Journal of Molecular Evolution

, Volume 70, Issue 4, pp 346–358 | Cite as

Nematode sbRNAs: Homologs of Vertebrate Y RNAs

  • Ilenia Boria
  • Andreas R. Gruber
  • Andrea Tanzer
  • Stephan H. Bernhart
  • Ronny Lorenz
  • Michael M. Mueller
  • Ivo L. Hofacker
  • Peter F. StadlerEmail author


Stem-bulge RNAs (sbRNAs) are a group of small, functionally yet uncharacterized noncoding RNAs first described in C. elegans, with a few homologous sequences postulated in C. briggsae. In this study, we report on a comprehensive survey of this ncRNA family in the phylum Nematoda. Employing homology search strategies based on both sequence and secondary structure models and a computational promoter screen we identified a total of 240 new sbRNA homologs. For the majority of these loci we identified both promoter regions and transcription termination signals characteristic for pol-III transcripts. Sequence and structure comparison with known RNA families revealed that sbRNAs are homologs of vertebrate Y RNAs. Most of the sbRNAs show the characteristic Ro protein binding motif, and contain a region highly similar to a functionally required motif for DNA replication previously thought to be unique to vertebrate Y RNAs. The single Y RNA that was previously described in C. elegans, however, does not show this motif, and in general bears the hallmarks of a highly derived family member.


sbRNA Nematodes Y RNA Homology search Noncoding RNA 



This research originated from an RNA Bioinformatics course at the University of Vienna in the fall semester 2008. Subsequently, it was then funded in part by the Austrian GEN-AU projects “Bioinformatics Integration Network III” and “Noncoding RNA”, the AMS Vienna and the DFG under the auspices of the SPPs 1174 “Deep Metazoan Phylogeny” and 1258 “Sensory and Regulatory RNAs”.

Supplementary material

239_2010_9332_MOESM1_ESM.pdf (189 kb)
Structure evolution of sbRNA loop regions. Gene duplication coincides with duplication of substructures within the loops regions as shown here for members ofthe long sbRNAs residing on C. elegans chromosome V. The ancestral gene of this family possibly consisted of four hairpins. During subsequent gene duplications,individual hairpins were lost. The hairpin B (yellow) shows high sequence similarity to the adjacent hairpin A (green) and probably arose by local duplication of astructural element. A,B,C,D: RNA secondary structures of representatives of each family. family ABCD: Cn4 (A); family AB_D: CeN73_1 (B); family A_CD: Cn8(C); family _BCD: Cr26 (D). (E) hand curated CLUSTAL W multiple sequence alignments including the consensus structure and location of structural motifs. PDF (188 KB)
239_2010_9332_MOESM2_ESM.eps (623 kb)
EPS (624 KB)


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Ilenia Boria
    • 1
    • 2
  • Andreas R. Gruber
    • 2
    • 3
  • Andrea Tanzer
    • 2
    • 3
  • Stephan H. Bernhart
    • 2
  • Ronny Lorenz
    • 2
  • Michael M. Mueller
    • 4
  • Ivo L. Hofacker
    • 2
  • Peter F. Stadler
    • 2
    • 3
    • 5
    • 6
    • 7
    Email author
  1. 1.Department of Medical Sciences and Interdisciplinary Research Centre for Autoimmune DiseasesUniversità del Piemonte OrientaleNovaraItaly
  2. 2.Institute for Theoretical ChemistryUniversity of ViennaWienAustria
  3. 3.Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for BioinformaticsUniversity of LeipzigLeipzigGermany
  4. 4.Department of Chromosome Biology, Max F. Perutz LaboratoriesUniversity of ViennaViennaAustria
  5. 5.Max-Planck Institute for Mathematics in the SciencesLeipzigGermany
  6. 6.Fraunhofer Institut für Zelltherapie und Immunologie (IZI)LeipzigGermany
  7. 7.Santa Fe InstituteSanta FeUSA

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