Evolution of vault RNAs

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

Research output: Contribution to journalArticle

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)1975-1991
Number of pages17
JournalMolecular biology and evolution
Volume26
Issue number9
DOIs
StatePublished - Sep 1 2009

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Keywords

  • Homology search
  • Micro RNA
  • RNA secondary structure
  • Vault RNA
  • Vault particle

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

Stadler, P. F., Chen, J., Hackermüller, J., Hoffmann, S., Horn, F., Khaitovich, P., Kretzschmar, A. K., Mosig, A., Prohaska, S. J., Qi, X., Schutt, K., & Ullmann, K. (2009). Evolution of vault RNAs. Molecular biology and evolution, 26(9), 1975-1991. https://doi.org/10.1093/molbev/msp112