Wei Zhu and Gerald Pao had questions about basic mechanisms that allow some human and animal cells to change identity, becoming more like stem cells. David M. Gardiner and S. Randal Voss had been chipping away for years at the mysteries of the salamander, a creature whose cells can repeatedly morph into an entire new body part. So when a chance at a data windfall that could help all their diverse investigations came along, these researchers, based in California and Kentucky, pooled their ideas and entered a contest.
Their bid went to Roche Biosciences in Palo Alto, Calif. Eager to demonstrate a new low-cost, high-speed DNA-sequencing technology, Roche held a competition seeking interesting projects last year, offering a first prize of a million DNA base pairs’ worth of free sequencing. Pao and Zhu, both postdoctoral researchers at the Salk Institute for Biological Studies in La Jolla, Calif., sent in the winning proposal for a project that would use multiple techniques to examine what goes on at the molecular level when salamander cells start rebuilding a lost limb.
The question is relevant not just to salamanders but to understanding whether humans could ever perform the same feat, perhaps by making our own cells revert to a stemlike state. Now that the collaborators have sifted some of their data, the serendipitous sequencing project is yielding nuggets of information valuable to each of them, while potentially reviving the study of salamander regeneration.
Pao and Zhu focused on the earliest stage of healing in cells at the site of an amputated salamander limb, examining stretches of DNA that were unwinding and presumably contained genes that were about to turn on. Sequencing this material revealed that genes seemingly involved in triggering the cellular regeneration program are some of the same ones active in embryonic stem cells, suggesting that the cells had reverted to a more primitive state. “We have several very interesting candidate genes that are basically almost exclusively active in germ cells,” Zhu says, “and we’re trying to define their function.”
“Obviously the goal is to understand which genes are turned on during regeneration and to understand more of the process,” explains Zhu’s boss, Tony Hunter. Figuring out which genes are important would be easier, though, if scientists knew what kinds of genes the salamander possesses. Unfortunately, Hunter remarks, “there is no complete sequence.”
That is because the salamander genome is huge, “10 times the size of the human genome sequence,” Hunter points out. Its size has always scared off would-be sequencers because of the cost of traditional sequencing methods, says Voss, a University of Kentucky biologist who maintains the Sal-Site repository for salamander gene data. He used some of the free sequencing prize to read large chunks of genome, in part to study its overall structure. The results revealed salamander genes to be organized much like human genes, with protein-encoding DNA stretches interrupted by noncoding sections, called introns. In salamanders, though, the introns are enormous and filled with repeated sequences, which helps to finally explain the genome’s extraordinary size.
The group has also been cataloguing newfound genes that have an obvious counterpart in humans and other vertebrates, a step toward figuring out if something unique to salamanders permits them to regenerate. “What the Roche contest did was take us from a little over 1,000 axolotl [salamander] genes that were clearly orthologues of human genes to now having 10,000,” says Gardiner of the University of California, Irvine. “It’s not all of them, but it’s a quantum leap.”
The tantalizing tidbits that came out of the sequencing prize have each of the researchers craving more. Pao and Zhu think further molecular studies of salamanders could yield insights into more universal mechanisms in embryonic stem cells, for instance. And after seeing what access to cheaper sequencing technology can accomplish, Gardiner thinks that the project will jump-start a new molecular era in salamander regeneration research, which he admits had reached something of an impasse using traditional biology techniques.
“Roche came along, and it was like a fairy godmother, sprinkling some fairy dust,” Gardiner remarks, “and now we can use the tools available in the bioinformatics community.”
Note: This story was originally printed with the title, "Getting a (New) Leg Up".