Nucleic Acids Research Advance Access originally published online on March 16, 2008
Nucleic Acids Research 2008 36(8):2677-2689; doi:10.1093/nar/gkn123
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Nucleic Acids Research, 2008, Vol. 36, No. 8 2677-2689
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis
1Innsbruck Biocenter, Division of Genomics and RNomics – Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, 2Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Wien, Austria, 3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Hartelstraße 16-18, D-04107 Leipzig, Germany, 4Santa Fe Institute, Santa Fe, NM 87501, USA, 5Fraunhofer Institut fuer Zelltherapie und Immunologie,Deutscher Platz 5e, 04103 Leipzig, Germany and 6Innsbruck Biocenter, Division of Molecular Biology – Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria
*To whom correspondence should be addressed. Tel: +43 512 9003 70250; Fax: +43 512 9003 73100; Email: alexander.huettenhofer{at}i-med.ac.at Correspondence may also be addressed to Hubertus Haas. Tel: +43 512 9003 70205; Email: hubertus.haas{at}i-med.ac.at
Received December 7, 2007. Revised February 4, 2008. Accepted March 4, 2008.
Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the pathogenic filamentous fungus Aspergillus fumigatus. To that aim, we experimentally screened for ncRNAs, expressed under various growth conditions or during specific developmental stages, by generating a specialized cDNA library from size-selected small RNA species. Our screen revealed 30 novel ncRNA candidates from known ncRNA classes such as small nuclear RNAs (snRNAs) and C/D box-type small nucleolar RNAs (C/D box snoRNAs). Additionally, several candidates for H/ACA box snoRNAs could be predicted by a bioinformatical screen. We also identified 15 candidates for ncRNAs, which could not be assigned to any known ncRNA class. Some of these ncRNA species are developmentally regulated implying a possible novel function in A. fumigatus development. Surprisingly, in addition to full-length tRNAs, we also identified 5'- or 3'-halves of tRNAs, only, which are likely generated by tRNA cleavage within the anti-codon loop. We show that conidiation induces tRNA cleavage resulting in tRNA depletion within conidia. Since conidia represent the resting state of A. fumigatus we propose that conidial tRNA depletion might be a novel mechanism to down-regulate protein synthesis in a filamentous fungus.
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