BYU researchers help toss theory that most DNA is 'junk' through ENCODE Project work

PROVO — The scientific community is rethinking its decade-old belief that most DNA is "junk," after an international consortium that included a BYU professor and one of his undergraduate students found at least 80 percent plays a role with genes.

That consortium finding was just published in the journal Genome Research. Other papers have been published all week in various journals.

When the Human Genome Project was completed a decade ago, researchers had 3 billion units of information and had identified 20,000 genes as crucial to human biology. Since those genes made up fewer than 2 percent of the human genome, it was widely concluded that most or all of the rest was useless. Some researchers even suggested that exploring them would be a waste of time and money.

The ENCODE Project (short for Encyclopedia of DNA Elements) was launched to learn what, if anything, all the parts of DNA do, including the presumably worthless 95-plus percent. Partway through, Brigham Young University assistant professor of microbiology and molecular biology Steven Johnson was tapped because at Stanford he'd developed an efficient way to isolate the DNA wrapped around nucleosomes to determine their positions across the entire genome. He taught then-undergraduate Elliot Winters, now a first-year medical student in Texas, to isolate the nucleosomes — "a couple billion" of them.

Nucleosomes are fundamental to taking 46 strands of DNA (23 pairs of chromosomes) that total 6 feet and placing them in a cell nucleus that's only 5 millionths of a meter in diameter. "Mind-boggling" is how Johnson described the fit, which relies on efficiently organizing the material. Nucleosome are like thread spools on which the DNA is wrapped, the result a bit like wax beads on a string.

That compaction process matters because where it is sitting and which piece of DNA is wrapped up determines which genes can turn on or off. The position is the "first order of genetic regulation," Johnson said. Both he and Winters are listed as "authors" on the research.

Undergrad experience

How the DNA is wrapped in a cell has a big impact on what the cell becomes, said Winters, who noted that BYU undergraduates get opportunities for hands-on research that is often reserved for graduate students at other universities. When he started the project, he had no idea what a big deal it would turn out to be or how proud he'd feel.

Nearly a third of BYU undergraduates have a research experience under the guidance of a professor. The university's Office of Research and Creative Activities last year awarded grants to 321 undergraduates for research projects. Winters and Johnson got one of those grants.

The research finding "is like a huge set of floodlights being switched on," the lead analysis coordinator for ENCODE, Ewan Birney of the European Bioinformatics Institute in the United Kingdom, told the Wall Street Journal. He said they've found several hundred previously unknown biological links, including some that point to what causes various conditions, like Crohn's disease. His prediction? All of DNA will prove to have purpose.

Dozens of papers based on ENCODE were published this week. The hope — and even expert expectation — is that new understanding of the human genome will lead to screening tools, prevention and treatment of disease.

Nearly 450 scientists from around the world have been part of ENCODE.

Meanwhile, earlier this week the National Genome Research Institute in the National Institute of Health awarded another round of grants to expand ENCODE. "We have already made tremendous progress, but much work remains to complete the catalog of functional elements," said Elise A. Feingold, program director for the project in the institute's Division of Extramural Research. "These grants, awarded over a four-year period, will allow us to build on those results and take the next significant steps in deepening our understanding of the entire human genome."

A bit of controversy

While the latest findings have kicked off great scientific excitement, it has also sparked some heat in the evolution/intelligent design debate about origins.

Those who believe in intelligent design — a world created by God — are heralding the findings as a major blow to evolutionary theory. For example, Christian Apologetics called it "a significant defeat for Darwinism because the evidence supporting evolution by random mutation and natural selection has been so sparse. Before the latest results, Darwinists could plausibly claim that junk DNA was their evidence. It 'encoded' the history of random mutations. No longer."

Jonathan Wells, a senior fellow at the Center for Science and Culture, has documented the decade-long debate in a book, "The Myth of Junk DNA."

Critics of intelligent design have called the findings "hyped." One of the most widely quoted critics, Larry Moran, a scientist at the University of Toronto, wrote on his blog, "The creationists are going to love this. This is going to make my life very complicated."

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