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 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”.
- Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud MC, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, Flutre T, Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G, Poulain J, Robinson-Rechavi M, Sallet E, Ségurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso MN, Schiex T, Smant G, Weissenbach J, Wincker P (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol 26:909–915CrossRefPubMedGoogle Scholar
- Deng W, Zhu X, Skogerbø G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R (2006) Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression. Genome Res 16:20–29CrossRefPubMedGoogle Scholar
- Mosig A, Chen JL, Stadler PF (2007b) Homology search with fragmented nucleic acid sequence patterns. In: Giancarlo R, Hannenhalli S (eds) Algorithms in bioinformatics (WABI 2007), Volume 4645 of Lecture Notes in Computer Science. Springer Verlag, Berlin, Heidelberg, pp 335–345Google Scholar
- Sönnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Röder M, Finell J, Häntsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gönczy P, Coulson A, Hyman AA, Echeverri CJ (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434:462–469CrossRefPubMedGoogle Scholar
- Sudhaus W, Kiontke K (2007) Comparison of the cryptic nematode species Caenorhabditis brenneri sp. n. and C. remanei (Nematoda: Rhabditidae) with the stem species pattern of the Caenorhabditis elegans group. Zootaxa 1456:45–62Google Scholar
- Tanzer A, Stadler PF (2006) Evolution of MicroRNAs. In: Ying SY (ed) MicroRNA protocols. Humana Press, Totowa, NJ, pp 335–350Google Scholar