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MBE Advance Access originally published online on June 2, 2009
Molecular Biology and Evolution 2009 26(9):1975-1991; doi:10.1093/molbev/msp112
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Evolution of Vault RNAs

Peter F. Stadler*,{dagger},{ddagger},§,||, Julian J.-L. Chen,#, Jörg Hackermüller{ddagger}, Steve Hoffmann*, Friedemann Horn{ddagger},**, Phillip Khaitovich{dagger}{dagger}, Antje K. Kretzschmar{ddagger}, Axel Mosig{dagger},{dagger}{dagger}, Sonja J. Prohaska*,§,||, Xiaodong Qi, Katharina Schutt{ddagger},** and Kerstin Ullmann{ddagger},**

* Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
{dagger} Max-Planck Institute for Mathematics in the Sciences, Leipzig, Germany
{ddagger} Fraunhofer Institut für Zelltherapie und Immunologie , Leipzig, Germany
§ Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
|| Santa Fe Institute, Santa Fe, New Mexico
Department of Chemistry and Biochemistry, Arizona State University
# School of Life Sciences, Arizona State University
** Institute of Clinical Immunology and Transfusion Medicine, Medical Faculty, University of Leipzig, Leipzig, Germany
{dagger}{dagger} CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, China

E-mail: studla{at}bioinf.uni-leipzig.de.

Accepted for publication May 14, 2009.

Vault RNAs (vtRNAs) are small, about 100 nt long, polymerase III transcripts contained in the vault particles of eukaryotic cells. Presumably due to their enigmatic function, they have received little attention compared with most other noncoding RNA (ncRNA) families. Their poor sequence conservation makes homology search a complex and tedious task even within vertebrates. Here we report on a systematic and comprehensive analysis of this rapidly evolving class of ncRNAs in deuterostomes, providing a comprehensive collection of computationally predicted vtRNA genes. We find that all previously described vtRNAs are located at a conserved genomic locus linked to the protocadherin gene cluster, an association that is conserved throughout gnathostomes. Lineage-specific expansions to small vtRNA gene clusters are frequently observed in this region. A second vtRNA locus is syntenically conserved across eutherian mammals. The vtRNAs at the two eutherian loci exhibit substantial differences in their promoter structures, explaining their differential expression patterns in several human cancer cell lines. In teleosts, expression of several paralogous vtRNA genes, most but not all located at the syntenically conserved protocadherin locus, was verified by reverse transcriptase–polymerase chain reaction.

Key Words: vault particle • vault RNA • micro RNA • homology search • RNA secondary structure

Hervé Philippe, Associate Editor


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