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Nucleic Acids Research Advance Access originally published online on August 9, 2006
Nucleic Acids Research 2006 34(14):3842-3852; doi:10.1093/nar/gkl448
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Nucleic Acids Research, 2006, Vol. 34, No. 14 3842-3852
© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Identification of small non-coding RNAs from mitochondria and chloroplasts

Birgit Lung, Anja Zemann1, Monika J. Madej, Markus Schuelke2, Sandra Techritz2, Stephanie Ruf3, Ralph Bock3,* and Alexander Hüttenhofer*

Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria 1 Institut für Experimentelle Pathologie/Molekulare Neurobiologie (ZMBE), Universität Münster Von-Esmarch Strasse 56, 48149 Münster, Germany 2 Department of Neuropediatrics, Charité University Hospital Augustenburger Platz 1, D-13353 Berlin, Germany 3 Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1 D-14476, Potsdam-Golm, Germany

*To whom correspondence should be addressed. Tel: +43 512 9003 70250; Fax: +43 512 9003 73100; Email: alexander.huettenhofer{at}i-med.ac.at

Received April 26, 2006. Revised June 12, 2006. Accepted June 12, 2006.

Small non-protein-coding RNAs (ncRNAs) have been identified in a wide spectrum of organisms ranging from bacteria to humans. In eukarya, systematic searches for ncRNAs have so far been restricted to the nuclear or cytosolic compartments of cells. Whether or not small stable non-coding RNA species also exist in cell organelles, in addition to tRNAs or ribosomal RNAs, is unknown. We have thus generated cDNA libraries from size-selected mammalian mitochondrial RNA and plant chloroplast RNA and searched for small ncRNA species in these two types of DNA-containing cell organelles. In total, we have identified 18 novel candidates for organellar ncRNAs in these two cellular compartments and confirmed expression of six of them by northern blot analysis or RNase A protection assays. Most candidate ncRNA genes map to intergenic regions of the organellar genomes. As found previously in bacteria, the presumptive ancestors of present-day chloroplasts and mitochondria, we also observed examples of antisense ncRNAs that potentially could target organelle-encoded mRNAs. The structural features of the identified ncRNAs as well as their possible cellular functions are discussed. The absence from our libraries of abundant small RNA species that are not encoded by the organellar genomes suggests that the import of RNAs into cell organelles is of very limited significance or does not occur at all.

*Correspondence may also be addressed to Ralph Bock. Tel: +49 331 567 8700; Fax: +49 331 567 8701; Email: rbock{at}mpimp-golm.mpg.de


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