Tiny, jumping bits of DNA are looking less like genomic junk and more like significant players in mammalian evolution, according to a new analysis.

Researchers have uncovered more than 10,000 short stretches of what may be functional DNA in parts of the human genome with no obvious role—the so-called junk DNA that makes up 95 percent of the genome. The segments appear to be fragments of transposons, pieces of DNA capable of copying themselves and inserting into new locations, up to millions of times.

"One of the big questions is: Where does novel functional DNA come about in the genome?" says evolutionary developmental biologist Gill Bejerano of Stanford University, a member of the team that performed the study. "We think we've hit on a force here that was underappreciated before."

Bejerano and his colleagues identified the transposon fragments by looking for sequences of junk DNA that were nearly identical across six mammalian species—human, chimp, rhesus monkey, dog, mouse and rat. Researchers consider such similarities a sign that evolution preserved DNA for some function, otherwise small errors would accumulate.

They compared the conserved sequences with those found in the chicken genome to weed out any that were present before mammals evolved. In a paper published online this week in Proceedings of the National Academy of Sciences USA, they report that 5 percent of the uniquely mammalian elements were similar in sequence to transposons. Bejerano says the source of the remaining 95 percent is unclear.

Although found in so-called gene deserts, where genes are sparse, the conserved transposon elements lay within striking distance of genes active during embryonic development, including all known members of a biochemical pathway that helps cells stick to one another.

The actual functions of the conserved elements remain untested, but the proximity suggests that evolution may have harnessed the bits of junk DNA to control the activities of the nearby genes, Bejerano says.

In this way, genes might become active in new places or at new times, contributing to the differences between species. Researchers had turned up a few examples of conserved transposon elements before, but they were isolated cases, says Bejerano. "This is a genome-wide phenomenon that appears to play a significant role."

Nevertheless, 95 percent of the mysterious conserved junk DNA remains. Next up: figuring out where it comes from.

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