Publications - Published papers

Please find below publications of our group. Currently, we list 501 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.

Evolution of vault RNAs

Peter F. Stadler, Julian J.-L. Chen, Jörg Hackermüller, Steve Hoffmann, Friedemann Horn, Phillip Khaitovich, Antje Kretzschmar, Axel Mosig, Sonja J. Prohaska, Xiaodong Qi, Katharina Schutt, Kerstin Ullmann

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Mol Biol Evol. 2009; 26(9):1975-91

Abstract


Vault RNAs (vRNAs) are small, about 100nt long, poly-III transcripts contained in the vault particles of eukaryotic cells. Presumably due to their enigmatic function they have received little attention compared to other ncRNA families. Here we report on a systematic study of this rapidly evolving class of ncRNAs in Deuterostomia, providing a comprehensive collection of computationally predicted vRNA genes. Previously known vRNAs are located at a conserved location linked to the protocadherin gene cluster, an association that is conserved throughout gnathostomes. Lineage specific expansion to small vRNA gene clusters are frequently observed at this locus. Expression of several paralogous vRNA genes, most but not all located at the canonical syntenically conserved locus, was verified by RT-PCR in both zebrafish and medaka. Homology search furthermore identifies an additional vRNA gene in eutheria that was misclassified as a microRNA. Lineage specific loss of one of the two loci in several eutherian lineages supports the annotation as novel vRNA. The comparative analysis of the promoter structure shows substantial differences between the two eutherian vRNA types, explaining their differential expression patterns in human cancer cell lines.