Top Story: October 5, 2012

Breaking the Code

ENCODE

By Barbara Tannebaum

An international consortium of researchers recently announced another milestone in the quest to unravel the genetic makeup of the human species. The project—ENCODE, for Encyclopedia of DNA Elements—is a collaborative effort among 440 researchers in 32 global institutions, coordinated by the National Human Genome Research Institute (NHGRI). The results of this international effort will stand alongside such research breakthroughs as Watson and Crick’s 1953 description of DNA’s double helix structure and the Human Genome Project’s 2003 complete sequencing of humanity’s 3.2 billion nucleotides.

ENCODE mapped more than four million non-coding regions of the genome that regulate and interact with protein-producing DNA. The scientific consortium also confirmed that 80 percent of the genome performs specific biological functions. This upends the previous consensus that long stretches of DNA were no more than “junk DNA.”

“This is one of the most important collections of information the world is trying to decode,” explains Brian Simison, head of the Academy’s Center for Comparative Genomics.

Not only does ENCODE solve a bit more of the human genome puzzle, but it offers the potential to accelerate medical research. “We’ve known for a long time that there is a genetic basis to many diseases,” says Simison. “What we didn’t realize is that the source of many diseases would be found in the vast regions of the genome previously known as junk DNA.”

While others describe the project as having found the on/off switches to our genes, Simison prefers the term ‘regulatory function.’

“We are learning that junk DNA has a regulatory role in dosage, duration, timing and other regulatory functions. Understanding these functions will transform Western medicine,” Simison adds. “ENCODE reveals that Western medicine is in its infancy.”

Simison points out that ENCODE is also altering our vision of the genetic composition of life. “Most people think all genetic material is passed down to us by our direct ancestors. Actually,” Simison explains, “the human species is filled with ‘fossil DNA’ transferred to us from viruses.”

As an example, Simison describes a retrovirus that has inserted its DNA into a person’s genome. These endogenous retroviruses (ERVs) are found throughout the genome and it is now believed that some of these have been repurposed.

Finally, Simison explains that it’s not just what ENCODE found but how they found it that is significant.

“The wow factor is enormous,” Simison laughs. As the National Institute of Health reports, hundreds of international researchers performed more than 1,600 sets of experiments on 147 types of tissue with technologies standardized across the consortium.

“Although technology has improved, no single institution could have analyzed the genome data on its own,” Simison remarks. “You need many people sifting through the many layers of data to decode the human genome.”

“I believe it is a positive development that so many nations are sharing this knowledge,” he said, lauding the consortium for its cooperative methods. “These illustrate how the path towards lofty ambitions is often as fruitful as the objectives themselves. Unlike the U.S. space program, the Human Genome Project and ENCODE were international projects where the benefits that emerge are shared with and benefit the world.”

ENCODE’s results were published last month in a wide range of scientific journals and posted online to ensure transparency and public access. To learn more, review the publications here.

Barbara Tannenbaum is a science writer working with the Academy's Digital Engagement Studio. Her work has appeared in the New York Times, San Francisco Magazine and many other publications.

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