TBI-p-2010-6

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Titel:
Nematode sbRNAs: homologs of vertebrate Y RNAs

Author(s):
Ilenia Boria , Andreas R. Gruber , Andrea Tanzer , Stephan H. Bernhart, Ronny Lorenz, Michael M. Mueller, Ivo L. Hofacker, Peter F. Stadler

submitted to:
J Mol Evol. 70(4):346-58 (2010).

Abstract:
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.


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