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PMID: 17139332 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Review

Editor meets silencer: crosstalk between RNA editing and RNA interference.

Nature reviews. Molecular cell biology ·Vol. 7 ·No. 12 ·2006-12-00 ·Pages 919-31

Nishikura K

Abstract

The most prevalent type of RNA editing is mediated by ADAR (adenosine deaminase acting on RNA) enzymes, which convert adenosines to inosines (a process known as A-->I RNA editing) in double-stranded (ds)RNA substrates. A-->I RNA editing was long thought to affect only selected transcripts by altering the proteins they encode. However, genome-wide screening has revealed numerous editing sites within inverted Alu repeats in introns and untranslated regions. Also, recent evidence indicates that A-->I RNA editing crosstalks with RNA-interference pathways, which, like A-->I RNA editing, involve dsRNAs. A-->I RNA editing therefore seems to have additional functions, including the regulation of retrotransposons and gene silencing, which adds a new urgency to the challenges of fully understanding ADAR functions.

MeSH Terms
Adenosine/chemistry,metabolism Adenosine Deaminase/chemistry,genetics,metabolism Alu Elements Animals Gene Expression Regulation Humans Inosine/chemistry,metabolism Introns RNA Editing RNA Interference RNA, Double-Stranded/metabolism RNA, Small Interfering/metabolism RNA-Binding Proteins Retroelements
Chemicals
RNA, Double-Stranded RNA, Small Interfering RNA-Binding Proteins Retroelements Inosine ADARB1 protein, human Adenosine Deaminase Adenosine
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Nishikura Kazuko
The Wistar Institute, Department of Gene Expression and Regulation, 3601 Spruce Street, Philadelphia, Pennsylvania 19104-4268, USA. [email protected]
References (112)
112 references, click to expand
  1. Editing the message from A to I.
    Nat Biotechnol. 2004 Aug;22(8):962-3 PMID: 15286646
  2. Widespread RNA editing of embedded alu elements in the human transcriptome.
    Genome Res. 2004 Sep;14(9):1719-25 PMID: 15342557
  3. Mechanisms of gene silencing by double-stranded RNA.
    Nature. 2004 Sep 16;431(7006):343-9 PMID: 15372041
  4. Substrate specificity of the dsRNA unwinding/modifying activity.
    EMBO J. 1991 Nov;10(11):3523-32 PMID: 1915306
  5. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency.
    Cell. 1993 Dec 31;75(7):1361-70 PMID: 8269514
  6. The cytoplasm of Xenopus oocytes contains a factor that protects double-stranded RNA from adenosine-to-inosine modification.
    Mol Cell Biol. 1994 Aug;14(8):5425-32 PMID: 8035819
  7. Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing.
    Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11457-61 PMID: 7972084
  8. Mutagenic analysis of double-stranded RNA adenosine deaminase, a candidate enzyme for RNA editing of glutamate-gated ion channel transcripts.
    J Biol Chem. 1995 Jul 21;270(29):17098-105 PMID: 7615504
  9. The Epstein-Barr virus nuclear protein 2 acidic domain forms a complex with a novel cellular coactivator that can interact with TFIIE.
    Mol Cell Biol. 1995 Sep;15(9):4735-44 PMID: 7651391
  10. Expression and regulation by interferon of a double-stranded-RNA-specific adenosine deaminase from human cells: evidence for two forms of the deaminase.
    Mol Cell Biol. 1995 Oct;15(10):5376-88 PMID: 7565688
  11. A mammalian RNA editing enzyme.
    Nature. 1996 Feb 1;379(6564):460-4 PMID: 8559253
  12. RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase.
    Nature. 1996 Apr 4;380(6573):454-6 PMID: 8602246
  13. RED2, a brain-specific member of the RNA-specific adenosine deaminase family.
    J Biol Chem. 1996 Dec 13;271(50):31795-8 PMID: 8943218
  14. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases.
    Mol Cell Biol. 1997 May;17(5):2413-24 PMID: 9111310
  15. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette.
    RNA. 1997 May;3(5):453-63 PMID: 9149227
  16. Regulation of serotonin-2C receptor G-protein coupling by RNA editing.
    Nature. 1997 May 15;387(6630):303-8 PMID: 9153397
  17. Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA.
    EMBO J. 1998 Feb 16;17(4):1120-7 PMID: 9463389
  18. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.
    Nature. 1998 Feb 19;391(6669):806-11 PMID: 9486653
  19. Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.
    EMBO J. 1998 Dec 15;17(24):7505-13 PMID: 9857205
  20. Altered G protein-coupling functions of RNA editing isoform and splicing variant serotonin2C receptors.
    J Neurochem. 2000 Mar;74(3):1290-300 PMID: 10693963
  21. The mle(napts) RNA helicase mutation in drosophila results in a splicing catastrophe of the para Na+ channel transcript in a region of RNA editing.
    Neuron. 2000 Jan;25(1):139-49 PMID: 10707979
  22. RNAi-mediated pathways in the nucleus.
    Nat Rev Genet. 2005 Jan;6(1):24-35 PMID: 15630419
  23. Is abundant A-to-I RNA editing primate-specific?
    Trends Genet. 2005 Feb;21(2):77-81 PMID: 15661352
  24. ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells.
    J Biol Chem. 2005 Feb 4;280(5):3946-53 PMID: 15556947
  25. Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin.
    Curr Biol. 2005 Feb 22;15(4):384-91 PMID: 15723802
  26. Evolutionarily conserved human targets of adenosine to inosine RNA editing.
    Nucleic Acids Res. 2005;33(4):1162-8 PMID: 15731336
  27. Regulation of serotonin 2C receptor pre-mRNA editing by serotonin.
    Int Rev Neurobiol. 2005;63:83-100 PMID: 15797466
  28. Identification of microRNAs of the herpesvirus family.
    Nat Methods. 2005 Apr;2(4):269-76 PMID: 15782219
  29. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors.
    Curr Opin Cell Biol. 2005 Jun;17(3):251-6 PMID: 15901493
  30. A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10.
    Bioinformatics. 2005 Jun 1;21(11):2590-5 PMID: 15797904
  31. Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts.
    Trends Genet. 2005 Jun;21(6):326-9 PMID: 15922830
  32. The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage.
    Nat Struct Mol Biol. 2005 Jun;12(6):489-96 PMID: 15895094
  33. MicroRNA biogenesis: coordinated cropping and dicing.
    Nat Rev Mol Cell Biol. 2005 May;6(5):376-85 PMID: 15852042
  34. Post-transcriptional gene silencing by siRNAs and miRNAs.
    Curr Opin Struct Biol. 2005 Jun;15(3):331-41 PMID: 15925505
  35. RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe.
    Trends Genet. 2005 Aug;21(8):450-6 PMID: 15979194
  36. ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation.
    Prog Nucleic Acid Res Mol Biol. 2005;79:299-338 PMID: 16096031
  37. High doses of siRNAs induce eri-1 and adar-1 gene expression and reduce the efficiency of RNA interference in the mouse.
    Biochem J. 2005 Sep 15;390(Pt 3):675-9 PMID: 16004606
  38. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing.
    Science. 2005 Sep 2;309(5740):1534-9 PMID: 16141067
  39. Antisense transcription in the mammalian transcriptome.
    Science. 2005 Sep 2;309(5740):1564-6 PMID: 16141073
  40. Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs.
    Nucleic Acids Res. 2005;33(16):5063-72 PMID: 16147990
  41. Is there any sense in antisense editing?
    Trends Genet. 2005 Oct;21(10):544-7 PMID: 16099531
  42. microPrimer: the biogenesis and function of microRNA.
    Development. 2005 Nov;132(21):4645-52 PMID: 16224044
  43. Regulating gene expression through RNA nuclear retention.
    Cell. 2005 Oct 21;123(2):249-63 PMID: 16239143
  44. Identification and characterization of small RNAs involved in RNA silencing.
    FEBS Lett. 2005 Oct 31;579(26):5830-40 PMID: 16153643
  45. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases.
    Nat Struct Mol Biol. 2006 Jan;13(1):13-21 PMID: 16369484
  46. Structure and specific RNA binding of ADAR2 double-stranded RNA binding motifs.
    Structure. 2006 Feb;14(2):345-55 PMID: 16472753
  47. ADAR2-dependent RNA editing of AMPA receptor subunit GluR2 determines vulnerability of neurons in forebrain ischemia.
    Neuron. 2006 Mar 2;49(5):719-33 PMID: 16504947
  48. Extensive adenosine-to-inosine editing detected in Alu repeats of antisense RNAs reveals scarcity of sense-antisense duplex formation.
    FEBS Lett. 2006 Apr 17;580(9):2301-5 PMID: 16574103
  49. An overview of cytidine deaminases.
    Int J Hematol. 2006 Apr;83(3):195-200 PMID: 16720547
  50. A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains.
    RNA. 2000 May;6(5):755-67 PMID: 10836796
  51. Double-stranded RNA as a template for gene silencing.
    Cell. 2000 Apr 28;101(3):235-8 PMID: 10847677
  52. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2.
    Nature. 2000 Jul 6;406(6791):78-81 PMID: 10894545
  53. A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity.
    Cell. 2000 Aug 18;102(4):437-49 PMID: 10966106
  54. Requirement of the RNA editing deaminase ADAR1 gene for embryonic erythropoiesis.
    Science. 2000 Dec 1;290(5497):1765-8 PMID: 11099415
  55. Human RNA-specific adenosine deaminase (ADAR1) gene specifies transcripts that initiate from a constitutively active alternative promoter.
    Gene. 2000 Nov 27;258(1-2):165-72 PMID: 11111054
  56. Functions and mechanisms of RNA editing.
    Annu Rev Genet. 2000;34:499-531 PMID: 11092837
  57. The RNA world meets behavior: A-->I pre-mRNA editing in animals.
    Trends Genet. 2001 Feb;17(2):53-6 PMID: 11173098
  58. Regulation of alternative splicing by RNA editing.
    Nature. 1999 May 6;399(6731):75-80 PMID: 10331393
  59. The importance of internal loops within RNA substrates of ADAR1.
    J Mol Biol. 1999 Aug 6;291(1):1-13 PMID: 10438602
  60. Polycistronic transcription and editing of the mitochondrial small subunit (SSU ) ribosomal RNA in Dictyostelium discoideum.
    Curr Genet. 1999 Aug;36(1-2):55-61 PMID: 10447595
  61. A survey of RNA editing in human brain.
    Genome Res. 2004 Dec;14(12):2379-87 PMID: 15545495
  62. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.
    PLoS Biol. 2004 Dec;2(12):e391 PMID: 15534692
  63. Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression.
    Annu Rev Biochem. 2006;75:243-69 PMID: 16756492
  64. RNA editing of human microRNAs.
    Genome Biol. 2006;7(4):R27 PMID: 16594986
  65. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes.
    Genes Dev. 2006 Jul 1;20(13):1732-43 PMID: 16766679
  66. A germline-specific class of small RNAs binds mammalian Piwi proteins.
    Nature. 2006 Jul 13;442(7099):199-202 PMID: 16751776
  67. A novel class of small RNAs bind to MILI protein in mouse testes.
    Nature. 2006 Jul 13;442(7099):203-7 PMID: 16751777
  68. Characterization of the piRNA complex from rat testes.
    Science. 2006 Jul 21;313(5785):363-7 PMID: 16778019
  69. A-to-I RNA editing and human disease.
    RNA Biol. 2006 Jan-Mar;3(1):1-9 PMID: 17114938
  70. Antisense RNA injections in fertilized frog eggs reveal an RNA duplex unwinding activity.
    Cell. 1987 Feb 27;48(4):599-605 PMID: 2434240
  71. A developmentally regulated activity that unwinds RNA duplexes.
    Cell. 1987 Feb 27;48(4):607-13 PMID: 2434241
  72. An unwinding activity that covalently modifies its double-stranded RNA substrate.
    Cell. 1988 Dec 23;55(6):1089-98 PMID: 3203381
  73. A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs.
    Proc Natl Acad Sci U S A. 1989 Apr;86(8):2647-51 PMID: 2704740
  74. RNA editing of the human serotonin 5-HT2C receptor. alterations in suicide and implications for serotonergic pharmacotherapy.
    Neuropsychopharmacology. 2001 May;24(5):478-91 PMID: 11282248
  75. RNA editing by base deamination: more enzymes, more targets, new mysteries.
    Trends Biochem Sci. 2001 Jun;26(6):376-84 PMID: 11406411
  76. RNA silencing in plants--defense and counterdefense.
    Science. 2001 Jun 22;292(5525):2277-80 PMID: 11423650
  77. Specific cleavage of hyper-edited dsRNAs.
    EMBO J. 2001 Aug 1;20(15):4243-52 PMID: 11483527
  78. The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs.
    Cell. 2001 Aug 24;106(4):465-75 PMID: 11525732
  79. CRM1 mediates the export of ADAR1 through a nuclear export signal within the Z-DNA binding domain.
    Mol Cell Biol. 2001 Nov;21(22):7862-71 PMID: 11604520
  80. RNAi is antagonized by A-->I hyper-editing.
    EMBO Rep. 2001 Dec;2(12):1107-11 PMID: 11743024
  81. Altered editing of serotonin 2C receptor pre-mRNA in the prefrontal cortex of depressed suicide victims.
    Neuron. 2002 Apr 25;34(3):349-56 PMID: 11988167
  82. RNA editing by adenosine deaminases that act on RNA.
    Annu Rev Biochem. 2002;71:817-46 PMID: 12045112
  83. tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli.
    EMBO J. 2002 Jul 15;21(14):3841-51 PMID: 12110595
  84. RNA interference.
    Nature. 2002 Jul 11;418(6894):244-51 PMID: 12110901
  85. The role of RNA editing by ADARs in RNAi.
    Mol Cell. 2002 Oct;10(4):809-17 PMID: 12419225
  86. RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans.
    EMBO J. 2002 Nov 15;21(22):6025-35 PMID: 12426375
  87. Editing site recognition and nucleotide insertion are separable processes in Physarum mitochondria.
    EMBO J. 2002 Nov 15;21(22):6154-61 PMID: 12426387
  88. Dynamic association of RNA-editing enzymes with the nucleolus.
    J Cell Sci. 2003 May 1;116(Pt 9):1805-18 PMID: 12665561
  89. Widespread inosine-containing mRNA in lymphocytes regulated by ADAR1 in response to inflammation.
    Immunology. 2003 May;109(1):15-23 PMID: 12709013
  90. Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA.
    J Biol Chem. 2003 May 9;278(19):17093-102 PMID: 12618436
  91. The dsRNA binding protein family: critical roles, diverse cellular functions.
    FASEB J. 2003 Jun;17(9):961-83 PMID: 12773480
  92. Regulation of ion channel/neurotransmitter receptor function by RNA editing.
    Curr Opin Neurobiol. 2003 Jun;13(3):279-83 PMID: 12850211
  93. Nervous system targets of RNA editing identified by comparative genomics.
    Science. 2003 Aug 8;301(5634):832-6 PMID: 12907802
  94. The small RNA profile during Drosophila melanogaster development.
    Dev Cell. 2003 Aug;5(2):337-50 PMID: 12919683
  95. Mutations of the RNA-specific adenosine deaminase gene (DSRAD) are involved in dyschromatosis symmetrica hereditaria.
    Am J Hum Genet. 2003 Sep;73(3):693-9 PMID: 12916015
  96. AMPA receptor tetramerization is mediated by Q/R editing.
    Neuron. 2003 Nov 13;40(4):763-74 PMID: 14622580
  97. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi.
    Nature. 2003 Nov 20;426(6964):310-4 PMID: 14628056
  98. Modulation of RNA editing by functional nucleolar sequestration of ADAR2.
    Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):14018-23 PMID: 14612560
  99. Mutations in RNAi rescue aberrant chemotaxis of ADAR mutants.
    Science. 2003 Dec 5;302(5651):1725 PMID: 14657490
  100. AluGene: a database of Alu elements incorporated within protein-coding genes.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D489-92 PMID: 14681464
  101. Recognition of small interfering RNA by a viral suppressor of RNA silencing.
    Nature. 2003 Dec 18;426(6968):874-8 PMID: 14661029
  102. Size selective recognition of siRNA by an RNA silencing suppressor.
    Cell. 2003 Dec 26;115(7):799-811 PMID: 14697199
  103. MicroRNAs: genomics, biogenesis, mechanism, and function.
    Cell. 2004 Jan 23;116(2):281-97 PMID: 14744438
  104. Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene.
    J Biol Chem. 2004 Feb 6;279(6):4952-61 PMID: 14613934
  105. Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1.
    J Biol Chem. 2004 Feb 6;279(6):4894-902 PMID: 14615479
  106. Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes.
    Genome Biol. 2004;5(2):209 PMID: 14759252
  107. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans.
    Nature. 2004 Feb 12;427(6975):645-9 PMID: 14961122
  108. Glutamate receptors: RNA editing and death of motor neurons.
    Nature. 2004 Feb 26;427(6977):801 PMID: 14985749
  109. Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.
    Mol Cell. 2004 Apr 23;14(2):221-31 PMID: 15099521
  110. Methods for analysis of mitochondrial tRNA editing in Acanthamoeba castellanii.
    Methods Mol Biol. 2004;265:315-31 PMID: 15103081
  111. RNA editing of a miRNA precursor.
    RNA. 2004 Aug;10(8):1174-7 PMID: 15272117
  112. Systematic identification of abundant A-to-I editing sites in the human transcriptome.
    Nat Biotechnol. 2004 Aug;22(8):1001-5 PMID: 15258596
Article Info
Journal
Nature reviews. Molecular cell biology
Abbr.
Nat Rev Mol Cell Biol
ISSN
1471-0072
Published
2006-12-00
Pages
919-31
Language
English
Region
England
NLM ID
100962782
PMCID
PMC2953463
Subset
IM
Grants
NIGMS NIH HHS · R01 GM040536 · United States
NHLBI NIH HHS · R01 HL070045 · United States
NIGMS NIH HHS · R01 GM040536-15 · United States
NCI NIH HHS · P01 CA072765 · United States
NCI NIH HHS · P01 CA072765-050002 · United States
NHLBI NIH HHS · R01 HL070045-04 · United States
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