Landmark Genome Study Shows Complexity of Human 'Code'

June 14, 2007 — -- In what is being hailed as a landmark in understanding the human genome, scientists from over 35 research centers around the world released a collaborative study Wednesday afternoon showing that our genetic makeup is much more complicated than previously thought.

The collaboration of researchers, known as the Encyclopedia of DNA Elements — or ENCODE — consortium, looked at roughly 1 percent of the entire human genome, concluding that the 95 percent of the genome previously believed to be superfluous actually plays a major role in regulating how DNA expresses itself.

The study brings a new dimension to determining both the impact of human genetics in clinical medicine and how humans evolved differently from animals.

When researchers announced they had mapped the human genome in 2003, they knew it was made up of over 3 billion base pairs of DNA.

However, only between 1.5 and 5 percent of that — encompassing the areas known as "genes" — was involved in actually making proteins. The rest was termed "junk DNA."

But researchers felt that the remaining part of the genome had to have a purpose. In a paper released in the journal Nature, scientists say they have found that much of that so-called junk DNA is actually involved in regulating how genes build and maintain the body.

"Several years ago, we had completion of the Human Genome Project, but we didn't know what to do with 95 percent of the DNA we'd found," said John Greally of the Albert Einstein College of Medicine, who reviewed the study in the same issue of Nature. "This is going to be a landmark."

Greally likens the genes to musical instruments, and the regulatory regions of the genome found in this study to an orchestral score — the instructions necessary to make the whole symphony come together.

Genes With Accessories

While Greally said the study is an important milestone in understanding the human genome, the fact that the other parts of the DNA play a regulatory role is not surprising; rather, it is something many scientists had expected.

He also said that this study begins to answer a question scientists have been asking for a while: How do cells in the body operate differently when they all have the exact same DNA?

"What we've known for a long time ... is that every cell in the body has the same DNA, but every cell uses different genes, and that's what defined them," said Greally.

While the current study mapped 1 percent of the genome and took four years, scientists feel that the remaining 99 percent of the genome's regulatory regions will be mapped within the next four to five years.

"It's just a matter of money," said Zhiping Weng, a biomedical engineering professor at Boston University, who was one of the study leaders.

She said the accelerating pace of technology for sequencing DNA, and the number of labs that will be interested in adding to the research, would speed up the remainder of the process.

"This is an enormous step forward," said Charles DeLisi, director of bioinformatics at Boston University, who played a major role in the Human Genome Project, but was not involved in the research for this particular study.

DeLisi sees this paper as the start of a new direction in the study of the human genome, where we gain a broader understanding of how DNA really dictates human physiology.

"You'll learn a lot well before this project is completed," he said, referring to what he termed a continuum of medical advances that would take place as researchers learned more about how genetic defects contribute to various diseases like diabetes, heart disease and certain forms of cancer.

Clinicians would then have a more accurate way of diagnosing patients for their risk of developing specific diseases, DeLisi said.

Working in Harmony

One of the most important parts of this study, DeLisi said, is the fact that many research labs came together to work on it.

"We're all working together to make this happen a lot more rapidly than it would otherwise happen," he said. "To me, that is exhilarating."

Francis Collins, head of the National Human Genome Research Institute, and Michael Snyder of Yale University, echoed that sentiment at a press conference on the study Wednesday morning. They indicated that having so many researchers working together so smoothly was key to completing this important work.

This level of collaboration will continue as scientists aim to complete the mapping of the human genome.

"One of the important results is that we can do this," said Ewan Birney, head of genome annotation at the European Molecular Biology Laboratory's European Bioinformatics Institute. "We can gain this information genomewide."

Evolving Understanding

Birney said that the genome research will take a number of different directions, leading to a variety of discoveries.

"Depending on your level of biological geekiness, you get excited about these stories at a different level," said Birney.

For him, an important finding was how different human and animal DNA are.

As many as half of the functional parts of the genome varied between different mammals, said Birney, who has looked at genomes for mice, rats, hedgehogs, platypuses and baboons, among others.

Despite that diversity between humans and animals, Birney stresses that humans are still very alike from one person to the next.

"Not only are we incredibly similar, the only sensible way to view our genetics is as one population," he said. "We are far, far more similar to each other than we are different."

While the new advance adds to the understanding of the genome, researchers point out that completing the mapping will take time. The complexity of the genome, Collins said, is something he feels all the researchers are in awe of.

"We are intended to be complicated," he said, "and we obviously are."