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Don't Call It Junk

14 July 2005 (All day)
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Trash is treasure. The more complex the organism, the more highly conserved its junk DNA.

How did simple organisms like yeast and worms evolve into ones as complex as birds and mammals? According to a broad comparative study of genomes, the answer may lie in their junk DNA.

Ever since the sequencing of the first genomes from eukaryotes--a group that includes yeast and humans--scientists have wondered why most of these creatures' DNA is devoid of genes. Possible explanations for this so-called junk DNA range from mutation protection to structural support of chromosomes. But the discovery last year that patches of junk DNA are identical in humans, mice, and rats indicated that the regions might contain important regulatory switches that control basic biochemistry and development, which might help organisms build sophisticated bodies. Strengthening that case is the fact that complicated animals don't sport vastly more genes than do simpler eukaryotes.

To gain further insight, a team led by David Haussler, a computational biologist at the University of California at Santa Cruz (UCSC), extended the junk DNA comparison to five vertebrate species--humans, mice, rats, chickens, and pufferfish--along with four insects, two worms, and seven species of yeast. A surprising pattern arose from the comparison: The more complex the organism, the more important junk DNA seems to be.

The underlying idea is that if different kinds of animals have the same DNA, that DNA must be doing something critical. Yeast and vertebrates share a fair amount of DNA--they both need to make proteins, after all--but only 15% of the shared DNA falls outside of genes. Compare yeast to more complicated worms, which have a multi-cellular body, however, and the fraction rises to 40%. Then compare those with vertebrates and insects, which are several notches more sophisticated than worms, and over 66% of the shared DNA consists of non-coding DNA, the team reports online today in Genome Research.

The worm result should be interpreted cautiously, says co-author Adam Siepel, a computational biologist at UCSC, because only two genomes were analyzed. Even so, Siepel thinks the finding supports the theory that increased biological complexity in vertebrates and insects derives mainly from elaborate forms of gene regulation.

Philip Green, a molecular biologist at the University of Washington in Seattle, agrees. "It's convincing," he says, but he notes that the purpose of all of the non-coding DNA that's not shared is still open.

Related sites
Haussler's webpage
Green's webpage

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