When you can’t trust the DNA: RNA editing changes transcript sequences

Knoop, Volker

doi:10.1007/s00018-010-0538-9

Cited by 181 publications

(141 citation statements)

References 255 publications

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“…in cox1 of Amphidinium carterae (Waller & Jackson 2009). Interestingly, beside land plants, dinoflagellates are the only group, for which plastid RNA editing has been reported, however, the process is not as widespread and elaborate as in their mitochondria (Knoop 2011;Smith & Keeling 2015).…”

Section: More Peculiarities: Missing Orfs Boundaries Rna Editing Trmentioning

confidence: 99%

Peculiarities within peculiarities – dinoflagellates and their mitochondrial genomes

Gagat

Mackiewicz

2017

Mitochondrial DNA Part B

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After the establishment of an endosymbiotic relationship between a proto-mitochondrion and its probable archaeal host, mitochondrial genomes underwent a spectacular reductive evolution. An interesting pathway was chosen by mitogenomes of unicellular protists called dinoflagellates, which experienced an additional wave of reduction followed by amplification and rearrangement leading to their secondary complexity. The former resulted in a mitogenome consisting of only three protein-coding genes, the latter in their multiple copies being scattered across numerous chromosomes and the evolution of complex processes for their expression. These stunning features raise a question about the future of the dinoflagellate mitochondrial genome. ARTICLE HISTORY

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Section: More Peculiarities: Missing Orfs Boundaries Rna Editing Trmentioning

confidence: 99%

Peculiarities within peculiarities – dinoflagellates and their mitochondrial genomes

Gagat

Mackiewicz

2017

Mitochondrial DNA Part B

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“…The modification of genetic information by the pyrimidineexchange type of RNA editing is common in land plant mitochondria and chloroplasts (Chateigner-Boutin and Small 2011;Knoop 2011;Finster et al 2012). Numerous cytidineto-uridine conversions in the organelle mRNAs (and in some plant clades also reverse uridine-to-cytidine exchanges) primarily serve to convert codon meanings to encode evolutionarily conserved amino acids.…”

Section: Introductionmentioning

confidence: 99%

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata

Oldenkott

Yamaguchi

Tsuji-Tsukinoki

et al. 2014

RNA

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105

113

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RNA editing in chloroplasts and mitochondria of land plants differs significantly in abundance. For example, some 200-500 sites of cytidine-to-uridine RNA editing exist in flowering plant mitochondria as opposed to only 30-50 such C-to-U editing events in their chloroplasts. In contrast, we predicted significantly more chloroplast RNA editing for the protein-coding genes in the available complete plastome sequences of two species of the spike moss genus Selaginella (Lycopodiophyta). To evaluate these predictions we investigated the Selaginella uncinata chloroplast transcriptome. Our exhaustive cDNA studies identified the extraordinary number of 3415 RNA-editing events, exclusively of the C-to-U type, in the 74 mRNAs encoding intact reading frames in the S. uncinata chloroplast. We find the overwhelming majority (61%) of the 428 silent editing events leaving codon meanings unaltered directly neighboring other editing events, possibly suggesting a sterically more flexible RNA-editing deaminase activity in Selaginella. No evidence of RNA editing was found for tRNAs or rRNAs but we identified a total of 74 editing sites in cDNA sequences of four group II introns (petBi6g2, petDi8g2, ycf3i124g2, and ycf3i354g2) retained in partially matured transcripts, which strongly contribute to improved base-pairing in the intron secondary structures as a likely prerequisite for their splicing.

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“…RNA editing has been shown to occur in a broad range of species, including animals, plants, fungi, protists, and viruses (Knoop 2010). Several types are known, differing considerably in their frequency, molecular mechanisms, and species distribution.…”

Section: Introductionmentioning

confidence: 99%

RNA editing of protein sequences: A rare event in human transcriptomes

Kleinman

Adoue

Majewski

2012

RNA

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RNA editing, the post-transcriptional recoding of RNA molecules, has broad potential implications for gene expression. Several recent studies of human transcriptomes reported a high number of differences between DNA and RNA, including events not explained by any known mammalian RNA-editing mechanism. However, RNA-editing estimates differ by orders of magnitude, since technical limitations of high-throughput sequencing have been sometimes overlooked and sequencing errors have been confounded with editing sites. Here, we developed a series of computational approaches to analyze the extent of this process in the human transcriptome, identifying and addressing the major sources of error of a large-scale approach. We apply the detection pipeline to deep sequencing data from lymphoblastoid cell lines expressing ADAR1 at high levels, and show that noncanonical editing is unlikely to occur, with at least 85%-98% of candidate sites being the result of sequencing and mapping artifacts. By implementing a method to detect intronless gene duplications, we show that most noncanonical sites previously validated originate in read mismapping within these regions. Canonical A-to-G editing, on the other hand, is widespread in noncoding Alu sequences and rare in exonic and coding regions, where the validation rate also dropped. The genomic distribution of editing sites we find, together with the lack of consistency across studies or biological replicates, suggest a minor quantitative impact of this process in the overall recoding of protein sequences. We propose instead a primary role of ADAR1 protein as a defense system against elements potentially damaging to the genome.

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When you can’t trust the DNA: RNA editing changes transcript sequences

Cited by 181 publications

References 255 publications

Peculiarities within peculiarities – dinoflagellates and their mitochondrial genomes

Peculiarities within peculiarities – dinoflagellates and their mitochondrial genomes

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata

RNA editing of protein sequences: A rare event in human transcriptomes

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