Talk abstracts
Talk on Friday 01:30-01:45pm submitted by Joshua Hatterschide
RiboCAT, a new RNA probing data analysis tool: Development and application to probing secondary structure of HTLV-1 5’UTR
Joshua Hatterschide (Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University), William Cantara (Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University), Weixin Wu (Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University), Karin Musier-Forsyth (Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University)
Abstract:
Human T-cell leukemia virus type-1 (HTLV-1) is the only retrovirus other than HIV known to cause human disease. Despite the well-known importance of genomic RNA (gRNA) elements in other retroviruses, comparatively little is known about the structure and function of HTLV-1 gRNA. We used selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) to probe the structure of the functionally important HTLV-1 5’ untranslated region (5’UTR). To facilitate processing of the large amount of data generated by capillary electrophoresis sample analysis, RiboCAT (Ribonucleic acid Capillary-electrophoresis Analysis Tool) and RiboDOG (RiboCAT Data Output Generator) were developed as user-friendly, Microsoft Excel-based tools. Relative to the most popular current software, QuShape, these new tools significantly reduce the time required for manual intervention during data analysis. This is accomplished with improvements to the algorithms used in RNA probing data processing and through the open architecture of Excel, which allows for simple user intervention. To validate these new tools, the secondary structure of the HIV-1 5′UTR was first determined by SHAPE, matching the results of previous work (Wilkinson et al, PLoS Biol, 2008). Finally, SHAPE/RiboCAT was used to determine the secondary structure of the HTLV-1 5’UTR, revealing RNA functional elements that include a new putative dimerization initiation site, the architecture of the primer binding site, and sites of HTLV-1 matrix protein binding.
References:
Wilkinson KA, Gorelick RJ, Vasa SM, Guex N, Rein A, Mathews DH, Giddings MC, Weeks KM. 2008. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol 6: e96.
Keywords: RNA Probing, SHAPE, HTLV-1