themselves, but that’s all they do. LINEs are part of a class called transposons, which also include stretches of DNA called SINEs (Short INterspersed Elements) and LTRs (Long Terminal Repeats). These are all similar in that they junk up the genome and are considered parasitic, useless DNA. When added together, these regions account for a whopping 45 percent of our genome. When you add in psuedogenes, introns, endogenous retrovirus and telomeres (which have a purpose, but are really wasteful), the percentage of junk climbs even higher. Most biologists think that about 15 percent of the genome is doing something useful and the rest is accumulated baggage. This conclusion is bolstered by the fact that genome size and complexity have no correlation in nature. There is an onion species with twice as much DNA as humans and another onion species with 10 times more than that. What is an onion doing with 20 times the DNA of a primate? The same goes for salamanders, which have huge genomes that dwarf ours. Why would they need that? Yet, the fugu fish has a nice compact genome with almost none of the typical junk DNA and gets along just fine. Everywhere biologists look, they find genome sizes with no correlation to complexity.

The amount of DNA an organism has seems quite random. But why? The predominant theory is that, through various mechanisms, animals and plants have randomly collected this useless DNA over eons, and although it doesn’t help them, it doesn’t harm them either, at least not much. If it caused a large enough survival or reproductive disadvantage, there would probably be better methods of deleting the useless stuff. Bacteria live right on the edge of life and death and need all the energy they can acquire. Wasting it by copying a bunch of useless genetic material isn’t an option for them, so they’ve managed to regulate what’s in their genome more closely and that makes them more efficient.

So why is junk DNA being called out this time? Far from the usual crank suspects simply misinterpreting a new discovery, much of the blame is being laid on a large consortium of research labs called The Encyclopedia of DNA Elements (ENCODE, whose purpose is to identify everything it can with regard to the human genome: what interacts with what, which proteins stick where, etc. It’s very important work, and it’s providing a wealth of badly needed information regarding interactions within the genome. What it can’t do is determine the ultimate biological consequences from the discoveries; that’s yet another level of research in the category of what’s deemed “functional,” as in what function does this particular interaction serve for the cell or organism? That isn’t what ENCODE is doing.

In the past, DNA said to be “functional” usually referred to a gene producing RNA or the function of a control sequence controlling another gene. Yet, the ENCODE lead paper (in a set of 30 recently released) decided that the word functional meant something else. It now means that any DNA is functional if it displays “a reproducible biochemical signature.” That definition is so vague it could mean almost anything, and it certainly can be applied to introns, LINEs, SINEs, LTRs and most of the junk DNA we know of. Right out of the gate, two paragraphs into its lead paper, ENCODE said that 80 percent of the genome has been found to be “functional.” Well, it didn’t take long for the headlines to start, even from ENCODE’s own publicity department. After all, if 80 percent of our DNA is functional, how can it be junk? The Intelligent Design crowd even proclaimed this to be the news item of the year.

Junk DNA is somewhat controversial, even among some biologists. We’re still understanding it and we will surely find more gems hidden in that mess. But the scientific consensus backs up what we’ve learned over the past 40 years, and it’s going to take more than redefining a word to change that. Molecular biologist Dr. John Timmer from the science site Ars Technica (arstechnica.com) sums things up nicely: “The ENCODE team itself bears a particular responsibility here. The scientists themselves should have known what the most critical part of the story was — the definition of ‘functional’ and all the nuance and caveats involved in that — and made sure the press officers understood it. Those press officers knew they would play a key role in shaping the resulting coverage, and should have made sure they got this right. More generally, the differences among non-coding DNA, regulatory DNA and junk DNA aren’t really that hard to get straight. And there’s no excuse for pretending that things we’ve known for decades are a complete surprise.”

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