ArticleRNA (New York, N.Y.)2016
High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Leishmania major virulence attenuation in vitro: An old conundrum revisited in the omics era.PLoS neglected tropical diseases · 2026Article
- Assembly and Annotation of Kinetoplastid and Diplonemid Mitochondrial Genomes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Evolutionary divergent kinetoplast genome structure and RNA editing patterns in the trypanosomatidProceedings of the National Academy of Sciences of the United States of America · 2025Article
- KRBP72 facilitates ATPase-dependent editing progression through a structural roadblock in mitochondrial A6 mRNA.Nucleic acids research · 2025Article
- KREH2 helicase represses ND7 mRNA editing in procyclic-stage Trypanosoma brucei by opposite modulation of canonical and 'moonlighting' gRNA utilization creating a proposed mRNA structure.Nucleic acids research · 2024Article
- RESC14 and RESC8 cooperate to mediate RESC function and dynamics during trypanosome RNA editing.Nucleic acids research · 2024Article
- RNA editing catalytic complexes edit multiple mRNA sites non-processively in Trypanosoma brucei.Molecular and biochemical parasitology · 2023Article
- Trypanosome RNA helicase KREH2 differentially controls non-canonical editing and putative repressive structure via a novel proposed 'bifunctional' gRNA in mRNA A6.Nucleic acids research · 2023Article
- KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing.Nucleic acids research · 2023Article
- Manipulation of mitochondrial poly(A) polymerase family proteins inFrontiers in parasitology · 2023Article
- Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing.RNA (New York, N.Y.) · 2022Article
- Organization of minicircle cassettes and guide RNA genes inRNA (New York, N.Y.) · 2022Article
- Mitochondrial RNA editing inComputational and structural biotechnology journal · 2022Article
- Trypanosome RNAEditing Substrate Binding Complex integrity and function depends on the upstream action of RESC10.Nucleic acids research · 2021Article
- Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events.Nucleic acids research · 2021Article
- Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples.Nucleic acids research · 2021Article
- Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes.RNA (New York, N.Y.) · 2020Article
- Developmental regulation of edited CYb and COIII mitochondrial mRNAs is achieved by distinct mechanisms in Trypanosoma brucei.Nucleic acids research · 2020Article
- Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes.Trends in parasitology · 2020Review
- Cell-line specific RNA editing patterns in Trypanosoma brucei suggest a unique mechanism to generate protein variation in a system intolerant to genetic mutations.Nucleic acids research · 2020Article
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5 authors.
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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.
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