Sequence and Structural Patterns in RNA

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"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)."Purdue University is awarded a grant to implement a complete informatics system for identifying conserved RNA structure topologies, and for finding new examples of similar topologies in sequence databases. This will allow RNA researchers the same loop of hypothesis/search/hypothesis-refinement that has been so powerful for DNA and proteins.RNA plays a central role in core biochemical process such as translation, RNA-splicing, gene regulation, and viral infection. Once thought to be only a structural scaffold, it is now appreciated that RNA can also act as an enzyme on its own or in ribonucleoprotein complexes. However, advances in understanding the role that RNA plays in the cell has been hampered by the difficulty in experimentally determining and computationally analyzing RNA structures. Approaches based on identifying conserved structures have been extremely powerful in deducing functional properties of DNA and proteins. This is because it is the function of the molecule that makes the sequence appear conserved over evolutionary time. Unfortunately, a similar analysis has not been possible for RNA structures because the conservation acts at the level of the base-paired structure rather than that of sequence per se.Since many other biological problems, such as systems biology, regulatory circuits, and some kinds of intermolecular binding, have strong graphical components, the ideas and software developed in this project will significantly advance other areas of biological research. Graph mining is also an important subject in Computer Science and other disciplines, which may also benefit from this work.Broader impact activities during this project include the research of three PhD students, cross-trained in both Biology and Computer Science, on aspects of this project. Outreach to high schools will include modules on RNA topology structure. Software from this project will be made publically available: http://wiki.genomics.purdue.edu/index.php/Gribskov::Main