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Nematode sbRNAs: Homologs of vertebrate Y RNAs

: Boria, I.; Gruber, A.R.; Tanzer, A.; Bernhart, S.H.; Lorenz, R.; Mueller, M.M.; Hofacker, I.L.; Stadler, P.F.


Journal of molecular evolution 70 (2010), No.4, pp.346-358
ISSN: 0022-2844
ISSN: 1432-1432
Journal Article
Fraunhofer IZI ()
sbRNA; nematode; Y-RNA; homology search; noncoding RNA

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.