Abstract

Nature has developed mechanisms to protect living organisms against external intruders such as viruses, or internal dysfunction leading to diseases, such as cancer. One such security mechanism is gene silencing, which is at the heart of organisms We aim to put these new powerful tools in the hands of the experimentalists, since rapidly and reliably producing RNA structures will yield immense benefits to the biomedical field's ability to understand and experiment with these recently discovered gene-silencing pathways.

Public Health Relevance

Accumulating evidence shows that RNA molecules are crucial players in the mechanisms that protect us against external intruders such as viruses, or internal dysfunction that leads to diseases. Determining RNA three-dimensional (3D) structures is key to study RNA function, but is costly and laborious using physical methods. In many ways, this situation hinders the RNA biomedical field, and the research here aims at providing to all computational tools to rapidly and reliably producing RNA 3D structures, yielding immense benefits to the researchers'ability to understand and manipulate RNAs including those in our own protection mechanisms.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM088813-01A1
Application #
7888537
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Preusch, Peter C
Project Start
2010-06-01
Project End
2015-05-31
Budget Start
2010-06-01
Budget End
2011-05-31
Support Year
1
Fiscal Year
2010
Total Cost
$203,138
Indirect Cost

  Institution

Name
University of Montreal
Department
Type
DUNS #
207622838
City
Montreal
State
PQ
Country
Canada
Zip Code
H3 3-J7

  Publications

Weill, Nathanaël; Lisi, Véronique; Scott, Nicolas et al. (2015) MiRBooking simulates the stoichiometric mode of action of microRNAs. Nucleic Acids Res 43:6730-8
Blanchet, Marc-Frédérick; St-Onge, Karine; Lisi, Véronique et al. (2014) Computational identification of RNA functional determinants by three-dimensional quantitative structure-activity relationships. Nucleic Acids Res 42:11261-71
Gkogkas, Christos G; Khoutorsky, Arkady; Ran, Israeli et al. (2013) Autism-related deficits via dysregulated eIF4E-dependent translational control. Nature 493:371-7
Parisien, Marc; Major, Francois (2012) Determining RNA three-dimensional structures using low-resolution data. J Struct Biol 179:252-60
Cruz, José Almeida; Blanchet, Marc-Frédérick; Boniecki, Michal et al. (2012) RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA 18:610-25
Reinharz, Vladimir; Major, Francois; Waldispuhl, Jerome (2012) Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics 28:i207-14
De Guire, Vincent; Caron, Maxime; Scott, Nicolas et al. (2010) Designing small multiple-target artificial RNAs. Nucleic Acids Res 38:e140
Yang, Sichun; Parisien, Marc; Major, Francois et al. (2010) RNA structure determination using SAXS data. J Phys Chem B 114:10039-48
Mullen, Melissa A; Olson, Kalee J; Dallaire, Paul et al. (2010) RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. Nucleic Acids Res 38:8149-63
Cruz-Toledo, Jose; Dumontier, Michel; Parisien, Marc et al. (2010) RKB: a Semantic Web knowledge base for RNA. J Biomed Semantics 1 Suppl 1:S2