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MBE Advance Access published online on June 19, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn140
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© The Author 2008. 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 ARTICLE

Arthropod 7SK RNA

Andreas R. Gruber*,a, Carsten Kilgusb,h, Axel Mosigb,c, Ivo L. Hofackera, Wolfgang Hennigb,h and Peter F. Stadlerd,e,f,a,g,*

a Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
b Department of Combinatorics and Geometry (DCG), CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Shanghai, China
c Max Planck Insitute for Mathematics in the Sciences, Inselstrasse 22, D-04103 Leipzig, Germany
d Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
e Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
f Fraunhofer Institut für Zelltherapie und Immunologie — IZI, Perlickstrasse 1, D-04103 Leipzig, Germany
g Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
h Institut für Genetik, Johannes Gutenberg-Universität Mainz, J.-J.-Becherweg 32, 55099 Mainz,Germany

* corresponding author: Tel.: +43 5277 52731 Fax: +43 4277 52793. e-mail: agruber{at}tbi.univie.ac.at

Received for publication April 21, 2008. Revision received May 30, 2008. Accepted for publication June 16, 2008.

The 7SK snRNA is a key player in the regulation of polymerase II transcription. 7SK RNA was long believed to be specific to vertebrates where it is highly conserved. Homologs in basal deuterostomes and a few lophotrochozoan species were only recently reported. On longer time scales 7SK evolves rapidly with only few conserved sequence and structure motifs. Previous attempts to identify the Drosophila homolog thus have remained unsuccessful despite considerable efforts. Here we report on the discovery of arthropod 7SK RNAs using a novel search strategy based on polymerase III promoters, as well as the subsequent verification of its expression. Our results demonstrate that a 7SK snRNA featuring two highly structured conserved domains was present already in the bilaterian ancestor.

Key Words: 7SK snRNA • homology search • non-coding RNA


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