Publications - Published papers

Please find below publications of our group. Currently, we list 508 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

Temperature-Dependent Structural Variability of RNAs: Spliced Leader RNAs and their Evolutionary History

Manja Marz, Nathalie Vanzo, Peter F. Stadler

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J Bioinform Comput Biol. 8: 1-17 (2010)

Abstract


The structures attained by RNA molecules depend not only on their sequence but also on environmental parameters such as their structure. So far, this effect has been largely neglected in bioinformatics studies. Here we show that structural comparisons can be facilitated and more coherent structural models can be obtained when differences in environmental parameters are taken into account. We re-evaluate the secondary structures of the spliced leader RNAs from the seven eukaryotic phyla in which SL RNA \emph{trans}-splicing has been described. Adjusting structure prediction to the natural growth temperatures and considering energetically similar secondary structures we observe striking similarities among Euglenida, Kinetoplastida, Dinophyceae, Cnidaria, Rotifera, Nematoda, Platyhelminthes, and Tunicata that cannot be explained easily by the independent innovation of SL RNAs in each of these phyla.

Keywords


RNA folding; temperature dependence; SL RNA; trans-splicing; evolution