New tool for profiling critical regulatory structures of RNA molecules

A paper by the research team -- led by Sarah M. Assmann, Waller Professor of Biology, and Philip Bevilacqua, professor of chemistry -- is scheduled for early online publication in the journal Nature on 24 November 2013.

"Scientists have studied a few individual RNA molecules, but now we have data on almost all the RNA molecules in a cell -- more than 10,000 different RNAs," Assmann said. "We are the first to determine, on a genome-wide basis, the structures of the RNA molecules in a plant, or in any living organism."

Temperature and drought are among the environmental stress factors that affect the structure of RNA molecules, thereby influencing how genes are "expressed" -- how their functions are turned on or turned off. "Climate change is predicted to cause increasingly extreme and unpredictable heat waves and droughts, which would impact our food crops, in part by affecting the structures of their RNA molecules and so influencing their translation into proteins," Bevilacqua said. "The more we understand about how environmental factors affect RNA structure and thereby influence gene expression, the more we may be able to breed -- or develop with biotechnological methods -- crops that are more resistant to those stresses. Such crops, which could perform better under more-marginal conditions, could help feed the world's growing population."

The scientific achievement of the Penn State research team -- postdoctoral scholar Yiliang Ding, graduate students Yin Tang and Chun Kit Kwok, and Professor of Statistics Yu Zhang, along with Assmann and Bevilacqua--involved determining the structures of the varieties of RNA molecules in a plant named Arabidopsis thaliana. This plant is used worldwide as a model species for scientific research.

Arabidopsis thaliana, commonly known as mouse-ear cress, is an ideal organism for RNA studies, the researchers say, because it is the first plant species to have its full genome sequenced and has the greatest number of genetic tools available.

RNA is the intermediate molecule between DNA and proteins in all living things. It is a critical component in the pathway of gene expression, which controls an organism's function. Unlike the double-stranded DNA molecule, which is compressed into cells by twisting and wrapping around proteins, RNA is single stranded, and folds back on itself. The researchers set out to answer the question, How exactly does RNA fold in a cell and how does that folding regulate gene function?

"We needed a tool to answer that question," says Bevilacqua. "That tool involves introducing a chemical into the plant that can modify some segments of the RNA but not others, which then gives a readout of the structure of the RNA. Using this technique we can figure out which classes of genes are associated with certain RNA structural traits. And we can try to understand how these RNA structural changes relate to certain biological functions."

"Previously, researchers would query the structures of individual RNAs in a cell one by one, and it was a tedious process," says Assmann. "You can't abstract rules or generalities about how RNAs are behaving just from knowing the structures of one or a few RNAs--you can't get a pattern. Now that we have genome-wide information for a particular organism, we can start to abstract patterns of how RNA structure influences gene expression and ultimately plant function. Other scientists can query their organisms of interest and ask what rules they can abstract. Are there universal rules that will be true for all organisms for how RNA structure influences gene expression?"

Bevilacqua adds, "Because RNA is so central in its role in gene regulation, the tools we've developed can be transferred to scientists who are working with essentially any biological system." Long-term potential implications of the methodology include human health--for example, how an infection-induced fever could affect the RNA structures of both humans and pathogens.