New App Shows 2D Structure of RNA Molecules, Reveals Complexity

Scientists now can enter a specific RNA from baker's yeast into their iPhone and see a depiction of its two-dimensional (2D) structure, but revealing much more.

While this application is exciting, the real advance is that for the first time, it is possible to capture experimentally a global snapshot of the conformation of thousands of RNA molecules in a cell. This is a significant development because RNA has recently been shown to be much more complex than once thought.

"We used to think of RNA as just a long, floppy string that delivers instructions from DNA to the protein-assembly points in the cell,” said associate Professor of Dermatology Howard Chang, M.D., Ph.D., from Stanford University (Palo Alto, CA, USA). "But now we're learning that often the molecule's structure--and not just its sequence of nucleotide letters--determines its function. So we set out to develop a method that can map the structure of all the RNA in a cell.”

Dr. Chang and Eran Segal, Ph.D., of the Weizmann Institute of Science (Rehovot, Israel), are the senior authors of the research, which was published September 2, 2010 in the journal Nature. Michael Kertesz, Ph.D., previously at the Weizmann Institute and currently a postdoctoral scholar in Stanford's department of bioengineering, and Stanford graduate student Yue Wan are the cofirst authors.

The researchers exploited the recent advance of deep-sequencing techniques that allow scientists to sequence simultaneously millions of nucleotide fragments for their analysis. They treated the pool of more than 3,000 protein-encoding RNA molecules from Saccharomyces cerevisiae, with structure-specific enzymes. They then sequenced the fragments and pieced together the structure of each RNA molecule in a process they call parallel analysis of RNA structure (PARS). "It's now possible to look at RNA structure much more quickly and comprehensively,” said Dr. Chang. "Now we can see patterns that were not previously evident, and begin to categorize RNAs by structure rather than sequence.”

Some of the patterns identified were surprising. The researchers discovered that regions of RNA that encode specific instructions for protein tend to have more secondary structure than do other regions, and that it is possible to identify the beginning, middle, and end of an RNA transcript simply by analyzing its structure. Finally, they found that RNA molecules that had similar functions often have similar structures--possibly to direct them better to specific locations within the cell.

The researchers assessed their technique on S. cerevisiae because it is a well-known organism with a relatively limited number of RNA molecules in action at any one time—about 3,000 (vs. 10,000 in humans). However, they plan to evaluate other organisms soon, and expand their analysis to include regulatory RNAs that do not carry protein-building instructions. "There's so much more information to be discovered,” said Dr. Chang. "This is just a snapshot of RNAs in isolation. But we can leverage this information for biological insight into how RNA structures may change under different conditions. There are levels of complexity that we're only just beginning to understand.”

The researchers are also developing a searchable website (please see related links below) with their data in addition to the iPhone (developed by Apple, Inc., Cupertino, CA, USA) application.


Related Links:
Stanford University
Weizmann Institute of Science
Weizmann Institute Segal Lab: PARS 2010