Publications - Published papers

Please find below publications of our group. Currently, we list 500 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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Nematode sbRNAs: homologs of vertebrate Y RNAs

Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan Bernhart, Ronny Lorenz, Michael M. Mueller, Ivo L. Hofacker, Peter F. Stadler


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J. Mol. Evol. 70: 346-358 (2010)


Stem bulge RNAs (sbRNAs) are a group of small, functionally yet uncharacterized noncoding RNAs found initially in C. elegans with a few homologous sequences postulated in C. briggsae. In this study we report on a comprehensive homology-based survey of this ncRNA family in the phylum Nematoda, resulting in a total of 233 new sbRNA homologs. For the majority of these hits promoter regions and transcription termination signals characteristic for pol-III transcripts were identified. Surprisingly, 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 have in addition 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.


sbRNA, nematodes, Y RNA, homology search, noncoding RNA