rna editing

Summary

Summary: A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).

Top Publications

  1. Ramaswami G, Li J. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 2014;42:D109-13 pubmed publisher
    We present RADAR--a rigorously annotated database of A-to-I RNA editing (available at http://RNAedit.com)...
  2. Kruse E, Voigt C, Leeder W, Göringer H. RNA helicases involved in U-insertion/deletion-type RNA editing. Biochim Biophys Acta. 2013;1829:835-41 pubmed publisher
    ..RNAs in kinetoplastid protozoa such as the disease-causing African trypanosomes are substrates of a unique RNA editing reaction...
  3. Wang W, Wu Y, Messing J. The mitochondrial genome of an aquatic plant, Spirodela polyrhiza. PLoS ONE. 2012;7:e46747 pubmed publisher
    ..There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses...
  4. Iyer L, Zhang D, Rogozin I, Aravind L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res. 2011;39:9473-97 pubmed publisher
    ..These observations greatly expand the distribution of possible unidentified mutagenic processes catalyzed by nucleic acid deaminases. ..
  5. Bhogal B, Jepson J, Savva Y, Pepper A, Reenan R, Jongens T. Modulation of dADAR-dependent RNA editing by the Drosophila fragile X mental retardation protein. Nat Neurosci. 2011;14:1517-24 pubmed publisher
    ..These results link dFMR1 with the RNA-editing pathway and suggest that proper NMJ synaptic architecture requires modulation of dADAR activity by dFMR1. ..
  6. Kiran A, Loughran G, O Mahony J, Baranov P. Identification of A-to-I RNA editing: dotting the i's in the human transcriptome. Biochemistry (Mosc). 2011;76:915-23 pubmed publisher
    The phenomenon of adenosine-to-inosine (A-to-I) RNA editing has attracted considerable attention from the scientific community due to its potential relationship to the evolution of cognition in animals...
  7. Jackson C, Gornik S, Waller R. A tertiary plastid gains RNA editing in its new host. Mol Biol Evol. 2013;30:788-92 pubmed publisher
    ..Transcription processes are also elaborately modified including extensive RNA editing and trans-splicing...
  8. Gommans W. A-to-I editing of microRNAs: regulating the regulators?. Semin Cell Dev Biol. 2012;23:251-7 pubmed publisher
    ..Inosine is interpreted as guanosine by the translational machinery, and when A-to-I RNA editing occurs in the coding region of pre-mRNA molecules this substitution can result in non-synonymous codon changes ..
  9. Chen L, Lin C, Chan T, Chow R, Song Y, Liu M, et al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med. 2013;19:209-16 pubmed publisher
    ..Transcriptome sequencing revealed that adenosine-to-inosine (A?I) RNA editing of AZIN1 (encoding antizyme inhibitor 1) is increased in HCC specimens...

More Information

Publications62

  1. Fang Y, Wu H, Zhang T, Yang M, Yin Y, Pan L, et al. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS ONE. 2012;7:e37164 pubmed publisher
    ..In addition, consistent with previous discoveries, there are three co-transcribed gene clusters-18S-5S rRNA, rps3-rpl16 and nad3-rps12-in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms. ..
  2. Nakamura T, Yagi Y, Kobayashi K. Mechanistic insight into pentatricopeptide repeat proteins as sequence-specific RNA-binding proteins for organellar RNAs in plants. Plant Cell Physiol. 2012;53:1171-9 pubmed publisher
    ..Here, we summarize recent studies addressing the mechanistic aspect of PPR proteins. ..
  3. Peng Z, Cheng Y, Tan B, Kang L, Tian Z, Zhu Y, et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol. 2012;30:253-60 pubmed publisher
    b>RNA editing is a post-transcriptional event that recodes hereditary information...
  4. Bentolila S, Oh J, Hanson M, Bukowski R. Comprehensive high-resolution analysis of the role of an Arabidopsis gene family in RNA editing. PLoS Genet. 2013;9:e1003584 pubmed publisher
    ..In plant organelles, RNA editing appears to be generally a correcting mechanism that restores the proper function of the encoded product...
  5. Jackman J, Gott J, Gray M. Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily. RNA. 2012;18:886-99 pubmed publisher
    ..We also discuss possible evolutionary origins of Thg1 family-catalyzed 3'-to-5' addition activities and their implications for the currently observed phylogenetic distribution of Thg1-related enzymes in biology. ..
  6. Kleinman C, Adoue V, Majewski J. RNA editing of protein sequences: a rare event in human transcriptomes. RNA. 2012;18:1586-96 pubmed publisher
    b>RNA editing, the post-transcriptional recoding of RNA molecules, has broad potential implications for gene expression...
  7. Daniel C, Venø M, Ekdahl Y, Kjems J, Ohman M. A distant cis acting intronic element induces site-selective RNA editing. Nucleic Acids Res. 2012;40:9876-86 pubmed publisher
    ..In human, thousands of genes are edited in duplexes formed by inverted repeats in non-coding regions. It is likely that numerous such duplexes can induce editing of coding regions throughout the transcriptome. ..
  8. Ling J, Peterson K, Simonovic I, Cho C, Soll D, Simonovic M. Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proc Natl Acad Sci U S A. 2012;109:3281-6 pubmed publisher
    ..Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria. ..
  9. Uthaipaisanwong P, Chanprasert J, Shearman J, Sangsrakru D, Yoocha T, Jomchai N, et al. Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.). Gene. 2012;500:172-80 pubmed publisher
    ..By aligning the cp genome sequence with oil palm cDNA sequences, we observed 18 non-silent and 10 silent RNA editing events among 19 cp protein-coding genes...
  10. Ramaswami G, Lin W, Piskol R, Tan M, Davis C, Li J. Accurate identification of human Alu and non-Alu RNA editing sites. Nat Methods. 2012;9:579-81 pubmed publisher
    We developed a computational framework to robustly identify RNA editing sites using transcriptome and genome deep-sequencing data from the same individual...
  11. Silberberg G, Lundin D, Navon R, Ohman M. Deregulation of the A-to-I RNA editing mechanism in psychiatric disorders. Hum Mol Genet. 2012;21:311-21 pubmed publisher
    ..Adenosine-to-inosine RNA editing is a cellular mechanism, which has been implicated in mental disorders and suicide...
  12. Wahlstedt H, Ohman M. Site-selective versus promiscuous A-to-I editing. Wiley Interdiscip Rev RNA. 2011;2:761-71 pubmed publisher
    b>RNA editing by adenosine deamination is acting on polymerase II derived transcripts in all metazoans. Adenosine-to-inosine (A-to-I) editing is mediated by the adenosine deaminase that acts on RNA (ADAR) enzymes...
  13. García López J, Hourcade J, del Mazo J. Reprogramming of microRNAs by adenosine-to-inosine editing and the selective elimination of edited microRNA precursors in mouse oocytes and preimplantation embryos. Nucleic Acids Res. 2013;41:5483-93 pubmed publisher
    ..These results provide new insight into how editing and Tudor-SN-mediated elimination of miRNA precursors is regulated during early development. ..
  14. Li X, Overton I, Baines R, Keegan L, O Connell M. The ADAR RNA editing enzyme controls neuronal excitability in Drosophila melanogaster. Nucleic Acids Res. 2014;42:1139-51 pubmed publisher
    b>RNA editing by deamination of specific adenosine bases to inosines during pre-mRNA processing generates edited isoforms of proteins. Recoding RNA editing is more widespread in Drosophila than in vertebrates...
  15. Mahajan S, Thai K, Chen K, Ziff E. Exposure of neurons to excitotoxic levels of glutamate induces cleavage of the RNA editing enzyme, adenosine deaminase acting on RNA 2, and loss of GLUR2 editing. Neuroscience. 2011;189:305-15 pubmed publisher
    ..Normally, an RNA editing step changes DNA-encoded glutamine to arginine, introduces arginine in the GluR2 pore apex...
  16. Flomen R, Makoff A. Increased RNA editing in EAAT2 pre-mRNA from amyotrophic lateral sclerosis patients: involvement of a cryptic polyadenylation site. Neurosci Lett. 2011;497:139-43 pubmed publisher
    ..We report adenine/inosine RNA editing at a novel site in intron 7 of EAAT2 pre-mRNA that appears to activate a cryptic alternative polyadenylation ..
  17. Tan M, Zhu B, Liu R, Chen X, Zhou X, Wang E. Interdomain communication modulates the tRNA-dependent pre-transfer editing of leucyl-tRNA synthetase. Biochem J. 2013;449:123-31 pubmed publisher
    ..These results also suggested a novel quality control mechanism of EcLeuRS which is achieved through the co-ordination between the synthetic and editing domains. ..
  18. Kiethega G, Yan Y, Turcotte M, Burger G. RNA-level unscrambling of fragmented genes in Diplonema mitochondria. RNA Biol. 2013;10:301-13 pubmed publisher
    ..Further, cox1 mRNA includes six non-encoded uridines indicating RNA editing. In the absence of recognizable cis-elements, we postulated that trans-splicing and RNA editing are directed by ..
  19. Vargas Rodriguez O, Musier Forsyth K. Exclusive use of trans-editing domains prevents proline mistranslation. J Biol Chem. 2013;288:14391-9 pubmed publisher
    ..These results highlight the diversity of approaches used to prevent proline mistranslation and reveal a novel triple-sieve mechanism of editing that relies exclusively on trans-editing factors. ..
  20. Chen L. Characterization and comparison of human nuclear and cytosolic editomes. Proc Natl Acad Sci U S A. 2013;110:E2741-7 pubmed publisher
    We developed a robust computational statistical framework to identify RNA editing events from RNA-Seq data with high specificity...
  21. Zhang T, Liu Z, Song W, Du Y, Dong K. Molecular characterization and functional expression of the DSC1 channel. Insect Biochem Mol Biol. 2011;41:451-8 pubmed publisher
    ..the 20 clones revealed nine optional exons, four of which contain in-frame stop codons; and 13 potential A-to-I RNA editing sites...
  22. Heale B, Keegan L, O Connell M. The effect of RNA editing and ADARs on miRNA biogenesis and function. Adv Exp Med Biol. 2010;700:76-84 pubmed
    ..Even where it is demonstratedthat RNA editing can affect biogenesis or targeting of a particular miRNA, effects may be limited by redundancy within the miRNA ..
  23. Yamashita T, Tadami C, Nishimoto Y, Hideyama T, Kimura D, Suzuki T, et al. RNA editing of the Q/R site of GluA2 in different cultured cell lines that constitutively express different levels of RNA editing enzyme ADAR2. Neurosci Res. 2012;73:42-8 pubmed publisher
    Adenosine deaminase acting on RNA 2 (ADAR2) catalyzes RNA editing at the glutamine/arginine (Q/R) site of GluA2, and an ADAR2 deficiency may play a role in the death of motor neurons in ALS patients...
  24. Shikanai T, Okuda K. In vitro RNA-binding assay for studying trans-factors for RNA editing in chloroplasts. Methods Mol Biol. 2011;774:199-208 pubmed publisher
    In plant organelles, specific C residues are modified to U by RNA editing. Short RNA sequences surrounding the target site (i.e...
  25. Farooq M, Kaswala R, Kleiman N, Kasinathan C, Frederikse P. GluA2 AMPA glutamate receptor subunit exhibits codon 607 Q/R RNA editing in the lens. Biochem Biophys Res Commun. 2012;418:273-7 pubmed publisher
    Regulated GluA2 AMPA receptor subunit expression, RNA editing, and membrane localization are fundamental determinants of neuronal Ca(2+) influx, and underlie basic functions such as memory and the primary brain disorder epilepsy...
  26. O Neil R, Emeson R. Quantitative analysis of 5HT(2C) receptor RNA editing patterns in psychiatric disorders. Neurobiol Dis. 2012;45:8-13 pubmed publisher
    ..anticodon loop of tRNAs from animal, plant and eubacterial origin, the deamination of adenosine-to-inosine by RNA editing has become increasingly recognized as an important RNA processing event to generate diversity in both the ..
  27. Verbitskiy D, Merwe J, Zehrmann A, Härtel B, Takenaka M. The E-class PPR protein MEF3 of Arabidopsis thaliana can also function in mitochondrial RNA editing with an additional DYW domain. Plant Cell Physiol. 2012;53:358-67 pubmed publisher
    In plants, RNA editing is observed in mitochondria and plastids, changing selected C nucleotides into Us in both organelles...
  28. Yang L, Huang P, Li F, Zhao L, Zhang Y, Li S, et al. c-Jun amino-terminal kinase-1 mediates glucose-responsive upregulation of the RNA editing enzyme ADAR2 in pancreatic beta-cells. PLoS ONE. 2012;7:e48611 pubmed publisher
    A-to-I RNA editing catalyzed by the two main members of the adenosine deaminase acting on RNA (ADAR) family, ADAR1 and ADAR2, represents a RNA-based recoding mechanism implicated in a variety of cellular processes...
  29. Mehedi M, Hoenen T, Robertson S, Ricklefs S, Dolan M, Taylor T, et al. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure. PLoS Pathog. 2013;9:e1003677 pubmed publisher
    ..This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding ..
  30. Samuel C. ADARs: viruses and innate immunity. Curr Top Microbiol Immunol. 2012;353:163-95 pubmed publisher
    ..In this chapter our current understanding of the role and significance of ADARs in the context of innate immunity, and as determinants of the outcome of viral infection, will be considered. ..
  31. Montiel Gonzalez M, Vallecillo Viejo I, Yudowski G, Rosenthal J. Correction of mutations within the cystic fibrosis transmembrane conductance regulator by site-directed RNA editing. Proc Natl Acad Sci U S A. 2013;110:18285-90 pubmed publisher
    ..This technology should spearhead powerful approaches to correcting a wide variety of genetic mutations and fine-tuning protein function through targeted nucleotide deamination. ..
  32. Gonzalez C, López Rodríguez A, Srikumar D, Rosenthal J, Holmgren M. Editing of human K(V)1.1 channel mRNAs disrupts binding of the N-terminus tip at the intracellular cavity. Nat Commun. 2011;2:436 pubmed publisher
    In the nervous system, A→I RNA editing has an important role in regulating neuronal excitability. Ligand-gated membrane receptors, synaptic proteins, as well as ion channels, are targets for recoding by RNA editing...
  33. Nejepinska J, Malik R, Filkowski J, Flemr M, Filipowicz W, Svoboda P. dsRNA expression in the mouse elicits RNAi in oocytes and low adenosine deamination in somatic cells. Nucleic Acids Res. 2012;40:399-413 pubmed publisher
    ..Expressed dsRNA did not cause transcriptional silencing in trans. Analysis of RNA editing revealed that a small fraction of long dsRNA is edited...
  34. Barbon A, Barlati S. Glutamate receptor RNA editing in health and disease. Biochemistry (Mosc). 2011;76:882-9 pubmed publisher
    b>RNA editing is a post-transcriptional process with an important role in gene modification...
  35. Penn A, Balik A, Greger I. Steric antisense inhibition of AMPA receptor Q/R editing reveals tight coupling to intronic editing sites and splicing. Nucleic Acids Res. 2013;41:1113-23 pubmed publisher
    Adenosine-to-Inosine (A-to-I) RNA editing is a post-transcriptional mechanism, evolved to diversify the transcriptome in metazoa...
  36. Kuttan A, Bass B. Mechanistic insights into editing-site specificity of ADARs. Proc Natl Acad Sci U S A. 2012;109:E3295-304 pubmed publisher
    ..Our studies set the stage for understanding the basis of altered editing levels in disease and for developing therapeutic reagents. ..
  37. Rieder L, Reenan R. The intricate relationship between RNA structure, editing, and splicing. Semin Cell Dev Biol. 2012;23:281-8 pubmed publisher
    Post-transcriptional modifications such as RNA editing and splicing diversify the proteome while limiting the necessary size of the genome...
  38. Park E, Williams B, Wold B, Mortazavi A. RNA editing in the human ENCODE RNA-seq data. Genome Res. 2012;22:1626-33 pubmed publisher
    ..data can be mined for sequence differences relative to the reference genome to identify both genomic SNPs and RNA editing events...
  39. Ammerman M, Downey K, Hashimi H, Fisk J, Tomasello D, Faktorová D, et al. Architecture of the trypanosome RNA editing accessory complex, MRB1. Nucleic Acids Res. 2012;40:5637-50 pubmed publisher
    Trypanosoma brucei undergoes an essential process of mitochondrial uridine insertion and deletion RNA editing catalyzed by a 20S editosome...
  40. Danecek P, Nellåker C, McIntyre R, Buendia Buendia J, Bumpstead S, Ponting C, et al. High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol. 2012;13:26 pubmed publisher
    ..account systematic biases in alignment, single nucleotide variant calling, and sequencing depth to identify RNA editing sites with high accuracy...
  41. Rosenthal J, Seeburg P. A-to-I RNA editing: effects on proteins key to neural excitability. Neuron. 2012;74:432-9 pubmed publisher
    b>RNA editing by adenosine deamination is a process used to diversify the proteome. The expression of ADARs, the editing enzymes, is ubiquitous among true metazoans, and so adenosine deamination is thought to be universal...
  42. Tang W, Fei Y, Page M. Biological significance of RNA editing in cells. Mol Biotechnol. 2012;52:91-100 pubmed publisher
    b>RNA editing is one of the post-transcriptional RNA processes. RNA editing generates RNA and protein diversity in eukaryotes and results in specific amino acid substitutions, deletions, and changes in gene expression levels...
  43. Ekdahl Y, Farahani H, Behm M, Lagergren J, Ohman M. A-to-I editing of microRNAs in the mammalian brain increases during development. Genome Res. 2012;22:1477-87 pubmed publisher
    Adenosine-to-inosine (A-to-I) RNA editing targets double-stranded RNA stem-loop structures in the mammalian brain. It has previously been shown that miRNAs are substrates for A-to-I editing...
  44. Palavicini J, Correa Rojas R, Rosenthal J. Extra double-stranded RNA binding domain (dsRBD) in a squid RNA editing enzyme confers resistance to high salt environment. J Biol Chem. 2012;287:17754-64 pubmed publisher
    A-to-I RNA editing is particularly common in coding regions of squid mRNAs...
  45. Kiran A, O Mahony J, Sanjeev K, Baranov P. Darned in 2013: inclusion of model organisms and linking with Wikipedia. Nucleic Acids Res. 2013;41:D258-61 pubmed publisher
    DARNED (DAtabase of RNa EDiting, available at http://darned.ucc.ie) is a centralized repository of reference genome coordinates corresponding to RNA nucleotides having altered templated identities in the process of RNA editing...
  46. Vesely C, Tauber S, Sedlazeck F, von Haeseler A, Jantsch M. Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res. 2012;22:1468-76 pubmed publisher
    ..Inosines are recognized as guanosines, and, hence, RNA editing alters the sequence information but also structure of RNAs...
  47. Marcucci R, Brindle J, Paro S, Casadio A, Hempel S, Morrice N, et al. Pin1 and WWP2 regulate GluR2 Q/R site RNA editing by ADAR2 with opposing effects. EMBO J. 2011;30:4211-22 pubmed publisher
    ..Pin1 and WWP2 also regulate the large subunit of RNA Pol II, so these proteins may also coordinately regulate other key cellular proteins. ..
  48. Heinemann I, Nakamura A, O Donoghue P, Eiler D, Soll D. tRNAHis-guanylyltransferase establishes tRNAHis identity. Nucleic Acids Res. 2012;40:333-44 pubmed publisher
    ..The crystal structure of human Thg1 revealed a fascinating structural similarity to 5'???3' polymerases, indicating that Thg1 derives from classical polymerases and evolved to assume its specific function in tRNA(His) processing. ..
  49. Sun T, Germain A, Giloteaux L, Hammani K, Barkan A, Hanson M, et al. An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize. Proc Natl Acad Sci U S A. 2013;110:E1169-78 pubmed publisher
    Plant RNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of both mitochondria and plastids...
  50. Liang G, Kitamura K, Wang Z, Liu G, Chowdhury S, Fu W, et al. RNA editing of hepatitis B virus transcripts by activation-induced cytidine deaminase. Proc Natl Acad Sci U S A. 2013;110:2246-51 pubmed publisher
    ..Taken together, the results indicate that AID can deaminate the nucleocapsid RNA of HBV. ..
  51. Zehrmann A, van der Merwe J, Verbitskiy D, Härtel B, Brennicke A, Takenaka M. The DYW-class PPR protein MEF7 is required for RNA editing at four sites in mitochondria of Arabidopsis thaliana. RNA Biol. 2012;9:155-61 pubmed publisher
    In plant mitochondria and plastids, RNA editing alters about 400 and about 35 C nucleotides into Us, respectively...
  52. Volchkova V, Dolnik O, Martínez M, Reynard O, Volchkov V. Genomic RNA editing and its impact on Ebola virus adaptation during serial passages in cell culture and infection of guinea pigs. J Infect Dis. 2011;204 Suppl 3:S941-6 pubmed publisher
    Synthesis of the structural, surface glycoprotein (GP) of Ebola virus (EBOV) is dependent on transcriptional RNA editing phenomenon...
  53. Lyddon R, Dwork A, Keddache M, Siever L, Dracheva S. Serotonin 2c receptor RNA editing in major depression and suicide. World J Biol Psychiatry. 2013;14:590-601 pubmed publisher
    ..The other, seen also in our previous study of suicide in BP and SZ, is linked to suicide alone and is associated with more editing and, therefore, less receptor function. ..