Substitutional A-to-I RNA editing

Wiley Interdisciplinary Reviews: RNA

Volumn 1, Issue 1, 2010, Pages 90-101

  Wulff, Bjorn Erik ^a   Nishikura, Kazuko ^a  

^a WISTAR INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE; ADENOSINE DEAMINASE; ADENOSINE DEAMINASE ACTING ON RNA 1; ADENOSINE DEAMINASE ACTING ON RNA 2; ADENOSINE DEAMINASE ACTING ON RNA 3; CYTIDINE DEAMINASE; DOUBLE STRANDED RNA; GUANOSINE; HOMODIMER; INOSINE; MESSENGER RNA; MICRORNA; RNA; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; RNA BINDING PROTEIN;

BASE PAIRING; BIOLOGICAL FUNCTIONS; CELLULAR DISTRIBUTION; CHEMICAL STRUCTURE; CODON; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; REVIEW; RNA EDITING; RNA SPLICING; RNA VIRUS; SIGNAL TRANSDUCTION; ANIMAL; BIOLOGICAL MODEL; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; POINT MUTATION;

RNA VIRUSES;

ADENOSINE; ANIMALS; BASE PAIRING; BASE SEQUENCE; HUMANS; INOSINE; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; POINT MUTATION; RNA EDITING; RNA-BINDING PROTEINS;

EID: 81855192230     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.10     Document Type: Review

References (64)

1. Bass BL, Weintraub H. A developmentally regulated activity that unwinds RNA duplexes. Cell 1987, 48: 607-613.
2. Rebagliati MR, Melton DA. Antisense RNA injections in fertilized frog eggs reveal an RNA duplex unwinding activity. Cell 1987, 48: 599-605; doi:10.1016/0092-8674(87)90238-8.
3. Wagner RW, Nishikura K. Cell cycle expression of RNA duplex unwindase activity in mammalian cells. Mol Cell Biol 1988, 8: 770-777.
4. Bass BL, Weintraub H. An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell 1988, 55: 1089-1098.
5. Sommer B, Köhler M, Sprengel R, Seeburg PH. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 1991, 67: 11-19; doi:10.1016/0092-8674(91)90568-J.
6. Kim U, Wang Y, Sanford T, Zeng Y, Nishikura K. Molecular cloning of cDNA for double-stranded RNA adenosine deaminase, a candidate enzyme for nuclear RNA editing. PNAS 1994, 91: 11457-11461.
7. Lai F, Chen CX, Carter KC, Nishikura K. Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases. Mol Cell Biol 1997, 17: 2413-2424.
8. Melcher T, Maas S, Herb A, Sprengel R, Higuchi M, et al. RED2, a brain-specific member of the RNA-specific adenosine deaminase family. J Biol Chem 1996, 271: 31795-31798; doi: 10.1074/jbc.271.50.31795.
9. Jin Y, Zhang W, Li Q. Origins and evolution of ADAR-mediated RNA editing. IUBMB Life 2009, 61: 572-578; doi:10.1002/iub.207.
10. Patterson JB, Thomis DC, Hans SL, Samuel CE. Mechanism of interferon action: double-stranded RNA-specific adenosine deaminase from human cells is inducible by alpha and gamma interferons. Virology 1995, 210: 508-511; doi:10.1006/viro.1995.1370.
11. Maas S, Gommans WM. Novel exon of mammalian ADAR2 extends open reading frame. PLoS ONE 2009, 4: e4225; doi:10.1371/journal.pone.0004225.
12. Cho DS, Yang W, Lee JT, Shiekhattar R, Murray JM, et al. Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA. J Biol Chem 2003, 208: 17093-17102; doi: 10.1074/jbc.M213127200.
13. Lehmann KA, Bass BL. Double-stranded RNA adenosine deaminase ADAR1 and ADAR2 have overlapping specificities. Biochemistry 2000, 39: 12875-12884; doi:10.1021/bi001383g.
14. Chen CX, Cho DS, Wang Q, Lai F, Carter KC, et al. A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains. RNA 2000, 6: 755-767.
15. Ryter JM, Schultz SC. Molecular basis of doublestranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA. EMBO J 1998, 17: 7505-7513.
16. Macbeth MR, Schubert HL, VanDemark AP, Lingam AT, Hill CP, et al. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science 1995, 309: 1534-1539; doi:10.1126/science.1113150.
17. Herbert A, Alfken J, Kim YG, Mian IS, Nishikura K, et al. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. PNAS 1997, 94: 8421-8426.
18. Brown BA, Lowenhaupt K, Wilbert CM, Hanlon EB, Rich A. 2nd The zalpha domain of the editing enzyme dsRNA adenosine deaminase binds left-handed Z-RNA as well as Z-DNA. PNAS 2000, 97: 13532-13536.
19. Maas S, Gerber AP, Rich A. Identification and characterization of a human tRNA-specific adenosine deaminase related to the ADAR family of pre-mRNA editing enzymes. PNAS 1999, 16: 8895-8900.
20. Eckmann CR, Neunteufl A, Pfaffstetter L, Jantsch MF. The human but not the Xenopus RNA-editing enzyme ADAR1 has an atypical nuclear localization signal and displays the characteristics of a shuttling protein. Mol Biol Cell 2001, 12: 1911-1924.
21. Fritz J, Strehblow A, Taschner A, Schopoff S, Pasierbek P. et al. RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1. Mol Cell Biol 2009, 29: 1487-1497.
22. Desterro JMP, Keegan LP, Lafarga M, Berciano MT, O'Connell M, et al. Dynamic association of RNA-editing enzymes with the nucleolus. J Cell Sci 2003, 116: 1805-1818; doi:10.1242/jcs.00371.
23. Poulsen H, Nilsson J, Damgaard CK, Egebjerg J, Kjems J. CRM1 mediates the export of ADAR1 through a nuclear export signal within the Z-DNA binding domain. Mol Cell Biol 2001, 21: 7862-7871; doi:10.1128/MCB.21.22.7862-7871.2001.
24. Sansam CL, Wells KS, Emeson RB. Modulation of RNA editing by functional nucleolar sequestration of ADAR2. PNAS 2003, 100: 14018-14023; doi:10.1073/pnas.2336131100.
25. Mian IS, Moser MJ, Holley WR, Chatterjee A. Statistical modelling and phylogenetic analysis of a deaminase domain. J Comp Biol 1998, 5: 57-72.
26. Nishikura K, Yoo C, Kim U, Murray JM, Estes PA, et al. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J 1991, 10: 3523-3532.
27. Wagner RW, Smith JE, Cooperman BS, Nishikura K. A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversions in mammalian cells and Xenopus eggs. PNAS 1989, 86: 2647-2651.
28. Lehmann KA, Bass BL. The Importance of internal loops within RNA substrates of ADAR1. J Mol Biol 1999, 291: 1-13.
29. Polson AG, Bass BL. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J 1994, 13: 5701-5711.
30. Wong SK, Shuji S, Lazinski DW. Substrate recognition by ADAR1 and ADAR2. RNA 2001, 7: 846-858.
31. Blow M, Futreal PA, Wooster R, Stratton MR. A survey of RNA editing in human brain. Genome Res 2004, 14: 2379-2387; doi:10.1101/gr.2951204.
32. Ensterö M, Daniel C, Wahlstedt H, Major F, Öhman M. Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA. Nucleic Acids Res 2009, 37: 6916-6926; doi:10.1093/nar/gkp731.
33. Higuchi M, Single FN, K̈hler M, Sommer B, Sprengel R, et al. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell 1993, 75: 1361-1370.
34. Burns CM, Chu H, Rueter SM, Hutchinson LK, Canton H, et al. Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature 1997, 387: 303-308; doi:10.1038/387303a0.
35. Higuchi M, Stefan M, Single FN, Hartner J, Rozov A, et al. Point mutation in an AMPA receptor gene rescues lethality in mice deficient in the RNA-editing enzyme ADAR2. Nature 2000, 406: 78-81.
36. Reuter SM, Dawson TR, Emeson RB. Regulation of alternative splicing by RNAediting. Nature 1999, 399: 75-80.
37. Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nature Reviews Molecular Cell Biology 2005, 6: 376-385; doi:10.1038/nrm1644.
38. Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, et al. Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 2006, 13: 13-21.
39. Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R, Nishikura K. RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep 2007, 8: 763-769.
40. Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG. et al. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 2007, 315: 1137-1140, doi:10.1126/science. 1138050.
41. Scadden AD, Smith CW. RNAi is antagonized by A-> I hyper-editing. EMBO Rep 2001, 2: 1107-1111.
42. Yang W, Wang Q, Howell KL, Lee JT, Cho DS, et al. ADAR1 RNA deaminase limits short interfering RNA efficacy in mammalian cells. J Biol Chem 2005, 280: 3946-3953, doi:10.1074/jbc.M407876200.
43. Cattaneo R, Schmid A, Eschle D, Baczko K, ter Meulen V, et al. Biased hypermutation and other genetic changes in defective measles viruses in human brain infections. Cell 1988, 55: 255-265, doi:10.1016/0092-8674(88)90048-7.
44. Bass BL, Weintraub H, Cattaneo R, Billeter MA. Biased hypermutation of viral RNA genomes could be due to unwinding/modification of double-stranded RNA. Cell 1989, 56: 331-331, doi:10.1016/0092-8674(89)90234-1.
45. Rueda P, García-Barreno B, Melero JA. Loss of conserved cysteine residues in the attachment (G) glycoprotein of two human respiratory syncytial virus escape mutants that contain multiple A-G substitutions (hypermutations). Virology 1994, 198: 653-662.
46. Zahn RC, Schelp I, Utermöhlen O, von Laer D. A-to-G hypermutation in the genome of lymphocytic choriomeningitis virus. J Virol 2007, 457-464, doi:10.1128/JVI.00067-06.
47. Polson AG, Bass BL, Casey JL. RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase. Nature 1996, 380: 454-456.
48. Hartwig D, Schütte C, Warnecke J, Dorn I, Hennig H, et al. The large form of ADAR 1 is responsible for enhanced hepatitis delta virus RNA editing in interferon-alpha-stimulated host cells. J Vir Hep 2005, 13: 150-157.
49. Doria M, Neri F, Gallo A, Farace MG, Michienzi A. Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection. Nucleic Acids Res 2009, 37: 5848-5858, doi:10.1093/nar/gkp604.
50. Phuphuakrat A, Kraiwong R, Boonarkart C, Lauhakirti D, Lee TH, et al. Double stranded RNA adenosine deaminases enhance HIV-1 expression of human immunodeficiency virus type 1 proteins. J Virol 2008, 82: 10864-10872, doi:10.1128/JVI.00238-08.
51. Toth AM, Li Z, Cattaneo R, Samuel CE. RNA-specific adenosine deaminase ADAR1 suppresses measles virus-induced apoptosis and activation of protein kinase PKR. J Biol Chem 2009, 284: 29350-29356, doi:10.1074/jbc.M109.045146.
52. Paul MS, Bass BL. Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J 1998, 17: 1120-1127, doi:10.1093/emboj/17.4.1120.
53. Athanasiadis A, Rich A, Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol 2004, 2: e391, doi:10.1371/journal.pbio.0020391.
54. Hoopengardner B, Bhalla T, Staber C, Reenan R. Nervous system targets of RNA editing identified by comparative genomics. Science 2003, 301: 832-836.
55. Li JB, Levanon EY, Yoon J-K, Aach J, Xie B, et al. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 2009, 324: 1210-1213, doi:10.1126/science.1170995.
56. Grover D, Mukerji M, Bhatnagar P, Kannan K, Brahmachari SK. Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics 2004, 20: 813-817, doi:10.1093/bioinformatics/bth005.
57. Eisenberg E, Nemzer S, Kinar Y, Sorek R, Rechavi G, et al. Is abundant A-to-I RNA editing primate-specific?. Trends Genet 2005, 21: 77-81, doi:10.1016/j.tig.2004.12.005.
58. Maas S, Patt S, Schrey M, Rich A. Underediting of glutamate receptor GluR-B mRNA in malignant gliomas. PNAS 2001, 98: 14687-14692.
59. Hartner JC, Schmittwolf C, Kispert A, Muller AM, Higuchi M, et al. Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1. J Biol Chem 2004, 279: 4894-4902, doi:10.1074/jbc.M311347200.
60. Palladino MJ, Keegan LP, O'Connell MA, Reenan RA. A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell 2000, 102: 437-449.
61. 2C receptor induced by interferon: implications for depression associated with cytokine therapy. Mol Brain Res 2004, 124: 70-78.
62. Miyamura Y, Suzuki T, Kono M, Inagaki K, Ito S, et al. Mutations of the RNA-specific adenosine deaminase gene (DSRAD) are involved in dyschromatosis symmetrica hereditaria. Am J Hum Genet 2003, 73: 693-699.
63. Kawahara Y, Ito K, Sun H, Aizawa H, Kanazawa I, et al. Glutamate receptors: RNA editing and death of motor neurons. Nature 2004, 427: 801-801, doi:10.1038/427801a.
64. Peng PL, Zhong XF, Tu WH, Soundarapandian MM, Molner P, et al. ADAR2-dependent RNA editing of AMPA receptor subunit GluR2 determines vulnerability of neurons in forebrain ischemia. Neuron 2006, 49: 719-733.