Nematode sbRNAs: Homologs of Vertebrate Y RNAs
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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.
KeywordssbRNA 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”.
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