title: High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing.
abstract: Uridine insertion/deletion RNA editing in kinetoplastids entails the addition and deletion of uridine residues throughout the length of mitochondrial transcripts to generate translatable mRNAs. This complex process requires the coordinated use of several multiprotein complexes as well as the sequential use of noncoding template RNAs called guide RNAs. The majority of steady-state mitochondrial mRNAs are partially edited and often contain regions of mis-editing, termed junctions, whose role is unclear. Here, we report a novel method for sequencing entire populations of pre-edited partially edited, and fully edited RNAs and analyzing editing characteristics across populations using a new bioinformatics tool, the Trypanosome RNA Editing Alignment Tool (TREAT). Using TREAT, we examined populations of two transcripts, RPS12 and ND7-5', in wild-typeTrypanosoma brucei We provide evidence that the majority of partially edited sequences contain junctions, that intrinsic pause sites arise during the progression of editing, and that the mechanisms that mediate pausing in the generation of canonical fully edited sequences are distinct from those that mediate the ends of junction regions. Furthermore, we identify alternatively edited sequences that constitute plausible alternative open reading frames and identify substantial variability in the 5' UTRs of both canonical and alternatively edited sequences. This work is the first to use high-throughput sequencing to examine full-length sequences of whole populations of partially edited transcripts. Our method is highly applicable to current questions in the RNA editing field, including defining mechanisms of action for editing factors and identifying potential alternatively edited sequences.
authors.affiliation: Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14214, USA.
authors.forename: Rachel M
authors.initials: RM
authors.lastname: Simpson
authors.affiliation: Center for Computational Research, University at Buffalo, Buffalo, New York 14203, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Bruno
authors.affiliation: University at Buffalo Genomics and Bioinformatics Core, Buffalo, New York 14222, USA.
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Bard
authors.affiliation: Deparment of Biochemistry, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14214, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Buck
authors.affiliation: Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York 14214, USA lread@buffalo.edu.
authors.forename: Laurie K
authors.initials: LK
authors.lastname: Read
mesh_terms: D000465:Algorithms; D000818:Animals; D059014:High-Throughput Nucleotide Sequencing; D017393:RNA Editing; D012333:RNA, Messenger / Q000235:genetics*; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D012333:RNA, Messenger
keywords: RNA editing; bioinformatics; kinetoplastid; mitochondria; trypanosome