Web Exclusives: Genetics
Zooming in on Gene Regulation
Ryan Tarpine's laptop screen looks like a scene from the movie The Matrix. Columns of brightly colored dots and dashes cascade down, connecting at intervals with bands that run horizontally.
The horizontal lines represent DNA sequences from two sea urchin species. The colored cascading columns—some narrow, others wider—are places where their genetic coding appears to match. More specifically, the matched areas show where the species share similar gene-regulating instructions.
Tarpine, a computer science graduate student at Brown University, developed this software system (cisGRN browser) and a genetic sequencing mapping tool (Solexa Mapper). Using these tools, biologists can take the DNA from one species, compare it with the genome of another species and discover where the genetic matches are. The results could help us understand how the genomes of different species—including humans—have evolved over time, as well as which genes were preserved and why.
"The computer is now an analytical tool guiding the next experiments. That is the beauty of it," says Tarpine's advisor and computer scientist Sorin Istrail. "It is showing the next piece of gold."
Tarpine and Istrail recently used the tools to help biologist Eric Davidson at the California Institute of Technology analyze transcription factors—a class of DNA-binding proteins that regulate gene expression. The scientists were able to overlay DNA segments from a pale green sea urchin onto the fully mapped genome of the purple sea urchin to hone in on matching regions.
"When you make those matches," Tarpine says, "you can be confident that those genes have been passed on."