'Junk' DNA: Not So Useless After All

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Junk. Barren. Non-functioning. Dark matter. Thats how scientists had described the 98% of human genome that lies between our 21,000 genes, ever since our DNA was first sequenced about a decade ago. The disappointment in those descriptors was intentional and palpable.

It had been believed that the human genome the underpinnings of the blueprint for the talking, empire-building, socially evolved species that we are would be stuffed with sophisticated genes, coding for critical proteins of unparalleled complexity. But when all was said and done, and the Human Genome Project finally determined the entire sequence of our DNA in 2001, researchers found that the 3 billion base pairs that comprised our mere 21,000 genes made up a paltry 2% of the entire genome. The rest, geneticists acknowledged with unconcealed embarrassment, was an apparent biological wasteland.

But it turns out they were wrong. In an impressive series of more than 30 papers published in several journals, including Nature, Genome Research, Genome Biology, Science and Cell, scientists now report that these vast stretches of seeming junk DNA are actually the seat of crucial gene-controlling activity changes that contribute to hundreds of common diseases. The new data come from the Encyclopedia of DNA Elements project, or ENCODE, a $123 million endeavor begun by the National Human Genome Research Institute (NHGRI) in 2003, which includes 442 scientists in 32 labs around the world.

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ENCODE has revealed that some 80% of the human genome is biochemically active. What is remarkable is how much of [the genome] is doing at least something. It has changed my perception of the genome, says Ewan Birney, ENCODEs lead analysis coordinator from the European Bioinformatics Institute.

Rather than being inert, the portions of DNA that do not code for genes contain about 4 million so-called gene switches, transcription factors that control when our genes turn on and off and how much protein they make, not only affecting all the cells and organs in our body, but doing so at different points in our lifetime. Somewhere amidst that 80% of DNA, for example, lie the instructions that coax an uncommitted cell in a growing embryo to form a brain neuron, or direct a cell in the pancreas to churn out insulin after a meal, or guide a skin cell to bud off and replace a predecessor that has sloughed off.

What we learned from ENCODE is how complicated the human genome is, and the incredible choreography that is going on with the immense number of switches that are choreographing how genes are used, Eric Green, director of NHGRI, told reporters during a teleconference discussing the findings. We are starting to answer fundamental questions like what are the working parts of the human genome, the parts list of the human genome and what those parts do.

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If the Human Genome Project established the letters of the human genome, ENCODE is providing the narrative of the genetic novel by fashioning strings of DNA into meaningful molecular words that together tell the story not just of how we become who we are, but how we get sick as well.

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'Junk' DNA: Not So Useless After All