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 at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa.de:bsz:15-qucosa-185322 |
| Date | 27 October 2015 |
| Creators | Berkemer, Sarah J., Höner zu Siederdissen, Christian, Amman, Fabian, Wintsche, Axel, Will, Sebastian, Hofacker, Ivo L., Prohaska, Sonja J., Stadler, Peter F. |
| Contributors | Universität Leipzig, Bioinformatik, Universität Wien, Institut für Theoretische Chemie, Universität Leipzig, Computational EvoDevo, Universität Leipzig, Interdisziplinäres Zentrum für Bioinformatik (IZBI), Universität Wien, Bioinformatics and Computational Biology, University of Copenhagen, Center for non-coding RNA in Technology and Health, Max-Planck-Institut für Mathematik,, Fraunhofer-Institut für Zelltherapie und Immunologie IZI,, Santa Fe Institute,, Kernel Press UG, |
| Publisher | Universitätsbibliothek Leipzig |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | doc-type:article |
| Format | application/pdf |
| Source | Genomics and computational biology Vol. 1, No. 1 (2015): e18 |
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