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Ontology Leontis wins grant to help establish RNA lexico

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Scientists studying protein structure have a language they can use to describe various folds — alpha helices and beta folds at the secondary level of structure, for example. But biologists interested in RNA structural analysis are a bit out of luck, says Neocles Leontis, a professor of chemistry at Bowling Green State University in Ohio. “There’s a sense that at some point, all or almost all of the protein folds will be found,” he says. “With RNA, we’re not even close.”

To help solve that discrepancy, Leontis has won an NSF grant worth $500,000 over five years to bring together an international group of RNA researchers to come up with a common ontology — or interrelated vocabulary — for describing the common set of folds an RNA molecule can obtain. Unlike proteins, which because of their polypeptide backbone can obtain a more limited number of basic conformations, the individual nucleotides that make up RNA molecules can rotate much more freely along their backbone, dramatically increasing the number of possible folds RNA can obtain.

Creating a standard ontology for RNA structure would also aid researchers in identifying genes that code for RNA, says Leontis. It’s becoming increasingly clear that RNA is involved in many more processes than researchers ever imagined, he adds, and detecting where these genes lie in an organism’s genome is limited by the understanding of which sequences represent RNA folds. Unlike protein-coding genes, which are more easily identified by start codons, for example, “you can get a lot of [genome] sequence, but not know where the RNA data is,” Leontis says.

Although $500,000 over five years may not seem like a lot of money, Leontis says the grant mechanism, known as a Research Coordination Network, will suffice to coordinate interactions between scientists with different approaches to assembling a common ontology for RNA structure. “It’s not a conventional grant, because the funding goes toward bringing many people together,” he adds. While the differences among the various participating scientists are not trivial, Leontis is confident he can succeed in promoting some consensus. “I’m confident the meetings we plan will be productive,” he says. “Scientists are rational people.”

— John S. MacNeil

Bowling Green State Univ. press release
http://www.bgsu.edu/offices/pr/news/2005/news8863.html
Neocles Leontis’ homepage
http://www.bgsu.edu/departments/chem/leontis.html
Funding award description
http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0443508

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