Featured Research

from universities, journals, and other organizations

New app shows 2-D structure of thousands of RNA molecules

Date:
September 2, 2010
Source:
Stanford University Medical Center
Summary:
For the first time, it's possible to experimentally capture a global snapshot of the conformation of thousands of RNA molecules in a cell. The finding is important because this scrappy little sister of DNA has recently been shown to be much more complex than previously thought.

"There's an app for that." To a cadre of scientists, the familiar phrase will soon mean they can enter a specific RNA from baker's yeast into their iPhone and see a depiction of its two-dimensional structure -- thanks to a new technology developed by scientists at Stanford University.

The application is cool, but it's just window dressing for the real advance: For the first time, it's possible to experimentally capture a global snapshot of the conformation of thousands of RNA molecules in a cell. The finding is important because this scrappy little sister of DNA has recently been shown to be much more complex than previously 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, MD, PhD. "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."

Chang, who was selected last year as a Howard Hughes Medical Institute Early Career Scientist, and Eran Segal, PhD, of the Weizmann Institute of Science in Israel, are the senior authors of the research, which will be published Sept. 2 in Nature. Michael Kertesz, PhD, previously at the Weizmann Institute and currently a postdoctoral scholar in Stanford's Department of Bioengineering, and Stanford graduate student Yue Wan are co-first authors.

For years, RNA was known only for its role in shuttling information in the form of nucleotide sequences from the DNA in a cell's nucleus to the protein factories in the cytoplasm. Now we know that RNAs control many aspects of gene regulation and function.

In comparison to DNA -- a relatively inflexible, double strand of paired nucleotides that spiral around one another in a helix formation -- RNA is a veritable circus contortionist. It can fold back on itself to form stem and loop structures, and these structures can bind to one another in pseudoknots, which can twist around and ... well, you get the idea. Until now, the only way to know what shape a particular RNA molecule preferred was to conduct a laborious series of experiments focused on just that molecule. But the effort was necessary to fully understand what it might be doing in the cell.

The researchers capitalized on the recent development of deep-sequencing techniques that allow scientists to simultaneously sequence millions of nucleotide fragments for their analysis. They treated the pool of more than 3,000 protein-encoding RNA molecules from Saccharomyces cerevisiae, also known as baker's yeast, with structure-specific enzymes (one cleaves only single-stranded nucleotides at specific sequences and while another cleaves only double-stranded, or paired, RNA sequences). They then sequenced the fragments and pieced together the structure of each RNA molecule in a process they call "parallel analysis of RNA structure" or PARS.

"It's now possible to look at RNA structure much more quickly and comprehensively," said 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 they identified were surprising. The researchers found 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 -- perhaps to better direct them to specific locations within the cell.

The researchers tested their technique on baker's yeast because it is a well-studied organism with a relatively limited number of RNA molecules in action at any one time (about 3,000 vs. 10,000 in humans). But they plan to tackle other organisms soon, and to expand their analysis to include regulatory RNAs that don't carry protein-building instructions.

"There's so much more information to be discovered," said 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 (http://genie.weizmann.ac.il/pubs/PARS10/index.html) with their data. And then there's that iPhone application. "Now you can use your phone to look up structures and pull up RNA sequences," said Chang.

In addition to the researchers at the Weizmann Institute, Stanford's scientists collaborated with colleagues at Harvard's Broad Institute and Life Technology in Foster City, Calif. The research was supported by the National Institutes of Health and Howard Hughes Medical Institute.


Story Source:

The above story is based on materials provided by Stanford University Medical Center. Note: Materials may be edited for content and length.


Cite This Page:

Stanford University Medical Center. "New app shows 2-D structure of thousands of RNA molecules." ScienceDaily. ScienceDaily, 2 September 2010. <www.sciencedaily.com/releases/2010/09/100901132151.htm>.
Stanford University Medical Center. (2010, September 2). New app shows 2-D structure of thousands of RNA molecules. ScienceDaily. Retrieved April 17, 2014 from www.sciencedaily.com/releases/2010/09/100901132151.htm
Stanford University Medical Center. "New app shows 2-D structure of thousands of RNA molecules." ScienceDaily. www.sciencedaily.com/releases/2010/09/100901132151.htm (accessed April 17, 2014).

Share This



More Health & Medicine News

Thursday, April 17, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Is Apathy A Sign Of A Shrinking Brain?

Is Apathy A Sign Of A Shrinking Brain?

Newsy (Apr. 17, 2014) A recent study links apathetic feelings to a smaller brain. Researchers say the results indicate a need for apathy screening for at-risk seniors. Video provided by Newsy
Powered by NewsLook.com
Could Even Casual Marijuana Use Alter Your Brain?

Could Even Casual Marijuana Use Alter Your Brain?

Newsy (Apr. 16, 2014) A new study conducted by researchers at Northwestern and Harvard suggests even casual marijuana use can alter your brain. Video provided by Newsy
Powered by NewsLook.com
Thousands Of Vials Of SARS Virus Go Missing

Thousands Of Vials Of SARS Virus Go Missing

Newsy (Apr. 16, 2014) A research institute in Paris somehow misplaced more than 2,000 vials of the deadly SARS virus. Video provided by Newsy
Powered by NewsLook.com
Formerly Conjoined Twins Released From Dallas Hospital

Formerly Conjoined Twins Released From Dallas Hospital

Newsy (Apr. 16, 2014) Conjoined twins Emmett and Owen Ezell were separated by doctors in August. Now, nearly nine months later, they're being released from the hospital. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins