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Nucleic Acids Research Advance Access published online on February 7, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm004
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© 2007 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.

RNA

Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae

Monika J. Madej1, Juan D. Alfonzo2 and Alexander Hüttenhofer1,*

1Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria and 2Department of Microbiology, Ohio State Biochemistry Program and The RNA Group, The Ohio State University, 484 West 12th Ave., Columbus, OH 43210, USA

To whom correspondence should be addressed. Tel: +43(0) 512 9003 70250; Fax: +43(0) 512 9003 73100; Email: alexander.huettenhofer{at}i-med.ac.at Correspondence may also be addressed to Juan D. Alfonzo. Tel: +1 614 292 0004; Fax: +1 614 292 0141; Email: Alfonzo.1{at}osu.edu

Received October 17, 2006. Revised December 21, 2006. Accepted December 22, 2006.

Gene expression in mitochondria of kinetoplastid protozoa requires RNA editing, a post-transcriptional process which involves insertion or deletion of uridine residues at specific sites within mitochondrial pre-mRNAs. Sequence specificity of the RNA editing process is mediated by oligo-uridylated small, non-coding RNAs, designated as guide RNAs (gRNAs). In this study, we have analyzed the small ncRNA transcriptome from kinetoplast mitochondria of Leishmania tarentolae by generating specialized cDNA libraries encoding size-selected RNA species. Through this screen, a significant number of novel oligo-uridylated RNA species, which we have termed oU-RNAs, has been identified. Most novel oU-RNAs are present as stable RNA species in mitochondria as assessed by northern blot analysis. Thereby, novel oU-RNAs show similar expression levels and sizes as previously reported for canonical gRNAs. Several oU-RNAs are transcribed from both strands of the maxicircle and minicircles components of the mitochondrial genome, from regions where up till now no transcription has been reported. Two stable oU-RNAs exhibit an anchor sequence in antisense orientation to known gRNAs and thus might regulate editing of respective pre-mRNAs. A number of oU-RNAs map in antisense orientation to non-edited protein-coding genes suggesting that they might function by a different mechanism. In addition, our screen shows that all kinetoplast-derived RNAs are prone to some degree of uridylation.


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