title: Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae.
abstract: 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.
authors.affiliation: Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Strasse. 3, 6020 Innsbruck, Austria.
authors.forename: Monika J
authors.initials: MJ
authors.lastname: Madej
authors.forename: Juan D
authors.initials: JD
authors.lastname: Alfonzo
authors.forename: Alexander
authors.initials: A
authors.lastname: Hüttenhofer
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D004270:DNA, Circular / Q000737:chemistry; D015723:Gene Library; D007891:Leishmania / Q000235:genetics* / Q000378:metabolism; D008928:Mitochondria / Q000235:genetics* / Q000378:metabolism; D009843:Oligoribonucleotides / Q000032:analysis; D015800:Protozoan Proteins / Q000235:genetics; D012313:RNA / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*; D016372:RNA, Antisense / Q000235:genetics; D017394:RNA, Guide, Kinetoplastida / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*; D000077278:RNA, Mitochondrial; D022661:RNA, Untranslated / Q000235:genetics; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D014500:Uracil Nucleotides / Q000032:analysis
chemical_list: D004270:DNA, Circular; D009843:Oligoribonucleotides; D015800:Protozoan Proteins; D016372:RNA, Antisense; D000077278:RNA, Mitochondrial; D022661:RNA, Untranslated; D014500:Uracil Nucleotides; C027916:oligo(U); D012313:RNA; D017394:RNA, Guide, Kinetoplastida