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February 12, 2001
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GENOME FINDINGS OPEN `BOOK OF LIFE'
GROUNDBREAKING STUDIES PROMISE DRAMATIC IMPACT


February 12, 2001

Two competing teams of scientists have released the first spectacular set of discoveries from the new catalog of the human genome, findings that promise to begin reshaping our view of who we are and where we came from.

Hundreds of researchers reporting Monday in the scientific journals Nature and Science have just scratched the surface of what the genome will eventually reveal. Even these early results, though, herald a sea change in thought about modern medicine and humanity's earliest roots.

We are genetically less complex than anyone dreamed--the entire set of genetic instructions for making a human is not much larger than that for a fruit fly or a roundworm.

We are more closely related to other organisms than anyone knew and even received some genes directly from bacteria, providing essential biological machinery that still ticks within us.

And we contain a sort of fossil record in our DNA of our evolutionary past.

Genes, the researchers learned, are far more lively, complicated, adaptable, universal and inventive than anyone ever thought.

The historic articles mark the first attempt to take the measure of the monumental genetic sequence since scientists announced its completion in June. But the new information in Monday's publications makes them more scientifically significant than last summer's milestone.

Scientists are looking both into the past and into the future, finding a family tree that goes back 500 million years, as well as discovering genes that predict how long a person is likely to live, what he or she may die from, and how that fate may be changed.

"This is for the first time having in front of us the human book of life and realizing that it's actually three books," said Dr. Francis Collins, director of the National Human Genome Research Center and mastermind of an international consortium of public investigators that is one of two major groups to publish its findings this week.

"It's a history book that tells us about where we came from, looking back hundreds of millions of years. It's a shop manual that contains within it a list of the parts that we're made of. And it's a textbook of medicine that contains within it clues to the causes of diabetes, heart disease, cancer and a variety of other disorders that we only at the moment barely glimpse."

Perhaps most surprisingly, the new estimate that each person carries about 30,000 distinct genes is far lower than expected--hardly greater than the figure for mustard weed or a worm.

The startlingly low gene number has some experts mystified at how nature can create a complete person with such minimal instructions.

"I'm hoping that historically, this change in our thinking will be somewhat equivalent in magnitude to Copernicus and Galileo proving that the Earth is not the center of the universe," said J. Craig Venter, CEO of the other research group, a private genomics company called Celera. "This is helping to show that humanity is not the center of the biological world."

The furious race to decode the human genome, which so far has cost more than $2 billion, is being run by scientists from the international public sector under Collins and those working for Celera.

Collins' group is reporting its results in Nature; Celera in Science. The findings were to be made public Monday, but the two journals ended their embargoes on the information when a London newspaper published the story early.

The treasures being uncovered inspired a moment of awe for the researchers writing in Nature. "We find it humbling to gaze upon the human sequence now coming into focus," they said. "In principle, the string of genetic bits holds long-sought secrets of human development, physiology and medicine."

Only 30,000 genes

Up to now, most scientists had guessed that the human genome contained 100,000 genes or more.

The research being published this week puts the long-sought figure at a paltry 30,000.

"Boy, that's an affront to our pride," said Eric Lander, director of the Whitehead Institute Center for Genome Research at the Massachusetts Institute of Technology and a main author of the public genome paper.

Active genes--little booklets of DNA code that, through the proteins they produce, shape everything from individual cells to major organs--comprise just a tiny fraction of the human genome's 3 billion DNA components.

Before the whole genome was sequenced, there was no way to know how many genes existed, leaving a yawning gap in knowledge about the complexity of human biology.

As recently as 1999, a paper in Nature by researchers from Incyte Pharmaceuticals put the gene figure at a whopping 142,634.

To get a more accurate estimate, researchers plugged the genome's huge sequence into sophisticated computer programs designed to look for anything resembling genes found in other organisms.

The scientists also looked at sequences of RNA, a chemical cousin of DNA that helps bring out the proteins encoded in genes. By matching known RNA sequences with DNA found in the genome, the teams isolated thousands of likely genes.

Having surveyed virtually the entire genome, scientists can tell where previous calculations went wrong.

It turns out that unlike bacteria or yeast, human genes are thrown in with a huge amount of inactive DNA that does not code for proteins. Some erroneous gene estimates in the past focused on two chromosomes that are unusually chock full of genes.

"Those are two of the most gene-dense regions of the genome," Venter said.

Although Celera and the public project used some different human samples and computer algorithms, their estimates are strikingly similar. Each group found rock-solid support for about 24,000 to 26,000 genes, with partial evidence raising the likely number to around 30,000.

"If we'd said there were 32,000 genes and they'd said there were 200,000, this would be a very different conversation," Collins said.

Beyond its implications for human biology, evolution and inheritance, determining the number of genes may affect the bottom line of biotechnology companies.

Many firms have bet huge fortunes on finding and patenting genes with medical uses; some believe the more genes there are, the more potential for profit.

Proteins solve puzzle

So if we have only 30,000 genes, a mustard weed has 25,706 and a fruit fly 13,338--and all the genes are pretty much alike--what is it that makes us human?

That's been a huge puzzle in biology, but now the answer is in--it's the proteins.

One of the biggest revelations to come out of decoding the human genome is that each of our genes can make three to 10 proteins, and possibly more, while the genes of simpler organisms average only one protein per gene.

Before, it was thought that one gene could make only one protein. So firm was the idea that the two scientists who first proposed it won a Nobel Prize.

But though a fruit fly essentially makes a little more than 13,000 proteins, humans make up to 250,000. What's more, those can be combined in different ways to produce millions of different potential proteins.

That is what accounts for the complexity of higher organisms.

Collins explains, "If an organism is going to develop a larger number of organ systems and tissues and functions, like an immune system and nervous system--all the things that are not present or present in a rudimentary form in worms and flies--you have a way of adding that additional potential for complexity."

The food we eat contains basic elements called amino acids that genes use to make instructions for building proteins. Those proteins then perform all the roles needed to build and maintain a body.

Some of them serve as construction workers that cut, join and move other proteins, which serve as the building blocks for everything from cell membranes to bones.

Take, for example, a protease protein that cuts other proteins. In worms and fruit flies it simply acts like a paring knife. It just cuts. But in humans, that same protein can be modified to perform like a Cuisinart. It can cut, chop and dice at different speeds.

The insulin gene, for instance, makes proinsulin, which gets cut into four parts to make insulin and two other proteins.

"If you look at how we're different from worms and flies, part of it seems to be this ability to add new functions to old proteins," Collins said. "Over the course of evolution, that may have been responsible for us becoming what we are. Without it we might still be in the roundworm stage."

Bacteria break the rules

One finding was so unexpected and unsettling that the researchers had trouble believing it: 223 of our genes appear to have come directly from bacteria.

In the Nature paper, Collins and Lander surmise that ancient bacteria passed DNA to our remote ancestors, perhaps fish swimming in primordial seas.

Those sequences are not present in more primitive organisms such as worms and insects, which should have inherited the genes if they had been passed along through normal evolution.

More remarkably, most of those genes now play central roles in the human body's basic metabolism and early development. Some have been connected to depression and other mental illness.

Several researchers were convinced that their samples had been contaminated by bacteria in the lab, said project leader Robert Waterston of Washington University in St. Louis.

"People basically didn't accept it--they wanted to just throw these sequences out," Waterston said. "It wasn't until we looked hard that we realized these weren't contaminants. They were actually human DNA."

No one knows exactly how or when the bacterial genes hopped across species. But the importance of those sequences for our survival probably means it was well over 200 million years ago.

Bacteria routinely exchange genes among themselves--a process biologists call horizontal transfer. But no one had thought that it could happen between bacteria and complex animals.

"This breaks all the rules," Collins said.

The bacterial genes play numerous essential roles in people, from the metabolism of nitrogen to the maintenance of mitochondria--the tiny power plants that supply energy to muscles and other tissues.

One of the genes produces an enzyme linked to depression and mental illness. Drugs that inhibit the enzyme, called monoamine oxidase, are used as antidepressants. And researchers in the early 1990s tied a defect in the gene to a disorder they dubbed Brunner syndrome, which is marked by aggressive behavior and exhibitionism.

"All of this should make us humble in a way, because it connects us with the rest of nature," Lander said. "We see within our own DNA our intimate connections with everything from chimpanzees to fish, to fruit flies, to baker's yeast. I don't think most people think of the chromosomes as being a paleontological dig. It's pretty amazing."

Men, women and heat

The Y chromosome, carried only by men, plays a unique role in evolution, researchers have found.

The Y is the littlest chromosome we have, carrying only a hundredth the genetic information of the female X chromosome and just a third the size.

It is the only part of the genome that is specific to one sex. And it is something of a genetic junkyard.

Only the Y does not recombine and swap DNA with its partner when eggs and sperm are made. Because 95 percent of the Y chromosome never swaps genes with a female X chromosome, it preserves the genes that allow it to determine gender.

But over time it also has degenerated, losing most of its active genetic material, and accumulating mutations. The public project shows that the Y chromosome contributes twice as many mutations as the X.

That, the genome researchers have determined, is good news and bad.

The bad: Men cause two-thirds of genetic diseases. The good: They also are responsible for two-thirds of evolution, because beneficial mutations are a driving force behind it.

Researcher David Page calls the Y chromosome "the Rodney Dangerfield of the genome--it has gotten no respect from scientists, and in fact, may have something of an attitude."

Page, of the Whitehead Institute at M.I.T., and Bruce Lahn, of the University of Chicago, have compared the DNA sequences of the sex chromosomes back to the time they were exactly the same, about 300 million years ago.

"In our reptilian ancestors, gender was most likely determined by the temperature of incubating eggs, like in today's turtles or crocodiles," Page said. Thus sex predated the sex chromosome.

"Then about the time mammals parted company with birds, a mutation occurred on one member of the chromosomal pair, creating a gene that when present always produced a male, no matter what the temperature was. That put sex in our DNA."

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