Processed Small RNAs in Archaea and BHB Elements

  • Sarah Juliane Berkemer Bioinformatics Group Leipzig, Department of Computer Science, University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany
  • Christian Höner zu Siederdissen Bioinformatics Group Leipzig, Department of Computer Science, University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany
  • Fabian Amman Institute for Theoretical Chemistry, University of Vienna, Waehringer Str. 17, 1090 Wien, Austria
  • Axel Wintsche Computational EvoDevo, Bioinformatics, Department of Computer Science, University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany
  • Sebastian Will Bioinformatics Group Leipzig, Department of Computer Science, University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany
  • Ivo Hofacker Institute for Theoretical Chemistry, University of Vienna, Waehringer Str. 17, 1090 Wien, Austria
  • Sonja Prohaska Computational EvoDevo, Bioinformatics, Department of Computer Science, University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany
  • Peter Stadler Bioinformatics Group Leipzig, Department of Computer Science, University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany http://orcid.org/0000-0002-5016-5191

Abstract

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.

Published
2015-09-18
How to Cite
BERKEMER, Sarah Juliane et al. Processed Small RNAs in Archaea and BHB Elements. Genomics and Computational Biology, [S.l.], v. 1, n. 1, p. e18, sep. 2015. ISSN 2365-7154. Available at: <https://genomicscomputbiol.org/ojs3/GCB/article/view/2>. Date accessed: 25 june 2019. doi: https://doi.org/10.18547/gcb.2015.vol1.iss1.e18.
Section
Research Articles