Journal
JOURNAL OF MOLECULAR EVOLUTION
Volume 70, Issue 4, Pages 346-358Publisher
SPRINGER
DOI: 10.1007/s00239-010-9332-4
Keywords
sbRNA; Nematodes; Y RNA; Homology search; Noncoding RNA
Funding
- Austrian GEN-AU
- AMS Vienna
- DFG [SPPs 1174, 1258]
- Austrian Science Fund (FWF) [W1207] Funding Source: Austrian Science Fund (FWF)
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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.
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