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The Unseen Genome:
Gems among the Junk

W. WAYT GIBBS / Scientific American v289, n.5 Nov03

 

Just when scientists thought they had DNA almost figured out, they are discovering in chromosomes two vast, but largely hidden, layers of information that affect inheritance, development and disease.

FLECKS OF DARK BROWN in an iris may be a telltale sign of the hidden genome at work. Certain traits are transmitted not through ordinary genes but rather through chemical modifications to the chromosomes, changes that are regulated in part by bits of "junk" DNA. Unlike genetic mutations, these heritable traits are often reversible and appear in some cells but not others. (The white sphere on the iris is a reflection of the light shining on the eye.)

About 20 years ago, astronomers became convinced that distant galaxies were moving in ways that made no sense, given the laws of gravity and the fabric of celestial objects visible in the sky. Gradually they were forced to conclude that the universe is not as empty as it appears, that in fact it must be dominated by some dark kind of matter. Although no one knew what the stuff is made of or how it works, scientists could see from its effects that it is out there. The quest to understand dark matter (and more recently, dark energy) meant revising or replacing theories, but it reenergized astrophysics and cosmology.

A similar revelation is now unfolding in molecular genetics. This year biologists celebrated the 50th anniversary of the discovery of the double helix, and the Human Genome Project announced its completion of a "final draft" of the DNA sequence for Homo sapiens. Scientists have clearly mastered DNA in the lab. Yet as they compare the DNA of distantly related species and look more closely at how chromosomes function in living cells, they are increasingly noticing effects that current theories cannot explain.

Overview/Hidden Gene

  • Geneticists have long focused on just the small part of DNA that contains blueprints for proteins. The remainder in humans, 98 percent of the DNA- was often dismissed as junk. But the discovery of many hidden genes that work through RNA, rather than protein, has overturned that assumption.

  • These RNA-only genes tend to be short and difficult to identify. But some of them play major roles in the health and development of plants and animals.

  • Active forms of RNA also help to regulate a separate "epigenetic" layer of heritable information that resides in the chromosomes but outside the DNA sequence.

Journals and conferences have been buzzing with new evidence that contradicts conventional notions that genes, those sections of DNA that encode proteins, are the sole mainspring of heredity and the complete blueprint for all life. Much as dark matter influences the fate of galaxies, dark parts of the genome exert control over the development and the distinctive traits of all organisms, from bacteria to humans. The genome is home to many more actors than just the protein-coding genes.

The extent of this unseen genome is not yet clear, but at least two layers of information exist outside the traditionally recognized genes. One layer is woven throughout the vast "noncoding" sequences of DNA that interrupt and separate genes. Though long ago written off as irrelevant because they yield no proteins, many of these sections have been preserved mostly intact through millions of years of evolution. That suggests they do something indispensable. And indeed a large number are transcribed into varieties of RNA that perform a much wider range of functions than biologists had imagined possible. Some scientists now suspect that much of what makes one person, and one species, different from the next are variations in the gems hidden within our "junk" DNA.

Above and beyond the DNA sequence there is another, much more malleable, layer of information in the chromosomes. "Epigenetic" marks, embedded in a mélange of proteins and chemicals that surround, support and stick to DNA, operate through cryptic codes and mysterious machinery. Unlike genes, epigenetic marks are routinely laid down, erased and rewritten on the fly. So whereas mutations last a lifetime, epigenetic mistakes-implicated in a growing list of birth defects, cancers and other diseases-may be reversible with drugs. In fact, doctors are already testing such experimental treatments on leukemia patients.

Researchers are also coming to realize that just about anything that can happen in the genome does happen, says Carmen Sapienza of Temple University, who started investigating epigenetic phenomena back when they were dismissed as minor anomalies. "There may even be fundamental mechanisms still to discover," Sapienza considers. "I think we are entering the most interesting time yet in genetics."

The Perils of Dogma

IT WILL TAKE YEARS, perhaps decades, to construct a detailed theory that explains how DNA, RNA and the epigenetic machinery all fit into an interlocking, self-regulating system. But there is no longer any doubt that a new theory is needed to replace the central dogma that has been the foundation of molecular genetics and biotechnology since the 1950s.

The central dogma, as usually stated, is quite simple: DNA makes RNA, RNA makes protein, and proteins do almost all the real work of biology. The idea is that information is stored in the twisted ladders of DNA, specifically in the chemical bases (commonly labeled A, T, G and C) that pair up to form the rungs of the ladders. A gene is just a particular sequence of bases on one side of the ladder that specifies a protein.

BIG DIFFERENCES in the appearance and health of organisms can arise from small changes to tiny, unconventional genes. Arabidopsis plants, for example, normally have spoon-shaped leaves (left). But when scientists interfered with the action of a microRNA, produced by an RNA-only gene, the mutant arabidopsis plants developed gross defects (right). The microRNA appears to control the activity levels of numerous genes.

The dogma holds that genes express themselves as proteins, which are made in four steps: First an enzyme docks to the chromosome and slides along the gene, transcribing the sequence on one strand of DNA into a single strand of RNA. Next, any introns-noncoding parts of the initial RNA transcript-are snipped out, and the rest is spliced together to make a piece of messenger RNA. The RNA message then moves out of the nucleus to the main part of the cell, where molecular machines translate it into chains of amino acids. Finally, each chain twists and folds into an intricate three-dimensional shape.

It is their shapes that make proteins so remarkably versatile. Some form muscles and organs; others work as enzymes to catalyze, metabolize or signal; and still others regulate genes by docking to specific sections of DNA or RNA. No great wonder, then, that many biologists (and journalists) have taken the central dogma to imply that, with very few exceptions, a DNA sequence qualifies as a gene only if it can produce a protein.

"Typically when people say that the human genome contains 27,000 genes or so, they are referring to genes that code for proteins," points out Michel Georges, a geneticist at the University of Liège in Belgium. But even though that number is still tentative-estimates range from 20,000 to 40,000-it seems to confirm that there is no clear correspondence between the complexity of a species and the number of genes in its genome. "Fruit flies have fewer coding genes than roundworms, and rice plants have more than humans," notes John S. Mattick, director of the Institute for Molecular Bioscience at the University of Queensland in Brisbane, Australia. "The amount of noncoding DNA, however, does seem to scale with complexity."

In higher organisms (such as humans), genes "are fragmented into chunks of protein-coding sequences separated by often extensive tracts of nonprotein-coding sequences," Mattick explains. In fact, protein-coding chunks account for less than 2 percent of the DNA in human chromosomes. Three billion or so pairs of bases that we all carry in nearly every cell are there for some other reason. Yet the introns within genes and the long stretches of intergenic DNA between genes, Mattick says, "were immediately assumed to be evolutionary junk."

That assumption was too hasty. "Increasingly we are realizing that there is a large collection of `genes' that are clearly functional even though they do not code for any protein" but produce only RNA, Georges remarks. The term "gene" has always been somewhat loosely defined; these RNA-only genes muddle its meaning further. To avoid confusion, says Claes Wahlestedt of the Karolinska Institute in Sweden, "we tend not to talk about `genes' anymore; we just refer to any segment that is transcribed [to RNA] as a 'transcriptional unit."'

Based on detailed scans of the mouse genome for all such elements, "we estimate that there will be 70,000 to 100,000," Wahlestedt announced at the International Congress of Genetics, held this past July in Melbourne. "Easily half of these could be noncoding." If that is right, then for every DNA sequence that generates a protein, another works solely through active forms of RNA-forms that are not simply intermediate blueprints for proteins but, rather, directly alter the behavior of cells.

What is true for mice is probably true for people and other animals as well. A team of scientists at the National Human Genome Research Institute (NHGRI) recently compared excerpts from the genomes of humans, cows, dogs, pigs, rats and seven other species. Their computer analysis turned up 1,194 segments that appear with only minor changes in several species, a strong indication that the sequences contribute to the species' evolutionary fitness. To the researchers' surprise, only 244 of the segments sit inside a protein-coding stretch of DNA. About two thirds of the conserved sequences lie in introns, and the rest are scattered among the intergenic "junk" DNA.

"I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century," Mattick says. "The failure to recognize the full implications of this-particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules-may well go down as one of the biggest mistakes in the history of molecular biology."

More than a Messenger

NOW THAT BIOLOGISTS have turned their attention back to RNA, they are finding it to be capable of impressive feats of cellular chemistry. Like proteins, some RNA transcripts can interact with other bits of RNA, with DNA, with proteins and even with small chemical compounds. Proteins are analog molecules, however; they bind to targets in much the way keys fit in locks. "The beauty of RNA is that it has a specific sequence, so it's digital, like a zip code," Mattick points out. A bit of RNA can float around until it bumps into a DNA (or another RNA) that has a complementary sequence; the two halves of the ladder then join rungs. (Two segments are complementary when all C bases mate with G's and all T or U bases join to A's.)

As an example of the unappreciated power of RNA, consider pseudogenes. Surveys of human DNA have found in it almost equal numbers of genes and pseudogenes-defective copies of functional genes. For decades, pseudogenes have been written off as molecular fossils, the remains of genes that were broken by mutation and abandoned by evolution. But this past May a group of Japanese geneticists led by Shinji Hirotsune of the Saitama Medical School reported their discovery of the first functional pseudogene.

Hirotsune was genetically engineering mice to carry a fruit fly gene called sex-lethal. Most mice did fine with this foreign gene, but in one strain sex-lethal lived up to its name; all the mice died in infancy. Looking closer, the scientists discovered that in those mice sex-lethal happened to get inserted right into the middle of a pseudogene, clobbering it. This pseudogene (named makorin1-p1) is a greatly shortened copy of makorin1, an ancient gene that mice share with fruit flies, worms and many other species. Although researchers don't know what makorin1 does, they do know that mice have lots of makorin1 pseudogenes and that none of them can make proteins. But if pseudogenes do nothing, why were these mice dying when they lost one?

For some reason, makorin1-and apparently only makorin1-all but shuts down when its pseudogene pl is knocked out. RNA made from the pseudogene, in other words, controls the expression of the "real" gene whose sequence it mimics, even though the two lie on different chromosomes. There is nothing pseudo about that.

A BESTIARY OF UNCONVENTIONAL GENES

GENES, according to conventional wisdom, are those sections of the DNA that encode functional proteins. Such sequences make up only about 2 percent of the human genome, however. The rest of the human genome is filled with DNA that is "noncoding"-but not useless. Scientists are discovering many noncoding genes that give rise to surprisingly active RNAs, including varieties that can silence or regulate conventional genes.

Antisense RNA is made from the complementary DNA strand that sits opposite a protein-coding gene on the double helix. Antisense RNAs can intercept the messenger RNA transcribed from the gene, preventing the mRNA from being translated into protein.

Protein-coding genes contain noncoding sections called introns. Introns are snipped out of the initial RNA transcript; the coding sections are then spliced to create a mature mRNA. Although many introns degrade, some contain active elements, such as microRNAs that can exploit the "RNA interference" effect to control other genes

Riboswitches are a newly discovered form of RNA that act as precision genetic switches. Produced in many cases from noncoding DNA between known genes, a riboswitch folds into a complex shape. One part of the folded RNA can bind to a specific target protein or chemical. Another part contains the RNA code for a protein product. The riboswitch turns "on" and produces the protein it encodes only when in the presence of its target.

It is too early to say whether many pseudogenes give rise to active RNA. But there are plenty of other sources scattered about the dark parts of the genome. Every normal protein-making gene, for instance, has a complementary DNA sequence that sits on the other side of the ladder and usually is not transcribed into RNA. Biologists like to think of this as a backup copy, because the cell can use it to repair damage to the gene.

In some cases, however, the backup has its own agenda. While the gene is producing a sensible RNA message, its alter ego can churn out an "antisense" RNA that has a complementary sequence. Whenever matched sense and antisense RNAs meet, they mesh to form their own double-stranded ladders-effectively interfering with the gene's ability to express its protein.

Biologists knew that bacteria and plants can produce antisense, but most thought that mammals rarely do. In April, Galit Rotman and her co-workers at CompuGen, a biotech firm in Tel Aviv, dashed that assumption. They screened human genome databases and concluded that at least 1,600 human genes (and probably many more) have a mate that yields antisense RNAs.

These competing RNAs may suppress a gene just by tying up the gene's messenger RNA. But Rotman speculates that they employ a built-in genome censor, known as the RNA interference machinery. Scientists are still enthralled by the discovery several years ago of this scheme for selectively silencing individual genes. When double-stranded RNA appears in a cell, enzymes dice it up, peel the two strands apart, and use one RNA fragment to seek out and destroy any other RNA messages that stick to its sequence. The system protects cells against viruses, which often deliver their payloads in the form of double-stranded RNA. But the censor also provides a handy way for scientists to shut off any gene at will [see "Censors of the Genome," by Nelson C. Lau and David P. Bartel; SCIENTIFIC AMERICAN, August].

Neither pseudogenes nor antisense RNAs, however, can explain the crinkled leaves that Detlef Weigel of the Max Planck Institute for Developmental Biology in Tübingen, Germany, and his collaborators saw in their arabidopsis plants this summer. These weeds of the mustard family normally have smooth, spoon-shaped leaves. The plants owe their gentle symmetrical curves, Weigel's group showed in Nature this past August, in part to a kind of active RNA called microRNA.

MicroRNAs, first observed a few years ago in roundworms, are short noncoding RNAs that fold back on themselves, like hairpins. In arabidopsis, the JAW microRNA doubles over and is then captured by the RNA interference machinery, just as if it had come out of a virus. But the JAW sequence matches a handful of different protein-making genes, members of a family that control the shape and size of the plant. The censor dutifully represses each of them by chopping up much (but not all) of the messenger RNA they produce. Thus, JAW, a tiny RNA-only gene, serves as the main lever by which arabidopsis cells adjust the volume of a suite of crucial protein genes. When Weigel's group engineered plants in which the microRNA could not do its job, the plants became sick and deformed.

In just the three years since researchers started looking in earnest, they have found hundreds of microRNAs-more than 150 in humans alone. They seem to be a well-established means for organisms to wrangle genes; about half the microRNAs in humans also appear, in nearly identical form, in the DNA of pufferfish, even though the two species went their separate ways some 400 million years ago.

Just what those 150-plus microRNAs do in people is a mystery. Anna M. Krichevsky of Harvard Medical School suspects that, among other things, they play an important role in brain development. Her lab used a "gene chip" to screen mouse neurons for 44 different kinds of microRNA. Krichevsky reported in September that levels of at least nine distinct microRNAs are precisely regulated in the mice as their brains grow. The link is still indirect, but as Diya Banerjee of Yale University noted last year in a review of microRNA science, "it seems that we are on the verge of an explosion of knowledge in this area."

Moving Genetics Forward

EVER SINCE THE INVENTION of recombinant DNA technology made genetic engineering feasible, most research in genetics has been run in "reverse." Reverse genetics begins with a particular gene of interest. The scientist fiddles with that gene in a cell culture or a living organism, watches what happens, and then tries to deduce the gene's function. It is a classic reductionist approach, and it can be very powerful.

But the gradual realization that the genome includes hidden genes functional sequences that were misclassified as junk highlights a major problem with reverse genetics: it can lead to tunnel vision. So recently a number of geneticists have been returning to the older practice of "forward" genetics as a way to identify the genes, both conventional and unconventional, that they don't know about.

Phenomix, a biotechnology company in La Jolla, Calif., founded last year by several prominent genetics teams, hopes to make a business out of the approach. The firm has set up a kind of production line for making mutant mice. In each group of mice, mutations to random points in the genome disable not just standard protein-coding genes but also hidden genes that make only active forms of RNA.

Phenomix starts with both healthy mice and mice that have diseases analogous to common human illnesses, such as diabetes, asthma, arthritis and Parkinson's disease. Some mutations induce or alleviate symptoms of these disorders in the mice. Researchers then do genetic screening to determine which mutations accounted for the effects. Whether the approach will inspire better drug designs remains to be seen. But forward genetics has already unearthed genetic phenomena, such as a functional pseudogene (see main text], that no one knew were possible. W.W.G.

Digital and Analog

PROTEINS MAY BE the draft horses of the cell, but active RNA sometimes wields the whip. And several kinds of RNA have turned up doing mules' work as well: catalyzing, signaling and switching as competently as any protein. In fact, some inherited diseases have stumped researchers because, in their diligent search for a mutant protein, the investigators ignored the active RNA right under their noses.

Doctors struggled for more than nine years, for example, to nail down the gene responsible for cartilage hair hypoplasia. This recessive disease was first identified in the Amish, one in 19 of whom carries a copy of the defective gene, which causes an unusual kind of dwarfism. People with CHH are not only small in stature but also at high risk for cancer and immune disorders. Geneticist Maaret Ridanpää of the University of Helsinki tracked the gene to chromosome nine, sequenced a large region and then proceeded to check all 10 protein-making genes in the area, one by one. None caused the disease.

Finally, in 2001, Ridanpää and his co-workers identified the culprit, an RNA-only gene called RMRP. The RNA transcribed from RMRP links up with proteins to form an enzyme that works inside a cell's energy generators, the mitochondria. A change to just a single base at a critical spot on this RNA can mean the difference between a full-size, healthy life and a short, abbreviated one (if the same mutation is inherited from both parents). Such "analog" RNAs, which fold up into complex shapes just as proteins do, have also been discovered recently to be essential to the function of enzymes that protect the chromosomes and that escort secreted protein signals out of cells' portholes.

Perhaps the most intriguing form of RNA yet discovered is the riboswitch, isolated last year by Ronald R. Breaker's lab at Yale. He and others have long wondered how, billions of years ago, the very earliest chemical precursors to life got along in the RNA world before DNA and proteins existed. They speculated that such proto-organisms would need to use RNA as sensors and switches to respond to changes in the environment and in their metabolism. To test the idea, they tried to create RNAs with such capabilities.

CLONES IN ALL BUT NAME, these littermates from a highly inbred strain of mice share practically identical DNA. Yet their coat colors run the spectrum from golden yellow to mahogany brown because of variations in the "epigenetic" chemical attachments each has to a particular segment of DNA that lies outside any known gene. The hair color of these mice cannot be predicted by current theories of genetics.

"Our laboratory successfully produced a number of synthetic RNA switches," Breaker recalls. Dubbed riboswitches, these long RNAs are both coding and noncoding at once. As the RNA folds up, the noncoding end becomes a sensitive receptor for a particular chemical target. A collision with the target flips the switch, causing the other end, which contains a standard blueprint for a protein, to change shape. The riboswitch thus gives rise to a protein, much like a normal gene does-but only when it senses its target.

Breaker's group started hunting for riboswitches in the wild and soon found them hiding in intergenic DNA. These precision genetic switches have been extracted now from species in all three kingdoms of life. "This implies that they were probably present in the last common ancestor," not long after the dawn of evolution, Breaker argues.

In August, Breaker and his co-workers reported that one family of riboswitches regulates the expression of no fewer than 26 genes in Bacillus subtilis, a common kitchen bacterium. These are not once-in-a-blue-moon genes, either, but genes that the bacterium relies on to metabolize such basic staples as sulfur and amino acids. Breaker estimates that B. subtilis has at least 68 genes, nearly 2 percent of its total, under the control of riboswitches. His lab has already begun engineering the hybrid digital-analog molecules to do useful things, such as selectively kill germs.

The Big Picture

AS BIOLOGISTS SIFT more and more novel kinds of active RNA genes out of the long-neglected introns and intergenic stretches of DNA, they are realizing that science is still far from having a complete parts list for humans or any other higher species. Unlike protein-making genes, which have standard "start" and "stop" codes, RNA-only genes vary so much that computer programs cannot reliably pick them out of DNA sequences. To spur the technology on, the NHGRI is launching this autumn an ambitious $36-million project to produce an "Encyclopedia of DNA Elements." The goal is to catalogue every kind of RNA and protein made from a select 1 percent of the human genome-in three years.

No one knows yet just what the big picture of genetics will look like once this hidden layer of information is made visible. "Indeed, what was damned as junk because it was not understood may, in fact, turn out to be the very basis of human complexity," Mattick suggests. Pseudogenes, riboswitches and all the rest aside, there is a good reason to suspect that is true. Active RNA, it is now coming out, helps to control the large-scale structure of the chromosomes and some crucial chemical modifications to them-an entirely different, epigenetic layer of information in the genome.

The exploration of that epigenetic layer is answering old conundrums: How do human beings survive with a genome horribly cluttered by seemingly useless, parasitic bits of DNA? Why is it so hard to clone an adult animal yet so easy to clone an embryo? Why do certain traits skip generations in an apparently unpredictable way? Next month the conclusion to this article will report on the latest discoveries about how the chromosomal layer of epigenetic phenomena works and on the initial attempts to exploit epigenetics in medicine and biotechnology. m

W. Wayt Gibbs is senior writer.

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