Life's Blueprint in Less Than an Inch

URL: http://www.washtech.com/news/biotech/7440-1.html

Date accessed: 21 March 2001

Sunday, February 11, 2001
By Rick Weiss ,
Washington Post Staff Writer
 
All the instructions for making a human being are packed within a surprisingly small number of genes — only about twice the number needed to grow a worm or a fly — according to the first detailed analysis of the entire human genetic code.

Moreover, hundreds of those genes, including one that's been implicated in depression, are actually genes from bacteria that infected human predecessors millions of years ago and left their microbial DNA behind.

But perhaps most remarkable, scientists said, is how little of the human genome — the 23 pairs of chromosomes that contain the blueprint for human life — is directly devoted to making human beings, and how much other biological activity is going on throughout the rest of the genome.

The genetic instructions for making a person take up less than one inch of the six-foot-long strand of DNA that's stuffed inside virtually every cell in the body, according to the new findings. Most of the rest of the human genome is filled with weird life-like entities that have settled in the genome like squatters. Among them are microscopic bits of foreign DNA that live like parasites on human DNA and even smaller bits that sponge off those parasites.

Although scientists have known that such critters existed in the human genome, only now have they been able to see how many there really are, how they are distributed among people's genes, and how these complex communities evolved inside the cells of human ancestors over millions of years.

Taken together, the new findings show the human genome to be far more than a mere sequence of biological code written on a twisted strand of DNA. It is a dynamic and vibrant ecosystem of its own, reminiscent of the thriving world of tiny Whos that Dr. Seuss's elephant, Horton, discovered on a speck of dust.

Scientists are scheduled to describe their results Monday at a Washington news conference to be Webcast live around the world. But details were released last night after a British newspaper ran a story about the findings in its Sunday edition. Additional news conferences are to be held in London, Paris, Berlin and Tokyo, and details of the work are being published this week as a thick collection of more than a dozen landmark articles in the journals Science and Nature.

The new work shows that some parts of the genome are rich in human genes, like biodiverse tropical rain forests, where genes crucial for human life — and some that cause disease — perform their jobs in the body. Scientists sifting through the newly unveiled genome with computerized search engines have discovered more than 40 previously unknown disease genes, including some for forms of epilepsy, deafness, color blindness and muscular dystrophy. Hundreds of others are expected to turn up in the next few years, speeding the development of new drugs and diagnostic tests.

Other regions of the genome are essentially genetic "deserts," where there is nary a human gene for as far as the eye can see but where life, of a sort, perseveres nonetheless. Like genes, the entities living in these vast stretches of the human genome are made of DNA, the doubly coiled molecule of heredity. But they don't contain coded messages to make anything useful for the human body.

Most are able to persist and replicate within the human genome but are so dependent on the genome that they can never leave it. Others are mere remnants of genes that were left behind by prehistoric viruses eons ago and have been passed down in increasingly degenerate condition from human generation to generation.

Now, like paleontologists studying a newly uncovered fossil trove, geneticists are dating and analyzing these genetic remnants, some of which have been in the human and pre-human genetic line for more than 500 million years. Through these studies, they are learning how genetic innovations during the course of evolution led to the handful of breakthroughs that allowed early backboned creatures to evolve into humans.

"We've called the human genome the book of life, but it's really three books," said Francis Collins, director of the National Human Genome Research Institute in Bethesda and a chief of the international human genome project. "It's a history book. It's a shop manual and parts list. And it's a textbook of medicine more profoundly detailed than ever."

The new findings come from the first comprehensive analyses of the human genetic code by the publicly funded human genome project — involving thousands of researchers around the globe and led in this country by the National Institutes of Health and the Department of Energy — and by Celera Genomics of Rockville, a private company. At a gala White House event in June, leaders of the competing public and private teams announced they each had determined the order of almost all the 3 billion "letters" of biochemical code in the human genome. Strung together along strands of DNA inside cells, those letters spell out the directions for making and maintaining human life.

The work answers some long-standing questions, such as why the human sense of smell is so crude compared with that of many other mammals: In the past 10 million years, it turns out, pre-humans have lost more than half of the 1,000 olfactory genes their ancestors once had, apparently choosing to concentrate on vision and other senses instead.

It also raises new and difficult questions, such as how human beings — with all their passions and fears, their capacity for art, music, culture and war — can be all that they are with just 30,000 or so genes, only five times as many as in baker's yeast.

One surprise is that the genome is populated with duplicate copies of many disease-causing genes — shadowy genetic "twins" that scientists had never seen before but that in many cases also cause diseases.

Another is that sperm carry twice as many mutations as eggs, suggesting that men are the major source of genetic errors in offspring but also the major source of evolutionary innovation.

And in one of the bigger surprises to come out of the new analysis, some of the "junk" DNA scattered throughout the genome that scientists had written off as genetic detritus apparently plays an important role after all, perhaps by helping humans respond to stress.

In short, said Celera president and chief executive J. Craig Venter, the human genome "is a lot more complicated than we thought."

Although it sounds paradoxical, Venter said, that complexity is due in part to humans having so few genes. The 30,000 estimate of both teams is a gross approximation; genes are not easy to identify in the genome, and the number may increase by a few thousand as the search continues.

But the final count will clearly be far below previous estimates, which only a year ago had centered around 80,000 and had stretched as high as 120,000. That raises the question of how just 30,000 "sentences" of coded instructions can direct the production of the hundreds of thousands of ingredients that together make up a human body.

The main answer, scientists said, is that the approximately 30,000 products (mostly proteins) made by those 30,000 human genes get cut into pieces after they're made, and those pieces are then shuffled around and pasted together in novel arrangements. Just as lots of different sentences can be composed with a limited number of words, this system enables the instructions, or genetic "words," in a single gene to produce 10 or more different proteins, depending on what the body needs.

By contrast, individual genes in simpler organisms such as flies and worms can generally make just one or two proteins each.

"We have the Cuisinart that can slice and dice and do lots of things, while worms and flies have paring knives," Collins said.

In addition, humans have a huge repertoire of regulatory mechanisms that simpler organisms lack, with which they can fine-tune their genes' activities from moment to moment. Studies indicate that a wide range of environmental influences are involved in these regulatory decisions — a reminder that biology and behavior are not genetically determined but are influenced by countless non-genetic variables.

By comparing the human genome to the genomes of simpler organisms such as the fly and the worm, scientists are also seeing with unprecedented detail how just a few genetic innovations helped launch early vertebrates ahead of the biological pack hundreds of millions of years ago. In one case, a few genes that probably helped flies and worms fight off invading microbes apparently copied and recopied and rearranged themselves inside newly evolving backboned creatures to create what is today the army of genes that together encode the human immune system, with its remarkable ability to recognize and attack a huge variety of invaders.

Similar duplications of genes led to the development of the blood clotting system, a complicated but crucial breakthrough for vertebrates. A third series of duplications gave rise to the spectrum of hormones and other molecules that today allow human cells to communicate with one another and coordinate their activities with exquisite precision. And yet another set of duplicated genes gave rise to the vertebrate nervous system and brain, the capstone of mammalian complexity.

Some human genes seem to have been ripped off wholesale from simpler organisms. By scanning the human genome for DNA sequences nearly identical to those in microbes, scientists found more than 200 genes whose origins can be traced to ancient infecting bacteria.

Apparently those genes' metabolic specialties were useful enough for them to be "hired" full time by the human genome. One, for example, controls production of a chemical called monoamine oxidase, which the body today uses to regulate brain chemicals affecting mood and is the target of a class of antidepressants called MAO inhibitors.

For all the evolutionary creativity that led to the human race, however, there is shockingly little variation from person to person, genome scientists said. Individuals around the world all are about 99.9 percent genetically identical, an indication of how recently the human species arose and how little time it has had to diversify.

Celera's analysis, which included genes from five people who identified themselves as Caucasian, Hispanic Mexican, Asian Chinese or African American, indicates that the number of harmless variations nestled in the human genome varies by race. On average, African Americans carry more variations than Caucasians — evidence that they have been around longer — and Caucasians have more than Asians. That's consistent with the prevailing theory that the human race got its start in Africa and radiated from there.

But Venter's data also strengthens the notion that race itself has no genetic basis. No genes, either by themselves or in concert with others, were able to predict which race each person had claimed to be.

Those genome findings could help temper cultural biases about the genetics of race, but other new results are likely to fan the flames of the gender wars: the finding that sperm cells are the main source of human genetic mutations.

Scientists said they are not certain why sperm are so loaded with genetic errors. One theory blames the fact that so many cell divisions occur in the making of sperm while eggs are the result of a single cell division. Each cell division offers chromosomes a new opportunity to break or mutate.

Whether men should be blamed or praised for their mutated sperm is an open question, scientists said. Mutations are usually harmful or neutral at best, suggesting that males are causing significant molecular mayhem. On the other hand, species count on occasional mutations to invent new things, so males may also be the species' prime innovators. In any case, daughters and sons equally inherit their dads' warped genes. So with the exception of their sperm, men are no more mutated than women.

But enough about you, the genome might say. What about me?

Indeed, the human genome is about much more than just humans. In the vast spaces between those scattered 30,000 genes, taking up the other 99 percent or so of the genome, is a molecular menagerie of genes and gene pieces. Some of them arose internally like warts on the genome while others hacked their way into human cells during the past several hundred million years and decided to stay.

Hundreds of thousands of these genes and gene fragments reside in the human genome in relative leisure while human genes toil away nearby, making new generations of people for all to live in. Most of them are just "freeloaders," said Eric Lander, director of the Whitehead Center for Genome Research in Cambridge, Mass. Having integrated themselves into the very fiber of the human genome, these interlopers can rest assured that every time a human cell divides and passes copies of its DNA to a daughter cell, they also will be replicated, thus keeping "alive" what to them are their family lines.

All told, the new analysis shows, at least 45 percent of the human genome consists of selfish genetic elements mooching off their human hosts. Scientists have grouped them into families, traced their lineages and are now tracking the migrations they've made over millions of years as they wandered from chromosome to chromosome through the wilderness of the genome.

In some cases, pieces of chromosomes have broken off, drifted away and attached themselves to other chromosomes, carrying their parasitic sequences along like penguins on ice floes. By tracing the routes these passengers have taken, scientists are identifying some of the large-scale genetic changes that correlate with key advances in human evolution.

"Humanity has a certain number of great classics of literature that are amazing historical stories and sources of insight and inspiration," Lander said. "Now for the first time we have an historical anthology of ourselves, some of it passed down for a billion years. We're just learning how to read the story, and it's sure to enthrall us for decades to come."

One story with an especially surprising ending has to do with ALU sequences, DNA fragments scattered about the human genome that don't make anything except more of themselves. The human genome is home to about a half a million of these entities, which take up fully 14 percent of the human genome.

Scientists had long written off ALUs as genetic "junk." But ALUs living near genes are preferentially retained, according to the new genome analysis, while ALUs that live in other areas of the genome are gradually weeded out. Recent but controversial experiments had suggested that ALUs might help their human hosts, perhaps by turning on protective genes in stressful situations. The new finding that ALUs are especially welcomed around genes is strong evidence that they are indeed helpful neighbors.

Many mysteries remain to be solved. Inexplicably, for example, few new families of genetic interlopers seem to have taken root in the human lineage in the past 50 million years. Also unexplained, some types of genetic parasites are becoming gradually extinct within the genome while others are apparently thriving. Entire civilizations, it seems, have risen and fallen within the human genome and are continuing to do so.

It's a humbling perspective, said Robert Waterston, director of Washington University's genome center in St. Louis. A person who gazes upon the human genome is likely to walk away feeling a little bit less the center of attention, he said — less certain about being the sole purpose of it all.

"You can't study the genome for very long before you start feeling that you're just a transient vehicle for making more DNA," Waterston said.

But not just any vehicle.

One with the curiosity, ingenuity and wherewithal to explore and decipher its own genetic code.

Staff writer Justin Gillis contributed to this report.

 

 
© 2001 The Washington Post Company

Category: 32. Genome Project and Genomics