Learning to Read the Book of Life
Genome signature tagging is one such method. Using “restriction” enzymes that recognize specific sequences in the genetic code, the scientists chop the genome into smaller segments that can be sequenced and used to differentiate species or traced back to the entire genome to identify important genes.
The segments, called “tags,” contain roughly 20 nucleotide base pairs. “Because these tags are so short, we ‘glue’ 10 to 30 of them together to sequence all at one time, making this a highly efficient, cost-effective technique,” says Daniel (Niels) van der Lelie, another Brookhaven biologist who is using the technique.
Finding the on/off switches
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In one recent example, John Dunn’s group used genome signature tagging to rapidly identify more than 6,000 sites where a particular regulatory protein binds to human DNA.
They first chemically cross-linked the protein and DNA in living cells. Then they added antibodies specific for the regulatory protein to identify the pieces of DNA that had the protein attached. Then they washed away all the segments without the protein bound, and chopped the pieces of DNA with the protein into smaller tags they could sequence. Because they knew these tag segments were within a certain distance of where the regulatory proteins attached, they were able trace the sequenced tags back to the original genome to identify the regulatory proteins’ binding sites.
Since the act of binding is thought to be a trigger for turning nearby genes on or off, “identifying the places where these regulators act — where these on/off switches are — should help us determine which genes are at work in different types of cells under different conditions,” Dunn says. That one test study identified several genes that may play an important role in cancer as well as the gene responsible for Huntington’s disease in mice, which is important for making advances in understanding Huntington’s disease in humans.
Sorting out microbes
In another example, van der Lelie’s group used genome signature tagging to quickly catalog the many species of microorganisms living in an unknown “microbial community.”
In this case the tags contained 16 nucleotide base pairs somewhat “upstream” from the beginning of a gene that is highly conserved among bacterial species. By sequencing these tags and comparing the sequenced code with databases of known bacterial genomes, the Brookhaven team determined that this specific 16-letter region contains enough unique genetic information to successfully identify all community members down to the genus level, and most to the species level as well.
This application has many potential uses — from assessing the microbes present in environmental samples and identifying species useful for cleaning up contamination, to identifying pathogens and distinguishing harmless bacteria from potential bioterror weapons.
Genome signature tagging “has no limits,” says Brookhaven Biology Department Chair Carl Anderson. He plans to use the technique to study genes associated with cancer, while others have approached Dunn’s group with ideas for using GST in studies of addiction, obesity, and diabetes.
As Dunn says, “it promises to be a really useful tool.”
