Enhancing non-coding RNA information content with ADAR editing

Neuroscience Letters

Volumn 466, Issue 2, 2009, Pages 89-98

  St Laurent III, Georges ^a,b   Savva, Yiannis A ^a   Reenan, Robert ^a  

^a BROWN UNIVERSITY   (United States)

^b UNIVERSIDAD DE ANTIOQUIA   (Colombia)

Author keywords

ADAR; ADAR activity during stress and inflammation; Nervous system transcriptome; Non coding RNA (ncRNA); RNA editing

Indexed keywords

TRANSCRIPTOME; UNTRANSLATED RNA;

CELL FUNCTION; HUMAN; INFLAMMATION; INFORMATION PROCESSING; MOLECULAR EVOLUTION; MOLECULAR MECHANICS; NERVOUS SYSTEM; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REVIEW; RNA EDITING; STRESS;

ADENOSINE; ADENOSINE DEAMINASE; ANIMALS; GENE EXPRESSION PROFILING; HUMANS; MODELS, MOLECULAR; NERVOUS SYSTEM; RNA EDITING; RNA, UNTRANSLATED; SIGNAL TRANSDUCTION;

EID: 70350131063     PISSN: 03043940     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neulet.2009.09.009     Document Type: Review

References (93)

1. Andersen P., and Moser E.I. Brain temperature and hippocampal function. Hippocampus 5 (1995) 491-498
2. Anderson P., and Kedersha N. Stress granules. Curr. Biol. 19 (2009) R397-398
3. Aon M.A., Cortassa S., Akar F.G., and O'Rourke B. Mitochondrial criticality: a new concept at the turning point of life or death. Biochim. Biophys. Acta 1762 (2006) 232-240
4. Athanasiadis A., Rich A., and Maas S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2 (2004) e391
5. Bhattacharyya S.N., Habermacher R., Martine U., Closs E.I., and Filipowicz W. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125 (2006) 1111-1124
6. Biamonti G., and Caceres J.F. Cellular stress and RNA splicing. Trends Biochem. Sci. 34 (2009) 146-153
7. Blow M.J., Grocock R.J., van Dongen S., Enright A.J., Dicks E., Futreal P.A., Wooster R., and Stratton M.R. RNA editing of human microRNAs. Genome Biol. 7 (2006) R27
8. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31 (2003) 365-370
9. Cam H.P., Chen E.S., and Grewal S.I. Transcriptional scaffolds for heterochromatin assembly. Cell 136 (2009) 610-614
10. Cao X., Yeo G., Muotri A.R., Kuwabara T., and Gage F.H. Noncoding RNAs in the mammalian central nervous system. Annu. Rev. Neurosci. 29 (2006) 77-103
11. Chang H.H., Hemberg M., Barahona M., Ingber D.E., and Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453 (2008) 544-547
12. Chang K.Y., and Ramos A. The double-stranded RNA-binding motif, a versatile macromolecular docking platform. FEBS J. 272 (2005) 2109-2117
13. Cheah M.T., Wachter A., Sudarsan N., and Breaker R.R. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447 (2007) 497-500
14. Cheng J., Kapranov P., Drenkow J., Dike S., Brubaker S., Patel S., Long J., Stern D., Tammana H., Helt G., Sementchenko V., Piccolboni A., Bekiranov S., Bailey D.K., Ganesh M., Ghosh S., Bell I., Gerhard D.S., and Gingeras T.R. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308 (2005) 1149-1154
15. Chowdhury S., Ragaz C., Kreuger E., and Narberhaus F. Temperature-controlled structural alterations of an RNA thermometer. J. Biol. Chem. 278 (2003) 47915-47921
16. Clutterbuck D.R., Leroy A., O'Connell M.A., and Semple C.A. A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10. Bioinformatics 21 (2005) 2590-2595
17. Crick F. Central dogma of molecular biology. Nature 227 (1970) 561-563
18. Dawson T.R., Sansam C.L., and Emeson R.B. Structure and sequence determinants required for the RNA editing of ADAR2 substrates. J. Biol. Chem. 279 (2004) 4941-4951
19. DeCerbo J., and Carmichael G.G. Retention and repression: fates of hyperedited RNAs in the nucleus. Curr. Opin. Cell Biol. 17 (2005) 302-308
20. Draper D.E. Protein-RNA recognition. Annu. Rev. Biochem. 64 (1995) 593-620
21. Faghihi M.A., Modarresi F., Khalil A.M., Wood D.E., Sahagan B.G., Morgan T.E., Finch C.E., St Laurent III G., Kenny P.J., and Wahlestedt C. Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 14 (2008) 723-730
22. Faulkner G.J., Kimura Y., Daub C.O., Wani S., Plessy C., Irvine K.M., Schroder K., Cloonan N., Steptoe A.L., Lassmann T., Waki K., Hornig N., Arakawa T., Takahashi H., Kawai J., Forrest A.R., Suzuki H., Hayashizaki Y., Hume D.A., Orlando V., Grimmond S.M., and Carninci P. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41 (2009) 563-571
23. Fejes-Toth. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457 (2009) 1028-1032
24. Fire A., Xu S., Montgomery M.K., Kostas S.A., Driver S.E., and Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
25. Gasser S., Orsulic S., Brown E.J., and Raulet D.H. The DNA damage pathway regulates innate immune system ligands of the NKG2D receptor. Nature 436 (2005) 1186-1190
26. Gingeras T.R., Higuchi R., Kricka L.J., Lo Y.M., and Wittwer C.T. Fifty years of molecular (DNA/RNA) diagnostics. Clin. Chem. 51 (2005) 661-671
27. 2+ signaling from growth cone to soma mediates reversal of neuronal migration induced by slit-2. Cell 129 (2007) 385-395
28. Hasler J., and Strub K. Alu RNP and Alu RNA regulate translation initiation in vitro. Nucleic Acids Res. 34 (2006) 2374-2385
29. Hoopengardner B., Bhalla T., Staber C., and Reenan R. Nervous system targets of RNA editing identified by comparative genomics. Science 301 (2003) 832-836
30. Hu Q., Kwon Y.S., Nunez E., Cardamone M.D., Hutt K.R., Ohgi K.A., Garcia-Bassets I., Rose D.W., Glass C.K., Rosenfeld M.G., and Fu X.D. Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 19199-19204
31. Huang S., Eichler G., Bar-Yam Y., and Ingber D.E. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys. Rev. Lett. 94 (2005) 128701
32. Huertas D., Cortes A., Casanova J., and Azorin F. Drosophila DDP1, a multi-KH-domain protein, contributes to centromeric silencing and chromosome segregation. Curr. Biol. 14 (2004) 1611-1620
33. Ingleby L., Maloney R., Jepson J., Horn R., and Reenan R. Regulated RNA editing and functional epistasis in Shaker potassium channels. J. Gen. Physiol. 133 (2009) 17-27
34. Jepson J.E., and Reenan R.A. RNA editing in regulating gene expression in the brain. Biochim. Biophys. Acta 1779 (2008) 459-470
35. Johnson J.M., Edwards S., Shoemaker D., and Schadt E.E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21 (2005) 93-102
36. Kallman A.M., Sahlin M., and Ohman M. ADAR2 A → I editing: site selectivity and editing efficiency are separate events. Nucleic Acids Res. 31 (2003) 4874-4881
37. Katayama S., Tomaru Y., Kasukawa T., Waki K., Nakanishi M., Nakamura M., Nishida H., Yap C.C., Suzuki M., Kawai J., Suzuki H., Carninci P., Hayashizaki Y., Wells C., Frith M., Ravasi T., Pang K.C., Hallinan J., Mattick J., Hume D.A., Lipovich L., Batalov S., Engstrom P.G., Mizuno Y., Faghihi M.A., Sandelin A., Chalk A.M., Mottagui-Tabar S., Liang Z., Lenhard B., and Wahlestedt C. Antisense transcription in the mammalian transcriptome. Science 309 (2005) 1564-1566
38. Kawahara Y., Megraw M., Kreider E., Iizasa H., Valente L., Hatzigeorgiou A.G., and Nishikura K. Frequency and fate of microRNA editing in human brain. Nucleic Acids Res. 36 (2008) 5270-5280
39. Kim D.D., Kim T.T., Walsh T., Kobayashi Y., Matise T.C., Buyske S., and Gabriel A. Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res. 14 (2004) 1719-1725
40. Kishore S., and Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311 (2006) 230-232
41. Kitano H. Towards a theory of biological robustness. Mol. Syst. Biol. 3 (2007) 137
42. Kuchibhotla K.V., Lattarulo C.R., Hyman B.T., and Bacskai B.J. Synchronous hyperactivity and intercellular calcium waves in astrocytes in Alzheimer mice. Science 323 (2009) 1211-1215
43. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., Funke R., Gage D., Harris K., Heaford A., Howland J., Kann L., Lehoczky J., LeVine R., McEwan P., McKernan K., Meldrim J., Mesirov J.P., Miranda C., Morris W., Naylor J., Raymond C., Rosetti M., Santos R., Sheridan A., Sougnez C., Stange-Thomann N., Stojanovic N., Subramanian A., Wyman D., Rogers J., Sulston J., Ainscough R., Beck S., Bentley D., Burton J., Clee C., Carter N., Coulson A., Deadman R., Deloukas P., Dunham A., Dunham I., Durbin R., French L., Grafham D., Gregory S., Hubbard T., Humphray S., Hunt A., Jones M., Lloyd C., McMurray A., Matthews L., Mercer S., Milne S., Mullikin J.C., Mungall A., Plumb R., Ross M., Shownkeen R., Sims S., Waterston R.H., Wilson R.K., Hillier L.W., McPherson J.D., Marra M.A., Mardis E.R., Fulton L.A., Chinwalla A.T., Pepin K.H., Gish W.R., Chissoe S.L., Wendl M.C., Delehaunty K.D., Miner T.L., Delehaunty A., Kramer J.B., Cook L.L., Fulton R.S., Johnson D.L., Minx P.J., Clifton S.W., Hawkins T., Branscomb E., Predki P., Richardson P., Wenning S., Slezak T., Doggett N., Cheng J.F., Olsen A., Lucas S., Elkin C., Uberbacher E., Frazier M., Gibbs R.A., Muzny D.M., Scherer S.E., Bouck J.B., Sodergren E.J., Worley K.C., Rives C.M., Gorrell J.H., Metzker M.L., Naylor S.L., Kucherlapati R.S., Nelson D.L., Weinstock G.M., Sakaki Y., Fujiyama A., Hattori M., Yada T., Toyoda A., Itoh T., Kawagoe C., Watanabe H., Totoki Y., Taylor T., Weissenbach J., Heilig R., Saurin W., Artiguenave F., Brottier P., Bruls T., Pelletier E., Robert C., Wincker P., Smith D.R., Doucette-Stamm L., Rubenfield M., Weinstock K., Lee H.M., Dubois J., Rosenthal A., Platzer M., Nyakatura G., Taudien S., Rump A., Yang H., Yu J., Wang J., Huang G., Gu J., Hood L., Rowen L., Madan A., Qin S., Davis R.W., Federspiel N.A., Abola A.P., Proctor M.J., Myers R.M., Schmutz J., Dickson M., Grimwood J., Cox D.R., Olson M.V., Kaul R., Shimizu N., Kawasaki K., Minoshima S., Evans G.A., Athanasiou M., Schultz R., Roe B.A., Chen F., Pan H., Ramser J., Lehrach H., Reinhardt R., McCombie W.R., de la Bastide M., Dedhia N., Blocker H., Hornischer K., Nordsiek G., Agarwala R., Aravind L., Bailey J.A., Bateman A., Batzoglou S., Birney E., Bork P., Brown D.G., Burge C.B., Cerutti L., Chen H.C., Church D., Clamp M., Copley R.R., Doerks T., Eddy S.R., Eichler E.E., Furey T.S., Galagan J., Gilbert J.G., Harmon C., Hayashizaki Y., Haussler D., Hermjakob H., Hokamp K., Jang W., Johnson L.S., Jones T.A., Kasif S., Kaspryzk A., Kennedy S., Kent W.J., Kitts P., Koonin E.V., Korf I., Kulp D., Lancet D., Lowe T.M., McLysaght A., Mikkelsen T., Moran J.V., Mulder N., Pollara V.J., Ponting C.P., Schuler G., Schultz J., Slater G., Smit A.F., Stupka E., Szustakowski J., Thierry-Mieg D., Thierry-Mieg J., Wagner L., Wallis J., Wheeler R., Williams A., Wolf Y.I., Wolfe K.H., Yang S.P., Yeh R.F., Collins F., Guyer M.S., Peterson J., Felsenfeld A., Wetterstrand K.A., Patrinos A., Morgan M.J., de Jong P., Catanese J.J., Osoegawa K., Shizuya H., Choi S., and Chen Y.J. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
44. Lein E.S., Hawrylycz M.J., Ao N., Ayres M., Bensinger A., Bernard A., Boe A.F., Boguski M.S., Brockway K.S., Byrnes E.J., Chen L., Chen T.M., Chin M.C., Chong J., Crook B.E., Czaplinska A., Dang C.N., Datta S., Dee N.R., Desaki A.L., Desta T., Diep E., Dolbeare T.A., Donelan M.J., Dong H.W., Dougherty J.G., Duncan B.J., Ebbert A.J., Eichele G., Estin L.K., Faber C., Facer B.A., Fields R., Fischer S.R., Fliss T.P., Frensley C., Gates S.N., Glattfelder K.J., Halverson K.R., Hart M.R., Hohmann J.G., Howell M.P., Jeung D.P., Johnson R.A., Karr P.T., Kawal R., Kidney J.M., Knapik R.H., Kuan C.L., Lake J.H., Laramee A.R., Larsen K.D., Lau C., Lemon T.A., Liang A.J., Liu Y., Luong L.T., Michaels J., Morgan J.J., Morgan R.J., Mortrud M.T., Mosqueda N.F., Ng L.L., Ng R., Orta G.J., Overly C.C., Pak T.H., Parry S.E., Pathak S.D., Pearson O.C., Puchalski R.B., Riley Z.L., Rockett H.R., Rowland S.A., Royall J.J., Ruiz M.J., Sarno N.R., Schaffnit K., Shapovalova N.V., Sivisay T., Slaughterbeck C.R., Smith S.C., Smith K.A., Smith B.I., Sodt A.J., Stewart N.N., Stumpf K.R., Sunkin S.M., Sutram M., Tam A., Teemer C.D., Thaller C., Thompson C.L., Varnam L.R., Visel A., Whitlock R.M., Wohnoutka P.E., Wolkey C.K., Wong V.Y., Wood M., Yaylaoglu M.B., Young R.C., Youngstrom B.L., Yuan X.F., Zhang B., Zwingman T.A., and Jones A.R. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445 (2007) 168-176
45. Leulliot N., and Varani G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40 (2001) 7947-7956
46. Lev-Maor G., Goren A., Sela N., Kim E., Keren H., Doron-Faigenboim A., Leibman-Barak S., Pupko T., and Ast G. The "alternative" choice of constitutive exons throughout evolution. PLoS Genet. 3 (2007) e203
47. Levanon E.Y., Eisenberg E., Yelin R., Nemzer S., Hallegger M., Shemesh R., Fligelman Z.Y., Shoshan A., Pollock S.R., Sztybel D., Olshansky M., Rechavi G., and Jantsch M.F. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 22 (2004) 1001-1005
48. Levanon K., Eisenberg E., Rechavi G., and Levanon E.Y. Letter from the editor: Adenosine-to-inosine RNA editing in Alu repeats in the human genome. EMBO Rep. 6 (2005) 831-835
49. Li C.L., Yang W.Z., Chen Y.P., and Yuan H.S. Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing. Nucleic Acids Res. 36 (2008) 3579-3589
50. Li J.B., Levanon E.Y., Yoon J.K., Aach J., Xie B., Leproust E., Zhang K., Gao Y., and Church G.M. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324 (2009) 1210-1213
51. Lin L., Shen S., Tye A., Cai J.J., Jiang P., Davidson B.L., and Xing Y. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet. 4 (2008) e1000225
52. Long D., Lee R., Williams P., Chan C.Y., Ambros V., and Ding Y. Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol. 14 (2007) 287-294
53. Lunde B.M., Moore C., and Varani G. RNA-binding proteins: modular design for efficient function. Nat. Rev. Mol. Cell Biol. 8 (2007) 479-490
54. Maas S., Kawahara Y., Tamburro K.M., and Nishikura K. A-to-I RNA editing and human disease. RNA Biol. 3 (2006) 1-9
55. Macbeth, et al. Science 309 (2005) 1534
56. Mattick J.S. A new paradigm for developmental biology. J. Exp. Biol. 210 (2007) 1526-1547
57. Mattick J.S., and Mehler M.F. RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci. 31 (2008) 227-233
58. Mehler M.F., and Mattick J.S. Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol. Rev. 87 (2007) 799-823
59. Mercer T.R., Dinger M.E., Sunkin S.M., Mehler M.F., and Mattick J.S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 716-721
60. Morris K.V. Non-coding RNAs, epigenetic memory, and the passage of information to progeny. RNA Biol. 6 (2009)
61. Nelson S.B., Sugino K., and Hempel C.M. The problem of neuronal cell types: a physiological genomics approach. Trends Neurosci. 29 (2006) 339-345
62. Newman M.A., Thomson J.M., and Hammond S.M. Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing. RNA 14 (2008) 1539-1549
63. Nishikura K. Editor meets silencer: crosstalk between RNA editing and RNA interference. Nat. Rev. Mol. Cell Biol. 7 (2006) 919-931
64. Olsen P.H., and Ambros V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216 (1999) 671-680
65. Owttrim G.W. RNA helicases and abiotic stress. Nucleic Acids Res. 34 (2006) 3220-3230
66. Parker R., and Sheth U. P bodies and the control of mRNA translation and degradation. Mol Cell. 25 (2007) 635-646
67. Patterson J.B., Thomis D.C., Hans S.L., and Samuel C.E. Mechanism of interferon action: double-stranded RNA-specific adenosine deaminase from human cells is inducible by alpha and gamma interferons. Virology 210 (1995) 508-511
68. Peng R., Dye B.T., Perez I., Barnard D.C., Thompson A.B., and Patton J.G. PSF and p54nrb bind a conserved stem in U5 snRNA. RNA 8 (2002) 1334-1347
69. Pollard K.S., Salama S.R., Lambert N., Lambot M.A., Coppens S., Pedersen J.S., Katzman S., King B., Onodera C., Siepel A., Kern A.D., Dehay C., Igel H., Ares Jr. M., Vanderhaeghen P., and Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443 (2006) 167-172
70. Polson A.G., and Bass B.L. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J. 13 (1994) 5701-5711
71. Prasanth K.V., Prasanth S.G., Xuan Z., Hearn S., Freier S.M., Bennett C.F., Zhang M.Q., and Spector D.L. Regulating gene expression through RNA nuclear retention. Cell 123 (2005) 249-263
72. Rajkowitsch L., and Schroeder R. Dissecting RNA chaperone activity. RNA 13 (2007) 2053-2060
73. Reenan R.A. Molecular determinants and guided evolution of species-specific RNA editing. Nature 434 (2005) 409-413
74. Reichow S.L., Hamma T., Ferre-D'Amare A.R., and Varani G. The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Res. 35 (2007) 1452-1464
75. Rybak A., Fuchs H., Smirnova L., Brandt C., Pohl E.E., Nitsch R., and Wulczyn F.G. A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nat. Cell Biol. 10 (2008) 987-993
76. Sasaki Y.T., Ideue T., Sano M., Mituyama T., and Hirose T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc. Natl. Acad. Sci. U.S.A. 106 (2009) 2525-2530
77. Scadden A.D. The RISC subunit Tudor-SN binds to hyper-edited double-stranded RNA and promotes its cleavage. Nat. Struct. Mol. Biol. 12 (2005) 489-496
78. Sengupta S., Parihar R., and Ganesh S. Satellite III non-coding RNAs show distinct and stress-specific patterns of induction. Biochem. Biophys. Res. Commun. 382 (2009) 102-107
79. Seong S.Y., and Matzinger P. Hydrophobicity: an ancient damage-associated molecular pattern that initiates innate immune responses. Nat. Rev. Immunol. 4 (2004) 469-478
80. Shamovsky I., Ivannikov M., Kandel E.S., Gershon D., and Nudler E. RNA-mediated response to heat shock in mammalian cells. Nature 440 (2006) 556-560
81. Shav-Tal Y., and Zipori D. PSF and p54(nrb)/NonO-multi-functional nuclear proteins. FEBS Lett. 531 (2002) 109-114
82. St Laurent III G., and Wahlestedt C. Noncoding RNAs: couplers of analog and digital information in nervous system function?. Trends Neurosci. 30 (2007) 612-621
83. Stefl R., Xu M., Skrisovska L., Emeson R.B., and Allain F.H. Structure and specific RNA binding of ADAR2 double-stranded RNA binding motifs. Structure 14 (2006) 345-355
84. Tian B., Bevilacqua P.C., Diegelman-Parente A., and Mathews M.B. The double-stranded-RNA-binding motif: interference and much more. Nat. Rev. Mol. Cell Biol. 5 (2004) 1013-1023
85. Tirosh I., Reikhav S., Levy A.A., and Barkai N. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324 (2009) 659-662
86. Valente L., and Nishikura K. ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. Prog. Nucleic Acid Res. Mol. Biol. 79 (2005) 299-338
87. Valente L., and Nishikura K. RNA binding-independent dimerization of adenosine deaminases acting on RNA and dominant negative effects of nonfunctional subunits on dimer functions. J. Biol. Chem. 282 (2007) 16054-16061
88. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., Gocayne J.D., Amanatides P., Ballew R.M., Huson D.H., Wortman J.R., Zhang Q., Kodira C.D., Zheng X.H., Chen L., Skupski M., Subramanian G., Thomas P.D., Zhang J., Gabor Miklos G.L., Nelson C., Broder S., Clark A.G., Nadeau J., McKusick V.A., Zinder N., Levine A.J., Roberts R.J., Simon M., Slayman C., Hunkapiller M., Bolanos R., Delcher A., Dew I., Fasulo D., Flanigan M., Florea L., Halpern A., Hannenhalli S., Kravitz S., Levy S., Mobarry C., Reinert K., Remington K., Abu-Threideh J., Beasley E., Biddick K., Bonazzi V., Brandon R., Cargill M., Chandramouliswaran I., Charlab R., Chaturvedi K., Deng Z., Di Francesco V., Dunn P., Eilbeck K., Evangelista C., Gabrielian A.E., Gan W., Ge W., Gong F., Gu Z., Guan P., Heiman T.J., Higgins M.E., Ji R.R., Ke Z., Ketchum K.A., Lai Z., Lei Y., Li Z., Li J., Liang Y., Lin X., Lu F., Merkulov G.V., Milshina N., Moore H.M., Naik A.K., Narayan V.A., Neelam B., Nusskern D., Rusch D.B., Salzberg S., Shao W., Shue B., Sun J., Wang Z., Wang A., Wang X., Wang J., Wei M., Wides R., Xiao C., Yan C., Yao A., Ye J., Zhan M., Zhang W., Zhang H., Zhao Q., Zheng L., Zhong F., Zhong W., Zhu S., Zhao S., Gilbert D., Baumhueter S., Spier G., Carter C., Cravchik A., Woodage T., Ali F., An H., Awe A., Baldwin D., Baden H., Barnstead M., Barrow I., Beeson K., Busam D., Carver A., Center A., Cheng M.L., Curry L., Danaher S., Davenport L., Desilets R., Dietz S., Dodson K., Doup L., Ferriera S., Garg N., Gluecksmann A., Hart B., Haynes J., Haynes C., Heiner C., Hladun S., Hostin D., Houck J., Howland T., Ibegwam C., Johnson J., Kalush F., Kline L., Koduru S., Love A., Mann F., May D., McCawley S., McIntosh T., McMullen I., Moy M., Moy L., Murphy B., Nelson K., Pfannkoch C., Pratts E., Puri V., Qureshi H., Reardon M., Rodriguez R., Rogers Y.H., Romblad D., Ruhfel B., Scott R., Sitter C., Smallwood M., Stewart E., Strong R., Suh E., Thomas R., Tint N.N., Tse S., Vech C., Wang G., Wetter J., Williams S., Williams M., Windsor S., Winn-Deen E., Wolfe K., Zaveri J., Zaveri K., Abril J.F., Guigo R., Campbell M.J., Sjolander K.V., Karlak B., Kejariwal A., Mi H., Lazareva B., Hatton T., Narechania A., Diemer K., Muruganujan A., Guo N., Sato S., Bafna V., Istrail S., Lippert R., Schwartz R., Walenz B., Yooseph S., Allen D., Basu A., Baxendale J., Blick L., Caminha M., Carnes-Stine J., Caulk P., Chiang Y.H., Coyne M., Dahlke C., Mays A., Dombroski M., Donnelly M., Ely D., Esparham S., Fosler C., Gire H., Glanowski S., Glasser K., Glodek A., Gorokhov M., Graham K., Gropman B., Harris M., Heil J., Henderson S., Hoover J., Jennings D., Jordan C., Jordan J., Kasha J., Kagan L., Kraft C., Levitsky A., Lewis M., Liu X., Lopez J., Ma D., Majoros W., McDaniel J., Murphy S., Newman M., Nguyen T., Nguyen N., Nodell M., Pan S., Peck J., Peterson M., Rowe W., Sanders R., Scott J., Simpson M., Smith T., Sprague A., Stockwell T., Turner R., Venter E., Wang M., Wen M., Wu D., Wu M., Xia A., Zandieh A., and Zhu X. The sequence of the human genome. Science 291 (2001) 1304-1351
89. Viswanathan S.R., Daley G.Q., and Gregory R.I. Selective blockade of microRNA processing by Lin28. Science 320 (2008) 97-100
90. Wang Q., Zhang Z., Blackwell K., and Carmichael G.G. Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. Curr. Biol. 15 (2005) 384-391
91. Yang J.H., Luo X., Nie Y., Su Y., Zhao Q., Kabir K., Zhang D., and Rabinovici R. Widespread inosine-containing mRNA in lymphocytes regulated by ADAR1 in response to inflammation. Immunology 109 (2003) 15-23
92. Zhang Z., and Carmichael G.G. The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell 106 (2001) 465-475
93. Zhang K., Chen X., Wu J., Sakaki K., Saunders T., Rutkowski D., Back S., and Kaufman R. Endoplasmic reticulum stress activates cleavage of CREBH to induce a systemic inflammatory response. Cell 124 (2006) 587-599