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Theory of Junk DNA Debunked:

The deepest look into the human genome so far shows it to be a richer, messier and more intriguing place than was believed just a decade ago, scientists said Wednesday.

While the findings underscore the challenges of tackling complex diseases, they also offer scientists new terrain to unearth better treatments.

The new insight is the product of Encode, or Encyclopedia of DNA Elements, a vast, multiyear project that aims to pin down the workings of the human genome in unprecedented detail.

Encode succeeded the Human Genome Project, which identified the 20,000 genes that underpin the blueprint of human biology. But scientists discovered that those 20,000 genes constituted less than 2% of the human genome. The task of Encode was to explore the remaining 98%—the so-called junk DNA—that lies between those genes and was thought to be a biological desert.

That desert, it turns out, is teeming with action. Almost 80% of the genome is biochemically active, a finding that surprised scientists.

In addition, large stretches of DNA that appeared to serve no functional purpose in fact contain about 400,000 regulators, known as enhancers, that help activate or silence genes, even though they sit far from the genes themselves.

The discovery "is like a huge set of floodlights being switched on" to illuminate the darkest reaches of the genetic code, said Ewan Birney of the European Bioinformatics Institute in the U.K., lead analysis coordinator for the Encode results….

The flood of scientific data is likely to keep researchers busy for a long time. More than 30 papers based on Encode were published Wednesday. Six of those, including an overview paper, appeared in the journal Nature, along with a total of 24 related papers in Genome Research and Genome Biology. Others journals, including Science, also published papers….

The unexpected level of activity seen in the genomic hinterlands may also help explain what makes us human. Compared with other species, the human genome has about 30 times as much "junk DNA."

When the human genome was first sequenced, scientists were surprised that its structure—based on fewer-than-expected genes—seemed uncomplicated, said Chris Ponting, a professor of genomics at the University of Oxford who wasn't involved in the latest research.

"Encode shows us how extraordinarily decorated the genome is," Dr. Ponting said.