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Us and them: junk DNA raises the question, whose life is it anyway? - The Evolutionary Front - genome research
Natural History, Nov, 2001 by Carl Zimmer
The February 15, 2001, issue of Nature was a peculiar one. Lodged in the middle of the journal was a kind of scientists' centerfold: a multipage foldout covered in long trains of tiny hatch marks, alphanumeric codes, and squiggly graph lines. Here, for the first time in print, was a rough draft of the human genome--what Francis Collins, head of the U.S. Human Genome Project (HGP), called "the first glimpses of our instruction book, previously known only to God."
It certainly gives one pause to look at this sprawling map and think about what it represents. It's even tempting to imagine we are peering at a biological version of the soul, the unique essence that determines us both as a species and as individuals. But be careful when you turn to your genome to search for your soul. Where you expect to find your true inner self, you will come face-to-face with a mob of strangers.
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Researchers now estimate that the human genome contains roughly 40,000 genes--those stretches of DNA that make the proteins that a cell needs to survive. That's up from the figure of 30,000 published last February, but these 40,000 genes still constitute only about 2 percent of the full human genome. What's the other 98 percent? In the 1970s, when geneticists first began to look at it, they dubbed this extra material "junk DNA."
The implication of the nickname was that there was nothing interesting or important about the stuff. It is true that a sizable portion of the DNA that isn't part of a gene fits this definition. Known as "pseudogenes," these segments of DNA are the mutated relics of genes that once encoded proteins. But a large portion of the junk DNA--amounting to about 40 percent of the human genome, in fact, according to an HGP estimate--actually has a life of its own.
An ordinary gene can duplicate itself only when a cell divides and makes a new copy of the entire genome. Certain kinds of junk DNA don't have to wait that long. Instead they may, for example, harness the cell to copy them in the form of a segment of RNA, the single-stranded version of the genetic code. Normally, RNA is used by the cell during the production of proteins. But in the case of some junk DNA, the cell uses this RNA to create another DNA copy of the junk segment, which it then inserts somewhere else in the genome. Researchers call such self-replicating pieces of junk DNA "transposable elements" because of the way they transpose copies of themselves into new places in the genome.
The more researchers have studied transposable elements, the more these bits of DNA have come to seem like a collection of parasites that use the genome as their host. We tend to think of parasites as autonomous organisms--hookworms or lice, for instance--not as our "own" genetic material. But during the 1980s and 1990s, the metaphor of genetic parasites turned out to be very powerful. Parasites tend to follow certain evolutionary paths, and these genetic parasites are no exception.
Like other parasites, transposable elements can cause a lot of harm to their host--such as by pasting a copy of themselves smack in the middle of a gene. When it comes time for the cell to build a protein based on that gene, it may be unable to do so because the inserted DNA has turned the gene's code to gibberish. Researchers are discovering more and more forms of human genetic disorders--ranging from hemophilia to breast cancer--that have come about because a transposable element has hopped into an unfortunate place in the genome.
Another hallmark of parasites is that hosts often evolve defenses against them. Transposable elements appear to be no exception to this rule. In certain regions of our genome, for example, our DNA is capped with hydrocarbon molecules. This capping (called methylation) prevents the cell's DNA-copying machinery from locking onto the genetic material in those parts of the chromosomes. Researchers suspect that in many cases, methylation is the genome's way of fighting against the damage caused by transposable elements--by stopping them from reproducing.
In the May 10, 2001, issue of Nature, for instance, a group of Japanese researchers described their study of methylation in the genome of the thale cress plant (Arabidopsis thaliana). They found that if a certain gene mutated, the plant could no longer methylate its DNA. Freed from their prisons, the transposable elements in these mutants started replicating themselves and inserting these new copies into the genome. The resultant plants were nothing more than shriveled clumps. Thanks only to methylation, it seems, can the thale cress withstand its genetic parasites.
This discovery points up a conundrum that arises as much in connection with transposable elements as with conventional parasites: if they can be so harmful to their hosts, why haven't they driven their hosts extinct--and made themselves extinct in the process? Part of the answer comes from their evolutionary history. Transposable elements can spread gradually through a genome over millions of years, but eventually their success at self-replication wanes. Copying errors creep in and undermine their ability to replicate themselves; in addition, the host genome evolves an ability to suppress them. Most of the transposable elements in the human genome, it now seems, are already dead or about to give up the ghost.
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