RNA helix indexes as a tool for RNA folding space analysis

• Applicant: Professor Dr. Björn Voß
• Subject Area: Bioinformatics and Theoretical Biology
• Term: from 2009 to 2013
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 164256295

• Final Report Year: 2014

Final Report Abstract

In the course of this project we developed various algorithms to study the structure of RNA. This is interesting, especially in the light of the discovery that RNA is much more than a passive information carrier from the DNA to proteins. RNA not encoding a protein (non-coding RNA, ncRNA) is the major transcriptional output in pro- and eukaryotes and serves many, mainly regulatory functions. With the help of our tools it is possible to study ncRNAs in various manners. One can predict distinct suboptimal structures, i.e., hishapes, to figure out functionally important conformations. Using HiPath2 and HiTeD one can compare these conformations based on barrier energy and structural similarity, respectively. HiPath2 also serves as the basis for our folding kinetics simulator HiKinetics, which simulates the structural dynamics in time. Finally, we developed variants of all these methods to study families of related RNAs. These methods exploit information about evolutionary conservation, which improves their performance. Preliminary results suggest that our methods may be helpful in the identification and analysis of riboswitches [8] and other RNA elements, whose function is based on substantial conformational changes. Furthermore, due to high-throughput methods, like RNA-seq, the number of known ncRNAs is and will be growing quickly and bioinformatics tools for their analysis are needed. Our algorithms will help to fill this gap.

Publications

• (2011) RNAHeliCes – Folding space analysis based on position aware structure abstraction. In Proceedings of the German Conference on Bioinformatics 2011 (GCB 2011).p. RT–31
  Huang, J. and Voß, B.
  
• (2012) Abstract folding space analysis based on helices. RNA, 18, 2135–2147
  Huang, J., Backofen, R. and Voß, B.
  (See online at https://doi.org/10.1261/rna.033548.112)
• (2012) Folding space analysis: Abstraction and Filtering. Benasque RNA Meeting 2012
  Voß, B.
  
• (2012) Reducing the search space in RNA helix based folding. European Conference on Computational Biology (ECCB) 2012
  Huang, J. and Voß, B.
  
• (2014) Analysing RNA-kinetics based on folding space abstraction. BMC Bioinformatics, 15, 60-74
  Huang, J. and Voß, B.
  (See online at https://doi.org/10.1186/1471-2105-15-60)