Nematode sbRNAs: Homologs of Vertebrate Y RNAs

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...

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Bibliographic Details
Published in:Journal of molecular evolution 2010-04, Vol.70 (4), p.346-358
Main Authors: Boria, Ilenia, Gruber, Andreas R, Tanzer, Andrea, Bernhart, Stephan H, Lorenz, Ronny, Mueller, Michael M, Hofacker, Ivo L, Stadler, Peter F
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Animals
Base Sequence
Biomedical and Life Sciences
Cell Biology
Chromosomes
Evolutionary Biology
Genes, Helminth
Genomics
Homology search
Humans
Life Sciences
Microbiology
Molecular biology
Molecular Sequence Data
Nematoda
Nematoda - genetics
Nematodes
Noncoding RNA
Nucleic Acid Conformation
Phylogenetics
Phylogeny
Plant Genetics and Genomics
Plant Sciences
Promoter Regions, Genetic
Ribonucleic acid
Ribonucleoproteins
RNA
RNA, Untranslated - genetics
sbRNA
Sequence Homology, Nucleic Acid
Synteny
Vertebrates
Y RNA
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Summary: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.
ISSN:0022-2844
1432-1432
DOI:10.1007/s00239-010-9332-4