Publications - Published papers

Please find below publications of our group. Currently, we list 53 papers. Some of the publications are in collaboration with the group of Peter Stadler and are also listed in the publication list for his group. Access to published papers (access) is restricted to our local network and chosen collaborators.
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Processed Small RNAs in Archaea and BHB Elements

Sarah J. Berkemer, Christian Höner zu Siederdissen, Fabian Amman, Axel Wintsche, Sebastian Will, Ivo L. Hofacker, Sonja J. Prohaska, Peter F. Stadler


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GCB, Vol. 1, No. 1 (2015): e18


Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piece-wise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although Archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB-elements of a phylogenetically diverse set of Archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is a least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to indentify common sequence and/or secondary structure features that could be characteristic for such a mechanism.