Navigation Links
Researchers discover the structural alphabet of RNA
Date:3/6/2008

This release is available in French.

A team of bioinformaticians at the Universit de Montral (UdeM) report in the March 6th edition of Nature the discovery of a structural alphabet that can be used to infer the 3D structure of ribonucleic acid (RNA) from sequence data, providing new tools to understand the role of this important class of cellular regulators.

The folding of a single-stranded RNA molecule is determined by the interactions between its constituent nucleotides. The classical approach to RNA modelling suffers from an important limitation: it only takes into account the canonical Watson-Crick interactions A:U and G:C, that is those where the nucleotides are facing each other. The non-canonical Hoogsteen and sugar interactions, those where the nucleotides are side by side or on top of each other, are not taken into account by conventional modelling algorithms. The result can be incomplete or erroneous models which can mislead researchers.

The attempt to remedy this problem led Franois Major, principal investigator at the Institute for Research in Immunology and Cancer of the UdeM and professor in the Department of Computer Science and Operations Research and Marc Parisien, a graduate student in his laboratory, to propose a radically different approach to model RNA structure. Their idea: assemble the structure in silico starting from motifs that combine all the possible interactions between a nucleotide and its neighbors.

The researchers implemented a first algorithm, MC-Fold, that systematically assigns the different motifs to each segment of the sequence and selects the most probable pair based on its frequency in known structures. A second algorithm, MC-Sym, then assembles the set of selected motifs, taking into account the constraints that are found in known structures.

"We introduced a new first-order object to represent nucleotide relationships, the nucleotide cyclic motif (NCM). We reasoned that using NCMs could allow us to arrive at better models of the 3D structure of RNA molecules, " explains Franois Major. "Compared to the thermodynamic approach, our algorithms make less false positives and negatives and predict structures that are closer to the empirical data in the case of sequences for which it is available. The improvement is due to the fact that NCMs incorporate more base-pairing context-dependent information."

The biological importance of RNA and the growing recognition of its therapeutic potential mean that the new modelling algorithms have many applications in biomedical research. For instance, Major and Parisien have shown that these tools can be used to study the biology of RNA viruses such as HIV. They have also used the MC-Fold:MC-Sym pipeline to identify microRNAs, an important class of regulatory molecules which is currently the focus of intense investigation. microRNAs inhibit target genes both efficiently and specifically and are often considered to be the next generation of therapeutic agents. Since microRNAs are notoriously difficult to identify based on sequence alone, the use of RNA modelling algorithms and structural features to do so represents an important breakthrough.


'/>"/>

Contact: Christian Lanctt
christian.lanctot@umontreal.ca
514-343-7770
University of Montreal
Source:Eurekalert

Related biology news :

1. Researchers identify proteins involved in new neurodegenerative syndrome
2. Texas researchers and educators head for Antarctica
3. MGH researchers describe new way to identify, evolve novel enzymes
4. University of Pennsylvania researchers develop formula to gauge risk of disease clusters
5. U of MN researchers discover noninvasive diagnostic tool for brain diseases
6. U of Minnesota researchers discover noninvasive diagnostic tool for brain diseases
7. Researchers discover new strategies for antibiotic resistance
8. Researchers find new taste in fruit flies: carbonated water
9. Binghamton University researchers investigate evolving malaria resistance
10. UIC researchers find promising new targets for antibiotics
11. Researchers develop simple method to create natural drug products
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:1/19/2017)... PUNE, India , January 19, 2017 According to ... Market, Opportunities and Forecast, 2014 - 2022," the global biometric sensor market is ... from 2016 to 2022. In 2015, Asia-Pacific dominated the ... public and private sectors. Continue Reading ... ...
(Date:1/18/2017)... Md. , Jan. 18, 2017  In vitro ... respect to mergers and acquisitions (M&A), and Kalorama Information ... for such acquisitions have been shifting. Generally, uncertainty in ... and the U.S. has changed the acquisitions landscape. ... has resulted in companies buying partners outside of their ...
(Date:1/13/2017)... 13, 2017 Sandata Technologies, LLC, a ... homecare industry, including Electronic Visit Verification™ (EVV™), announced ... Jugs, as Senior Vice President of Product Management. ... of homecare experience to Sandata, where he will ... to align Sandata,s suite of solutions with the ...
Breaking Biology News(10 mins):
(Date:1/21/2017)... Colo. , Jan. 20, 2017 ... or the "Company"), announced that on January 14, 2017 ... plan under which the Company will terminate certain employees ... Bioptix Diagnostics, Inc.  The Company commenced terminations on January ... within 30 days.  The Company may pay severance benefits ...
(Date:1/21/2017)... , Jan. 21, 2017   Boston Biomedical , ... designed to target cancer stemness pathways, today presented data ... napabucasin, at the 2017 American Society of Clinical Oncology ... . In a Phase Ib/II ... designed to inhibit cancer stemness pathways by targeting STAT3 ...
(Date:1/20/2017)... , January 20, 2017 Stock-Callers.com ... conditions have influenced the most recent performances of select ... (NASDAQ: RGLS ), Abeona Therapeutics Inc. (NASDAQ: ... TBPH ), and Sage Therapeutics Inc. (NASDAQ: ... by Grand View Research, global Biotech market size is expected to ...
(Date:1/20/2017)... NEW YORK , January 20, 2017 ... Health Organization, cancer is one of leading causes of ... in 2012. Although the number of cancer related deaths ... since 1990. Rising in incidence rate of various cancers ... According to a research report by Global Market Insights, ...
Breaking Biology Technology: