Talk about payoff. Mark Batzer has been intrigued by interspersed, repeated DNA sequences since his postdoc days — and now, 17 years later, he and his group at Louisiana State University have rewritten a major theory about the evolution and spread of the most common such sequences.
“My group has done a lot of research trying to sort out the amplification of the mobile elements within the human lineage,” says Batzer, who recently published work comparing primate genomes to better understand mobile elements. Batzer’s crew found that a particular group of Alu elements, known as the AluYb subfamily, originated 15 million or 20 million years ago, he says. “They effectively lay dormant in the genome of many nonhuman primates,” he adds.
That dormancy lasted for millions of years. Some amplification of these elements can be seen in the chimpanzee genome, Batzer says, but the real retrotransposon activity began with the divergence of the human and chimp lineages between 4 million and 7 million years ago. After that, Alus became a decidedly frisky component of the human genome, and today they comprise more than 10 percent of the sequence content of the human genome.
The prevailing theory on the spread of Alus, according to Batzer, was that “Alu repeats that were highly capable of duplicating was a real key to success for the family in the genomes.” The source of all these elements must have made as many copies of itself as possible, the theory went.
But Batzer says the work his team has done shows that Alus have been successful because they’ve been more like the tortoise than the hare. Batzer refers to it as a “genomic arms race” in which “it’s a battle between the mobile elements that are trying to expand in copy number and the genome that is trying to control them.” In other words, if a particular element copies itself like crazy and tries to insert copies all over, “the genome perceives those as damaging agents” and neutralizes them. But elements that make just a few copies of themselves every few million years “are the stealth agents that stick around,” Batzer says. “They’re duplicating at a level that the genome is comfortable with.”
Batzer, who was recently made an endowed professor at LSU, where he’s worked for the past five years, says the work to understand Alus and other mobile sequence elements is still ongoing in his lab. Alus are a particularly “rich source of genetic variation,” Batzer says.
— Meredith Salisbury