Dysregulated A to I RNA editing and non-coding rnas in neurodegeneration

Frontiers in Genetics

Volumn 3, Issue JAN, 2013, Pages

  Singh, Minati ^a  

^a UNIVERSITY OF IOWA   (United States)

Author keywords

Adars; Long non coding RNA; Micrornas; Non coding rnas; RNA editing; Snornas

Indexed keywords

ANIMALIA; CAENORHABDITIS ELEGANS; EUKARYOTA; MAMMALIA; MUS;

EID: 84876178165     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00326     Document Type: Review

References (187)

1. Abelson, J. F., Kwan, K. Y., O'Roak, B. J., Baek, D. Y., Stillman, A. A., Morgan, T. M., et al. (2005). Sequence variants in SLITRK1 are associated with Tourette's syndrome. Science 310,317-320.
2. Akbarian, S., Huntsman, M. M., Kim, J. J., Tafazzoli, A., Potkin, S. G., Bun-ney, W. E., Jr., et al. (1995a). GABAA receptor subunit gene expression in human prefrontal cortex: comparison of schizophrenics and controls. Cereb. Cortex 5, 550-560.
3. Akbarian, S., Smith, M. A., and Jones, E. G. (1995b). Editing for an AMPA receptor subunit RNA in prefrontal cortex and striatum in Alzheimer's disease, Huntington's disease and schizophrenia. Brain Res. 699,297-304.
4. Alon, S., Mor, E., Vigneault, F., Church, G. M., Locatelli, F., Galeano, F., et al. (2012). Systematic identification of edited microRNAs in the human brain. Genome Res. 22,1533-1540.
5. Athanasiadis, A., Rich, A., and Maas, S. (2004). Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2:e391. doi: 10.1371/jour-nal.pbio.0020391
6. Barraud, P., and Allain, E H. (2012). ADAR proteins: double-stranded RNA and Z-DNA binding domains. Curr. Top. Microbiol. Immunol. 353, 35-60.
7. Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
8. Bass, B. L. (2002). RNA editing by adenosine deaminases that act on RNA. Annu. Rev. Biochem. 71, 817-846.
9. Beal, P. A., Maydanovych, O., and Pokharel, S. (2007). The chemistry and biology of RNA editing by adenosine deaminases. Nucleic Acids Symp. Ser. (Oxf) 83-84.
10. Bernard, A., Ferhat, L., Dessi, F., Charton, G., Represa, A., Ben-Ari, Y., et al. (1999). Q/R editing of the rat GluR5 and GluR6 kainate receptors in vivo and in vitro: evidence for independent developmental, pathological and cellular regulation. Eur. J. Neurosci. 11, 604-616.
11. Bian, S., and Sun, T. (2011). Functions of noncoding RNAs in neural development and neurological diseases. Mol. Neurobiol. 44, 359-373.
12. Blow, M. J., Grocock, R. J., Van Dongen, S., Enright, A. J., Dicks, E., Futreal, P. A., et al. (2006). RNA editing of human microRNAs. Genome Biol. 7,R27.
13. Borthwick, G. M., Taylor, R. W., Walls, T. J., Tonska, K., Taylor, G. A., Shaw, P. J., et al. (2006). Motor neuron disease in a patient with a mitochondrial tRNAIle mutation. Ann. Neurol. 59, 570-574.
14. Brook, J. D., Mccurrach, M. E., Harley, H. G., Buckler, A. J., Church, D., Abu-ratani, H., et al. (1992). Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3; end of a transcript encoding a protein kinase family member. Cell 68, 799-808.
15. Buckley, N. J., Johnson, R., Zuccato, C., Bithell, A., and Cattaneo, E. (2010). The role of REST in transcriptional and epigenetic dysregula-tion in Huntington's disease. Neurobiol. Dis. 39, 28-39.
16. Burns, C. M., Chu, H., Rueter, S. M., Hutchinson, L. K., Canton, H., Sanders-Bush, E., et al. (1997). Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature 387, 303-308.
17. Carthew, R. W., and Sontheimer, E. J. (2009). Origins and Mechanisms of miRNAs and siRNAs. Cell 136, 642-655.
18. Cavaille, J., Buiting, K., Kiefmann, M., Lalande, M., Brannan, C. I., Hors-themke, B., et al. (2000). Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl. Acad. Sci. U.S.A. 97, 14311-14316.
19. Cavaille, J., Seitz, H., Paulsen, M., Ferguson-Smith, A. C., and Bachel-lerie, J. P. (2002). Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum. Mol. Genet. 11, 1527-1538.
20. Chandler, V. L. (2007). Paramuta-tion: from maize to mice. Cell 128, 641-645.
21. Chen, C. X., Cho, D. S., Wang, Q., Lai, F., Carter, K. C., and Nishikura,K. (2000).Athirdmember of the RNA-specific adenosine deam-inase gene family, ADAR3, contains both single- and double-stranded RNA binding domains. RNA 6, 755-767.
22. Chen, L. L., and Carmichael, G. G. (2008). Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle 7, 3294-3301.
23. Chen, L. L., Decerbo, J. N., and Carmichael, G. G. (2008). Alu element-mediated gene silencing. EMBOJ. 27, 1694-1705.
24. Chen, Z., Wu, J., Yang, C., Fan, P., Balazs, L., Jiao, Y., et al. (2012). DiGeorge syndrome critical region 8 (DGCR8) protein-mediated microRNA Biogenesis Is Essential for Vascular Smooth Muscle Cell Development in Mice. J. Biol. Chem. 287, 19018-19028.
25. Chilibeck, K. A., Wu, T., Liang, C., Schellenberg, M. J., Gesner, E. M., Lynch, J. M., et al. (2006). FRET analysis of in vivo dimerization by RNA-editing enzymes. J. Biol. Chem. 281,16530-16535.
26. Cho, D. S., Yang, W., Lee, J. T., Shiekhattar, R., Murray, J. M., and Nishikura, K. (2003). Requirement of dimerization for RNA editing activity of adenosine deaminases acting on RNA. J. Biol. Chem. 278, 17093-17102.
27. Clark, S. J. (2007). Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis. Hum. Mol. Genet. 16, R88-R95.
28. Costa, E E (2005). Non-coding RNAs: new players in eukaryotic biology. Gene 357, 83-94.
29. Cuzin, F., Grandjean, V., and Ras-soulzadegan, M. (2008). Inherited variation at the epigenetic level: para-mutation from the plant to the mouse. Curr. Opin. Genet. Dev 18, 193-196.
30. D'Angelo, M. G., and Bresolin, N. (2006). Cognitive impairment in neuromuscular disorders. Muscle Nerve 34,16-33.
31. Davies, W., Isles, A. R., Burgoyne, P. S., and Wilkinson, L. S. (2006). X-linked imprinting: effects on brain and behaviour. Bioessays 28, 35-44.
32. Davies, W., Isles, A. R., and Wilkinson, L. S. (2005). Imprinted gene expression in the brain. Neurosci. Biobehav. Rev. 29,421-430.
33. Davies, W., Smith, R. J., Kelsey, G., and Wilkinson, L. S. (2004). Expression patterns of the novel imprinted genes Nap1l5 and Peg13 and their non-imprinted host genes in the adult mouse brain. Gene Expr. Patterns 4, 741-747.
34. Davis, E., Caiment, F., Tordoir, X., Cavaille, J., Ferguson-Smith, A., Cockett, N., et al. (2005). RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg1 1 locus. Curr. Biol. 15, 743-749.
35. Desterro, J. M., Keegan, L. P., Lafarga, M., Berciano, M. T., O'Connell, M., and Carmo-Fonseca, M. (2003). Dynamic association of RNA-editing enzymes with the nucleolus. J. Cell Sci. 116, 1805-1818.
36. Dimauro, S. (2004). Mitochondrial medicine. Biochim. Biophys. Acta 1659, 107-114.
37. Dimauro, S., and Davidzon, G. (2005). Mitochondrial DNA and disease. Ann. Med. 37, 222-232.
38. Ding, F., Prints, Y., Dhar, M. S., Johnson, D. K., Garnacho-Montero, C., Nicholls, R. D., et al. (2005). Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader-Willi syndrome mouse models. Mamm. Genome 16,424-431.
39. Dinger, M. E., Pang, K. C., Mercer, T. R., and Mattick, J. S. (2008). Differentiating protein-coding and noncod-ing RNA: challenges and ambiguities. PLoS Comput. Biol. 4:e1000176. doi: 10.1371/journal.pcbi.1000176
40. Doe, C.M., Relkovic, D., Garfield, A. S., Dalley, J. W., Theobald, D. E., Humby, T., et al. (2009). Loss of the imprinted snoRNA mbii-52 leads to increased 5htr2c pre-RNA editing and altered 5HT2CR-mediated behaviour. Hum. Mol. Genet. 18, 2140-2148.
41. Dostie, J., Mourelatos, Z., Yang, M., Sharma, A., and Dreyfuss, G. (2003). Numerous microRNPs in neuronal cells containing novel microRNAs. RNA 9, 180-186.
42. Du, Y., Davisson, M. T., Kafadar, K., and Gardiner, K. (2006). A-to-I pre-mRNA editing of the serotonin 2C receptor: comparisons among inbred mouse strains. Gene 382, 39-46.
43. Eacker, S. M., Dawson, T. M., and Dawson, V. L. (2009). Understanding microRNAs in neurodegenera-tion. Nat. Rev. Neurosci. 10, 837-841.
44. Eisenberg, E., Nemzer, S., Kinar, Y., Sorek, R., Rechavi, G., and Lev-anon,E.Y. (2005). Is abundant A-to-I RNA editing primate-specific? Trends Genet 21, 77-81.
45. Emeson, R. B., and Singh, M. (2001). "Adenosine to inosine RNA editing: substrates and consequences.," in RNA Editing: Frontiers in Molecular Biology, ed. B. L. Bass (London: Oxford University Press), 109-138.
46. Enciu, A. M., Popescu, B. O., and Gheorghisan-Galateanu, A. (2012). MicroRNAs in brain development and degeneration. Mol. Biol. Rep. 39, 2243-2252.
47. Englander, M. T., Dulawa, S. C., Bhansali, P., andSchmauss, C. (2005). How stress and fluoxetine modulate serotonin 2C receptor pre-mRNA editing. J. Neurosci. 25, 648-651.
48. Faghihi, M. A., Modarresi, F., Khalil, A. M., Wood, D. E., Sahagan, B. G., Morgan, T. E., et al. (2008). Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 14, 723-730.
49. Fattal, O., Budur, K., Vaughan, A. J., and Franco, K. (2006). Review of the literature on major mental disorders in adult patients with mitochondrial diseases. Psychosomatics 47, 1-7.
50. Fedoriw, A., Mugford, J., and Magnu-son, T. (2012). Genomic imprinting and epigenetic control of development. Cold Spring Harb. Perspect. Biol. 4,a008136.
51. Feng, Y., Sansam, C. L., Singh, M., and Emeson, R. B. (2006). Altered RNA editing in mice lacking ADAR2 autoregulation. Mol. Cell. Biol. 26, 480-488.
52. Fernandez, H. R., Kavi, H. H., Xie, W., and Birchler, J. A. (2005). Het-erochromatin: on the ADAR radar? Curr. Biol. 15,R132-R134.
53. Flomen, R., and Makoff, A. (2011). Increased RNA editing in EAAT2 pre-mRNA from amyotrophic lateral sclerosis patients: involvement of a cryptic polyadenylation site. Neurosci. Lett. 497, 139-143.
54. Fu, Y H., Pizzuti, A., Fenwick, R. G. Jr., King, J., Rajnarayan, S., Dunne, P. W., et al. (1992). An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science 255, 1256-1258.
55. Furuno, M., Pang, K. C., Ninomiya, N., Fukuda, S., Frith, M. C., Bult, C., et al. (2006). Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet. 2:e37. doi: 10.1371/journal.pgen.0020037
56. Gallo, J. M., Jin, P., Thornton, C. A., Lin, H., Robertson, J., D'Souza, I., et al. (2005). The role of RNA and RNA processing in neurodegeneration. J. Neurosci. 25, 10372-10375.
57. Gardiner, K., and Du, Y. (2006). A-to-I editing of the 5HT2C receptor and behaviour. Brief. Funct. Genomic Proteomic 5, 37-42.
58. Gatchel, J. R., and Zoghbi, H. Y (2005). Diseases of unstable repeat expansion: mechanisms and common principles. Nat. Rev. Genet. 6, 743-755.
59. George, C. X., Wagner, M. V., and Samuel, C. E. (2005). Expression of interferon-inducible RNA adenosine deaminase ADAR1 during pathogen infection and mouse embryo development involves tissue-selective promoter utilization and alternative splicing. J. Biol. Chem. 280, 15020-15028.
60. Ghildiyal,M.,and Zamore,P. D. (2009). Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10, 94-108.
61. Guibert, S., Forne, T., and Weber, M. (2012). Global profiling of DNA methylation erasure in mouse primordial germ cells. Genome Res. 22, 633-641.
62. Gurevich, I., Tamir, H., Arango, V., Dwork, A. J., Mann, J. J., and Schmauss, C. (2002). Altered editing of serotonin 2C receptor pre-mRNA in the prefrontal cortex of depressed suicide victims. Neuron 34, 349-356.
63. Hackler, E. A., Airey, D. C., Shannon, C. C., Sodhi, M. S., and Sanders-Bush, E. (2006). 5-HT(2C) receptor RNA editing in the amygdala of C57BL/6J, DBA/2J, and BALB/cJ mice. Neurosci. Res. 55, 96-104.
64. Hagerman, R. J., Ono, M. Y., and Hager-man, P. J. (2005). Recent advances in fragile X: a model for autism and neurodegeneration. Curr. Opin. Psychiatry 18, 490-496.
65. Han, J., Kim, D., and Morris, K. V. (2007). Promoter-associated RNA is required for RNA-directed transcrip-tional gene silencing in human cells. Proc. Natl. Acad. Sci. U.S.A. 104, 12422-12427.
66. Hansen, K. F., Karelina, K., Sakamoto, K., Wayman, G. A., Impey, S., and Obrietan, K. (2012). miRNA-132: a dynamic regulator of cognitive capacity. Brain Struct. Funct. doi: 10.1007/s00429-012-0431-4 [Epub ahead of print].
67. Haramati, S., Chapnik, E., Sztainberg, Y., Eilam, R., Zwang, R., Gershoni, N.,et al. (2010). miRNA malfunction causes spinal motor neuron disease. Proc. Natl. Acad. Sci. U.S.A. 107, 13111-13116.
68. Harraz, M. M., Dawson, T. M., and Dawson, V. L. (2011). MicroRNAs in Parkinson's disease. J. Chem. Neu-roanat. 42, 127-130.
69. Heale, B. S., Keegan, L. P., Mcgurk, L., Michlewski, G., Brindle, J., Stan-ton, C. M., et al. (2009). Editing independent effects of ADARs on the miRNA/siRNA pathways. EMBO J. 28,3145-3156.
70. Hideyama, T., Yamashita, T., Aizawa, H., Tsuji, S., Kakita, A., Takahashi, H., et al. (2012). Profound downreg-ulation of the RNA editing enzyme ADAR2 in ALS spinal motor neurons. Neurobiol. Dis. 45, 1121-1128.
71. Holmes, S. E., O'Hearn, E., and Mar-golis, R. L. (2003). Why is SCA12 different from other SCAs? Cytogenet. Genome Res. 100,189-197.
72. Holmes, S. E., O'Hearn, E. E., Mcin-nis, M. G., Gorelick-Feldman, D. A., Kleiderlein, J. J., Callahan, C., et al. (1999). Expansion of a novel CAG trinucleotide repeat in the 5' region of PPP2R2B is associated with SCA12. Nat. Genet. 23,391-392.
73. Honda, K., Smith, M. A., Zhu, X., Baus, D., Merrick, W C, Tar-takoff,A. M.,et al. (2005). Ribosomal RNA in Alzheimer disease is oxidized by bound redox-active iron. J. Biol. Chem. 280,20978-20986.
74. Horsch, M., Seeburg, P. H., Adler, T., Aguilar-Pimentel, J. A., Becker, L., Calzada-Wack, J., et al. (2011). Requirement of the RNA-editing Enzyme ADAR2 for Normal Physiology in Mice. J. Biol. Chem. 286, 18614-18622.
75. Huang, Y., Liu, N., Wang, J. P., Wang, Y Q., Yu, X. L., Wang, Z. B., et al. (2012). Regulatory long non-coding RNA and its functions. J. Physiol. Biochem. 68,611-618.
76. Ideker, T., and Sharan, R. (2008). Protein networks in disease. Genome Res. 18,644-652.
77. Irimia, M., Denuc, A., Ferran, J. L., Per-naute, B., Puelles, L., Roy, S. W., et al. (2012). Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1. RNA Biol. 9, 12-21.
78. Iwamoto, K., and Kato, T. (2003). RNA editing of serotonin 2C receptor in human postmortem brains of major mental disorders. Neurosci. Lett. 346, 169-172.
79. Iwamoto, K., Nakatani, N., Bundo, M., Yoshikawa, T., and Kato, T. (2005). Altered RNA editing of serotonin 2C receptor in a rat model of depression. Neurosci. Res. 53, 69-76.
80. Jacobs, M. M., Fogg, R. L., Eme-son, R. B., and Stanwood, G. D. (2009). ADAR1 and ADAR2 expression and editing activity during fore-brain development. Dev. Neurosci. 31,223-237.
81. Jepson, J. E., and Reenan, R. A. (2010). Unraveling pleiotropic functions of A-to-I RNA editing in Drosophila. Fly (Austin) 4, 154-158.
82. Jiang, H., Mankodi, A., Swanson, M. S., Moxley, R. T., and Thornton, C. A. (2004). Myotonic dystrophy type 1 is associated with nuclear foci of mutant RNA, sequestration of muscleblind proteins and deregulated alternative splicing in neurons. Hum.Mol. Genet. 13,3079-3088.
83. Johnson, R. (2012). Long non-coding RNAs in Huntington's disease neu-rodegeneration. Neurobiol Dis. 46, 245-254.
84. Johnson, R., Richter, N., Jauch, R., Gaughwin, P. M., Zuccato, C., Cattaneo, E., et al. (2010). The Human Accelerated Region 1 non-coding RNA is repressed by REST in Huntington's disease. Physiol. Genomics doi: 10.1152/physiolge-nomics.00019.2010 [Epub ahead of print].
85. Junn, E., and Mouradian, M. M. (2012). MicroRNAs in neurodegen-erative diseases and their therapeutic potential. Pharmacol Ther. 133, 142-150.
86. Kanduri, C., Whitehead, J., and Mohammad, F. (2009). The long and the short of it: RNA-directed chro-matin asymmetry in mammalian X-chromosome inactivation. FEBS Lett. 583,857-864.
87. Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., et al. (2007). RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316,1484-1488.
88. Kawahara, Y., Ito, K., Ito, M., Tsuji, S., and Kwak, S. (2005). Novel splice variants of human ADAR2 mRNA: skipping of the exon encoding the dsRNA-binding domains, and multiple C-terminal splice sites. Gene 363, 193-201.
89. Kawahara, Y., Sun, H., Ito, K., Hideyama, T., Aoki, M., Sobue, G., et al. (2006). Underediting of GluR2 mRNA, a neuronal death inducing molecular change in sporadic ALS, does not occur in motor neurons in ALS1 or SBMA. Neurosci. Res. 54, 11-14.
90. Kawahara, Y., Zinshteyn, B., Chendri-mada, T. P., Shiekhattar, R., and Nishikura, K. (2007). RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep. 8, 763-769.
91. Keegan, L. P., Brindle, J., Gallo, A., Leroy, A., Reenan, R. A., and O'Connell, M. A. (2005). Tuning of RNA editing by ADAR is required in Drosophila. EMBOJ. 24,2183-2193.
92. Kennett, G. A., Wood, M. D., Bright, E, Trail, B., Riley, G., Holland, V., et al. (1997). SB 242084, a selective and brain penetrant 5-HT2C receptor antagonist. Neuropharmacology 36,609-620.
93. Kiesel, P., Kues, A., Kaup, E J., Bode-mer, W., Gibson, T. J., and Zis-chler, H. (2012). A comparative analysis to study editing of small noncoding BC200- and Alu transcripts in brain of prion-inoculated rhesus monkeys (M. Mulatta). J. Toxicol. Environ. Health A 75, 391-401.
94. Kim, D. D., Kim, T. T., Walsh, T., Kobayashi, Y., Matise, T. C., Buyske, S., et al. (2004a). Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res. 14, 1719-1725.
95. Kim, J., Krichevsky, A., Grad, Y., Hayes, G. D., Kosik, K. S., Church, G. M., et al. (2004b). Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl. Acad. Sci. U.S.A. 101, 360-365.
96. Kishore, S., Khanna, A., Zhang, Z., Hui, J., Balwierz, P. J., Stefan, M., et al. (2010). The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum. Mol. Genet. 19, 1153-1164.
97. Kishore, S., and Stamm, S. (2006). Regulation of alternative splicing by snoRNAs. Cold. Spring Harb. Symp. Quant. Biol. 71, 329-334.
98. Kiss, A. M., Jady, B. E., Bertrand, E., and Kiss, T. (2004). Human box H/ACA pseudouridylation guide RNA machinery. Mol. Cell. Biol. 24, 5797-5807.
99. Kiss, A. M., Jady, B. E., Darzacq, X., Verheggen, C., Bertrand, E., and Kiss, T. (2002). A Cajal body-specific pseudouridylation guide RNA is composed of two box H/ACA snoRNA-like domains. Nucleic Acids Res. 30, 4643-4649.
100. Koob, M. D., Moseley, M. L., Schut, L. J., Benzow, K. A., Bird, T. D., Day, J. W., et al. (1999). An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8). Nat. Genet. 21,379-384.
101. Kubota, T., Miyake, K., and Hirasawa, T. (2012). Epigenetic understanding of gene-environment interactions in psychiatric disorders: a new concept of clinical genetics. Clin. Epigenetics 4, 1.
102. Kuersten, S., and Goodwin, E. B. (2003). The power of the 3' UTR: transla-tional control and development. Nat. Rev. Genet. 4, 626-637.
103. Kwak, S., and Kawahara, Y (2005). Deficient RNA editing of GluR2 and neuronal death in amyotropic lateral sclerosis. J. Mol. Med. (Berl.) 83, 110-120.
104. Kwak, S., Nishimoto, Y., and Yamashita, T. (2008). Newly identified ADAR-mediated A-to-I editing positions as a tool for ALS research. RNA Biol. 5, 193-197.
105. Lau, P., and de Strooper, B. (2010). Dys-regulated microRNAs in neurode-generative disorders. Semin. Cell Dev. Biol. 21, 768-773.
106. Lee, J. W., Beebe, K., Nangle, L. A., Jang, J., Longo-Guess, C. M., Cook, S. A., et al. (2006). Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 443, 50-55.
107. Levanon, E. Y., Eisenberg, E., Yelin, R., Nemzer, S., Hallegger, M., Shemesh, R., et al. (2004). Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22, 1001-1005.
108. Lewis, A., and Reik, W. (2006). How imprinting centres work. Cytogenet. GenomeRes. 113,81-89.
109. Luciano, D. J., Mirsky, H., Vendetti, N. J., and Maas, S. (2004). RNA editing of a miRNA precursor. RNA 10, 1174-1177.
110. Luco, R. F., Allo, M., Schor, I. E., Korn-blihtt, A. R., and Misteli, T. (2011). Epigenetics in alternative pre-mRNA splicing. Cell 144, 16-26.
111. Luco, R. F., and Misteli, T. (2011). More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation. Curr. Opin. Genet. Dev. 21,366-372.
112. Macbeth, M. R., Schubert, H. L., Vande-mark, A. P., Lingam, A. T., Hill, C. P., and Bass, B. L. (2005). Inositol hexak-isphosphate is bound in the ADAR2 core and required for RNA editing. Science 309, 1534-1539.
113. Mahadevan, M., Tsilfidis, C., Sabourin, L., Shutler, G., Amemiya, C., Jansen, G., et al. (1992). Myotonic dystrophy mutation: an unstable CTG repeat in the 3' untranslated region of the gene. Science 255, 1253-1255.
114. Martin, J. R., Bos, M., Jenck, F., Moreau, J., Mutel, V., Sleight, A. J., et al. (1998). 5-HT2C receptor agonists: pharmacological characteristics and therapeutic potential. J. Pharmacol. Exp. Ther. 286,913-924.
115. Matsuura, T., Yamagata, T., Burgess, D. L., Rasmussen, A., Grewal, R. P., Watase, K., et al. (2000). Large expansion of the ATTCT pentanucleotide repeat in spinocerebellar ataxia type 10. Nat Genet. 26, 191-194.
116. Mattick, J. S. (2003). Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25, 930-939.
117. Mattick, J. S., and Gagen, M. J. (2001). The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol. 18, 1611-1630.
118. Mattick, J. S., and Makunin, I. V. (2005). Small regulatory RNAs in mammals. Hum.Mol. Genet. 14, R121-R132.
119. Mattick, J. S., and Makunin, I. V. (2006). Non-coding RNA. Hum. Mol. Genet. 15,R17-R29.
120. Mattick, J. S., and Mehler, M. F. (2008). RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci. 31,227-233.
121. Matzke, M., Kanno, T., Huettel, B., Daxinger, L., and Matzke, A. J. (2007). Targets of RNA-directed DNA methylation. Curr. Opin. Plant Biol. 10,512-519.
122. Mehler, M. F. (2008). Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog. Neurobiol. 86, 305-341.
123. Mehler, M. F., and Mattick, J. S. (2007). Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol. Rev. 87, 799-823.
124. Meier, U. T. (2005). The many facets of H/ACA ribonucleoproteins. Chromo-soma 114,1-14.
125. Melcher, T., Maas, S., Herb, A., Spren-gel, R., Higuchi, M., and Seeburg, P. H. (1996). RED2, a brain-specific member of the RNA-specific adeno-sine deaminase family. J. Biol. Chem. 271,31795-31798.
126. Mercer, T. R., Qureshi, I. A., Gokhan, S., Dinger, M. E., Li, G., Mattick, J. S., et al. (2010). Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci. 11:14. doi: 10.1186/1471-2202-11-14
127. Mette, M. F., Aufsatz, W., Van Der Winden, J., Matzke, M. A., and Matzke, A. J. (2000). Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBOJ. 19,5194-5201.
128. Migicovsky, Z., and Kovalchuk, I. (2011). Epigenetic memory in mammals. Front. Genet. 2:28. doi: 10.3389/fgene.2011.00028
129. Miyake, K., Hirasawa, T., Koide, T., and Kubota, T. (2012). Epigenetics in autism and other neurodevelopmen-tal diseases. Adv. Exp. Med. Biol. 724, 91-98.
130. Morabito, M. V., Abbas, A. I., Hood, J. L., Kesterson, R. A., Jacobs, M. M., Kump, D. S., et al. (2010). Mice with altered serotonin 2C receptor RNA editing display characteristics of Prader-Willi syndrome. Neurobiol. Dis. 39, 169-180.
131. Morse, D. P., Aruscavage, P. J., and Bass, B. L. (2002). RNA hairpins in noncoding regions of human brain and Caenorhabditis elegans mRNA are edited by adenosine deaminases that act on RNA. Proc. Natl. Acad. Sci. U.S.A. 99,7906-7911.
132. Mutsuddi, M., Marshall, C. M., Ben-zow, K. A., Koob, M. D., and Rebay, I. (2004). The spinocerebellar ataxia 8 noncoding RNA causes neu-rodegeneration and associates with staufen in Drosophila. Curr. Biol. 14, 302-308.
133. Neeman, Y., Levanon, E. Y., Jantsch, M. F., and Eisenberg, E. (2006). RNA editing level in the mouse is determined by the genomic repeat repertoire. RNA 12, 1802-1809.
134. Nemes, J. P., Benzow, K. A., Moseley, M. L., Ranum, L. P., and Koob, M. D. (2000). The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1). Hum. Mol. Genet.9, 1543-1551.
135. Nishikura, K. (2006). Editor meets silencer: crosstalk between RNA editing and RNA interference. Nat. Rev. Mol. Cell Biol. 7,919-931.
136. Niswender, C. M., Copeland, S. C., Herrick-Davis, K., Emeson, R. B., and Sanders-Bush, E. (1999). RNA editing of the human serotonin 5-hydroxytryptamine 2C receptor silences constitutive activity. J. Biol. Chem. 274, 9472-9478.
137. O'Neill, M. J. (2005). The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum. Mol Genet. 14, R113-R120.
138. Ohman, M. (2007). A-to-I editing challenger or ally to the microRNA process. Biochimie 89, 1171-1176.
139. Pal-Bhadra, M., Bhadra, U., and Birch-ler, J. A. (2002). RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila. Mol. Cell. 9, 315-327.
140. Palladino, M. J., Keegan, L. P., O'Connell, M. A., and Reenan, R. A. (2000). A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity. Cell 102, 437-449.
141. Pang, K. C., Frith, M. C., and Mattick, J. S. (2006). Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet. 22, 1-5.
142. Paro, S., Li, X., O'Connell, M. A., and Keegan, L. P. (2012). Regulation and functions of ADAR in Drosophila. Curr. Top. Microbiol Immunol 353, 221-236.
143. Pascual, M., Vicente, M., Monfer-rer, L., and Artero, R. (2006). The Muscleblind family of proteins: an emerging class of regulators of developmentally programmed alternative splicing. Differentiation 74, 65-80.
144. Paul, M. S., and Bass, B. L. (1998). Ino-sine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBOJ. 17,1120-1127.
145. Paupard, M. C., O'Connell, M. A., Ger-ber, A. P., and Zukin, R. S. (2000). Patterns of developmental expression of the RNA editing enzyme rADAR2. Neuroscience 95, 869-879.
146. Poulsen, H., Jorgensen, R., Heding, A., Nielsen, F. C., Bonven, B., and Egebjerg, J. (2006). Dimerization of ADAR2 is mediated by the double-stranded RNA binding domain. RNA 12,1350-1360.
147. Prasanth, K. V., Prasanth, S. G.,Xuan,Z., Hearn, S., Freier, S. M., Bennett, C. F., et al. (2005). Regulating gene expression through RNA nuclear retention. Cell 123, 249-263.
148. Qureshi, I. A., and Mehler, M. F. (2011). Non-coding RNA networks underlying cognitive disorders across the lifespan. Trends Mol. Med. 17, 337-346.
149. Qureshi, I. A., and Mehler, M. F. (2012). Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat. Rev. Neu-rosci. 13,528-541.
150. Ranum, L. P., Rasmussen, P. F., Benzow, K. A., Koob, M. D., and Day, J. W. (1998). Genetic mapping of a second myotonic dystrophy locus. Nat. Genet. 19,196-198.
151. Reenan, R. A. (2001). The RNA world meets behavior: A → I pre-mRNA editing in animals. Trends Genet. 17, 53-56.
152. Rogelj, B., and Giese, K. P. (2004). Expression and function of brain specific small RNAs. Rev. Neurosci. 15, 185-198.
153. Rogelj, B., Hartmann, C. E., Yeo, C. H., Hunt, S. P., and Giese, K. P. (2003). Contextual fear conditioning regulates the expression of brain-specific small nucleolar RNAs in hippocampus. Eur. I Neurosci. 18, 3089-3096.
154. Rueter, S. M., Dawson, T. R., and Emeson, R. B. (1999). Regulation of alternative splicing by RNA editing. Nature 399, 75-80.
155. Saito, Y., and Saito, H. (2012). MicroR-NAs in cancers and neurodegenera-tive disorders. Front. Genet. 3:194. doi: 10.3389/fgene.2012.00194
156. Salta, E., and De Strooper, B. (2012). Non-coding RNAs with essential roles in neurodegenerative disorders. Lancet Neurol. 11, 189-200.
157. Sansam, C. L., Wells, K. S., and Emeson, R. B. (2003). Modulation of RNA editing by functional nucleolar sequestration of ADAR2. Proc. Natl. Acad. Sci. U.S.A. 100, 14018-14023.
158. Satoh, J. (2012). Molecular network of microRNA targets in Alzheimer's disease brains. Exp. Neurol. 235, 436-446.
159. Scadden, A. D., and Smith, C.W. (2001). RNAi is antagonized by A -→ I hyper-editing. EMBORep. 2, 1107-1111.
160. Schellekens, H., Finger, B. C., Dinan, T. G., and Cryan, J. F. (2012). Ghrelin signalling and obesity: at the interface of stress, mood and food reward. Pharmacol Ther.135, 316-326.
161. Sie, C. P., and Kuchka, M. (2011). RNA editing adds flavor to complexity. Biochemistry (Mosc) 76, 869-881.
162. Simpson, L., and Emeson, R. B. (1996). RNA editing. Annu. Rev. Neurosci. 19, 27-52.
163. Singh, M., Kesterson, R. A., Jacobs, M. M., Joers, J. M., Gore, J. C., and Emeson, R. B. (2007). Hyperpha-gia-mediated obesity in transgenic mice misexpressing the RNA-editing enzyme ADAR2. J. Biol. Chem. 282, 22448-22459.
164. Singh, M., Singh, M. M., Na, E., Agas-sandian, K., Zimmerman, M. B., and Johnson,A.K. (2011). Altered ADAR 2 equilibrium and 5HT(2C) R editing in the prefrontal cortex of ADAR 2 transgenic mice. Genes Brain Behav. 10, 637-647.
165. Singh, M., Zimmerman, M. B., Beltz, T. G., and Johnson, A. K. (2009). Affect-related behaviors in mice misexpressing the RNA editing enzyme ADAR2. Physiol Behav. 97, 446-454.
166. Sleutels, F., Barlow, D. P., and Lyle, R. (2000). The uniqueness of the imprinting mechanism. Curr. Opin. Genet. Dev 10, 229-233.
167. Sodhi, M. S., Airey, D. C., Lambert, W., Burnet, P. W., Harrison, P. J., and Sanders-Bush, E. (2005). A rapid new assay to detect RNA editing reveals antipsychotic-induced changes in serotonin-2C transcripts. Mol. Pharmacol. 68, 711-719.
168. Sodhi, M. S., Burnet, P. W., Makoff, A. J., Kerwin, R. W., and Harrison, P. J. (2001). RNA editing of the 5-HT(2C) receptor is reduced in schizophrenia. Mol. Psychiatry 6, 373-379.
169. Song, X., Wang, X., Arai, S., and Kurokawa, R. (2012). Promoter-associated noncoding RNA from the CCND1 promoter. Methods Mol. Biol. 809, 609-622.
170. Sonntag, K. C. (2010). MicroRNAs and deregulated gene expression networks in neurodegeneration. Brain Res. 1338,48-57.
171. Tonkin, L. A., Saccomanno, L., Morse, D. P., Brodigan, T., Krause, M., and Bass, B. L. (2002). RNA editing by ADARs is important for normal behavior in Caenorhabditis elegans. EMBO J. 21, 6025-6035.
172. Tran, V. G., Court, F., Duputie, A., Antoine, E., Aptel, N., Milligan, L., et al. (2012). H19 antisense RNA can up-regulate igf2 transcription by activation of a novel promoter in mouse myoblasts. PLoS ONE 7:e37923. doi:10.1371/journal.pone.0037923
173. Valente, L., and Nishikura, K. (2005). ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. Prog. Nucleic Acid Res. Mol. Biol. 79,299-338.
174. Valente, L., and Nishikura, K. (2007). RNA binding-independent dimerization of adenosine deaminases acting on RNA and dominant negative effects of nonfunctional subunits on dimer functions. J. Biol. Chem. 282, 16054-16061.
175. Van Esch, H. (2006). The Fragile X pre-mutation: new insights and clinical consequences. Eur. J. Med. Genet. 49, 1-8.
176. Vesely, C., Tauber, S., Sedlazeck, F. J., Von Haeseler, A., and Jantsch, M. F. (2012). Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res. 22,1468-1476.
177. Vitali, P., Basyuk, E., Le Meur, E., Bertrand, E., Muscatelli, F., Cavaille, J.,et al. (2005). ADAR2-mediatedediting of RNA substrates in the nucle-olus is inhibited by C/D small nucleolar RNAs. J. Cell Biol. 169, 745-753.
178. Wang, G., Van Der Walt, J. M., Mayhew, G., Li, Y J., Zuchner, S., Scott, W. K., et al. (2008). Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpres-sion of alpha-synuclein. Am. J. Hum. Genet. 82, 283-289.
179. Wang, Q., Miyakoda, M., Yang, W., Khillan, J., Stachura, D. L., Weiss, M. J., et al. (2004a). Stress-induced apoptosis associated with null mutation of ADAR1 RNA editing deaminase gene. J. Biol Chem. 279, 4952-4961.
180. Wang, Y., Joh, K., Masuko, S., Yatsuki, H., Soejima, H., Nabetani, A., et al. (2004b). The mouse Murr1 gene is imprinted in the adult brain, presumably due to transcriptional interference by the antisense-oriented U2af 1-rs1 gene. Mol. Cell. Biol. 24, 270-279.
181. Wang, Y., Li, S., Chen, L., You, G., Bao, Z., Yan, W., et al. (2012). Glioblas-toma with an oligodendroglioma component: distinct clinical behavior, genetic alterations, and outcome. Neurooncol. 14,518-525.
182. Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agar-wal, P., et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature420,520-562.
183. Wright, A., and Vissel, B. (2012). The essential role of AMPA receptor GluR2 subunit RNA editing in the normal and diseased brain. Front. Mol. Neurosci. 5:34. doi: 10.3389/fnmol.2012.00034
184. Yang, J. H., Nie, Y., Zhao, Q., Su, Y., Pypaert, M., Su, H., et al. (2003). Intracellular localization of differentially regulated RNA-specific adenosine deaminase isoforms in inflammation. J. Biol. Chem. 278, 45833-45842.
185. Yang, P. K., and Kuroda, M. I. (2007). Noncoding RNAs and intranuclear positioning in monoal-lelic gene expression. Cell 128, 777-786.
186. Yang, W., Chendrimada, T. P., Wang, Q., Higuchi, M., Seeburg, P. H., Shiekhattar, R., et al. (2006). Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat. Struct. Mol. Biol. 13,13-21.
187. Zhou, J., Wang, Q., Chen, L. L., and Carmichael, G. G. (2008). On the mechanism of induction of heterochromatin by the RNA-binding protein vigilin. RNA 14, 1773-1781.