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Biological Chemistry

Editor-in-Chief: Brüne, Bernhard

Editorial Board Member: Buchner, Johannes / Lei, Ming / Ludwig, Stephan / Sies, Helmut / Turk, Boris / Wittinghofer, Alfred

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Traces of post-transcriptional RNA modifications in deep sequencing data

Sven Findeiß
  • Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelsrtraße 16-18, D-04107 Leipzig, Germany
/ David Langenberger
  • Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelsrtraße 16-18, D-04107 Leipzig, Germany
  • LIFE, Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
/ Peter F. Stadler
  • Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelsrtraße 16-18, D-04107 Leipzig, Germany
  • LIFE, Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
  • Max-Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
  • Fraunhofer Institut für Zelltherapie und Immunologie, Perlickstraße 1, D-04103 Leipzig, Germany
  • Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, A-1090 Wien, Austria
  • Center for non-coding RNA in Technology and Health, University of Copenhagen, Gønnegårdsvej 3, 1870 Frederiksberg C, Denmark
  • Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
  • :
/ Steve Hoffmann
  • Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelsrtraße 16-18, D-04107 Leipzig, Germany
  • LIFE, Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
Published Online: 2011-07-25 | DOI: https://doi.org/10.1515/bc.2011.043

Abstract

Many aspects of the RNA maturation leave traces in RNA sequencing data in the form of deviations from the reference genomic DNA. This includes, in particular, genomically non-encoded nucleotides and chemical modifications. The latter leave their signatures in the form of mismatches and conspicuous patterns of sequencing reads. Modified mapping procedures focusing on particular types of deviations can help to unravel post-transcriptional modification, maturation and degradation processes. Here, we focus on small RNA sequencing data that is produced in large quantities aimed at the analysis of microRNA expression. Starting from the recovery of many well known modified sites in tRNAs, we provide evidence that modified nucleotides are a pervasive phenomenon in these data sets. Regarding non-encoded nucleotides we concentrate on CCA tails, which surprisingly can be found in a diverse collection of transcripts including sub-populations of mature microRNAs. Although small RNA sequencing libraries alone are insufficient to obtain a complete picture, they can inform on many aspects of the complex processes of RNA maturation.

Keywords: CCA enzyme; high throughput sequencing; microRNAs; RNA editing; RNA modification; tRNAs

Corresponding author


Published Online: 2011-07-25

Published in Print: 2011-04-01


Citation Information: Biological Chemistry. Volume 392, Issue 4, Pages 305–313, ISSN (Online) 1437-4315, ISSN (Print) 1431-6730, DOI: https://doi.org/10.1515/bc.2011.043, July 2011

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