Noncoding RNAs in the mammalian central nervous system

Annual Review of Neuroscience

Volumn 29, Issue , 2006, Pages 77-103

  Cao, Xinwei ^a   Yeo, Gene ^a   Muotri, Alysson R ^a   Kuwabara, Tomoko ^b   Gage, Fred H ^a  

^a SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Base pairing; Comparative genomics; Evolution; Genome tiling microarray; LINE 1 elements

Indexed keywords

MICRORNA; SMALL INTERFERING RNA; SMALL NUCLEAR RNA; UNTRANSLATED RNA; BC1 RNA; SMALL CYTOPLASMIC RNA; SMALL NUCLEOLAR RNA;

CENTRAL NERVOUS SYSTEM; DNA MICROARRAY; GENETIC TRANSCRIPTION; GENOMICS; MAMMAL; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; REVIEW; RNA SEQUENCE; ANIMAL; HUMAN; METABOLISM; NEUROLOGIC DISEASE; PHYSIOLOGY;

ANIMALS; CENTRAL NERVOUS SYSTEM; HUMANS; MAMMALS; MICRORNAS; NERVOUS SYSTEM DISEASES; RETROELEMENTS; RNA, SMALL CYTOPLASMIC; RNA, SMALL NUCLEOLAR; RNA, UNTRANSLATED;

EID: 33745602880     PISSN: 0147006X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.neuro.29.051605.112839     Document Type: Review

References (149)

1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. 2002. Molecular Biology of the Cell. New York: Garland Publishing. 4th ed.
2. Ambros V. 2004. The functions of animal microRNAs. Nature 431:350-55
3. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. 2003. A uniform system for microRNA annotation. RNA 9:277-79
4. Andres ME, Burger C, Peral-Rubio MJ, Battaglioli E, Anderson ME, et al. 1999. CoREST: a functional corepressor required for regulation of neural-specific gene expression. Proc. Natl. Acad. Sci. USA 96:9873-78
5. Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, et al. 2001. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol. 11:941-50
6. Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR. 2004. Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 10:1813-19
7. Bachellerie J-P, Cavaille J, Huttenhofer A. 2002. The expanding snoRNA world. Biochimie 84:775-90
8. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, et al. 2005. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122:553-63
9. Ballas N, Grunseich C, Lu DD, Speh JC, Mandel G. 2005. REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell 121:645-57
10. Barad O, Meiri E, Avniel A, Aharonov R, Barzilai A, et al. 2004. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14:2486-94
11. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-97
12. Bartel DP, Chen CZ. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5:396-400
13. Bernstein E, Kim SY, Carmell MA, Murchison EP, Alcorn H, et al. 2003. Dicer is essential for mouse development. Nat. Genet. 35:215-17
14. Bertone P, Gerstein M, Snyder M. 2005. Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Res. 13:259-74
15. Brenner S, Jacob F, Meselson M. 1961. An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 190:576-81
16. Bruce AW, Donaldson IJ, Wood IC, Yerbury SA, Sadowski MI, et al. 2004. Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc. Natl. Acad. Sci. USA 101:10458-63
17. Calderone A, Jover T, Noh KM, Tanaka H, Yokota H, et al. 2003. Ischemic insults derepress the gene silencer REST in neurons destined to die. J. Neurosci. 23:2112-21
18. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309:1559-63
19. Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, et al. 2000. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl. Acad. Sci. USA 97:14311-16
20. Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116:499-509
21. Chen J-L, Blasco MA, Greider CW. 2000. Secondary structure of vertebrate telomerase RNA. Cell 100:503-14
22. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149-54
23. Chien P, Weissman JS, DePace AH. 2004. Emerging principles of conformation-based prion inheritance. Annu. Rev. Biochem. 73:617-56
24. Copley RR. 2004. Evolutionary convergence of alternative splicing in ion channels. Trends Genet. 20:171-76
25. Cost GJ, Boeke JD. 1998. Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure. Biochemistry 37:18081-93
26. Cost GJ, Feng Q, Jacquier A, Boeke JD. 2002. Human L1 element target-primed reverse transcription in vitro. EMBO J. 21:5899-910
27. Cost GJ, Golding A, Schlissel MS, Boeke JD. 2001. Target DNA chromatinization modulates nicking by L1 endonuclease. Nucleic Acids Res. 29:573-77
28. Cullen BR. 2004. Transcription and processing of human microRNA precursors. Mol. Cell 16:861-65
29. D'Amour KA, Gage FH. 2003. Genetic and functional differences between multipotent neural and pluripotent embryonic stem cells. Proc. Natl. Acad. Sci. USA 100:11866-72
30. Deleault NR, Geoghegan JC, Nishina K, Kascsak R, Williamson RA, Supattapone S. 2005. Protease-resistant prion protein amplification reconstituted with partially purified substrates and synthetic polyanions. J. Biol. Chem. 280:26873-79
31. Deleault NR, Lucassen RW, Supattapone S. 2003. RNA molecules stimulate prion protein conversion. Nature 425:717-20
32. Dermitzakis ET, Reymond A, Lyle R, Scamuffa N, Ucla C, et al. 2002. Numerous potentially functional but non-genie conserved sequences on human chromosome 21. Nature 420:578-82
33. Dhavan R, Tsai LH. 2001. A decade of CDK5. Nat. Rev. Mol. Cell Biol. 2:749-59
34. Ding F, Prints Y, Dhar MS, Johnson DK, Garnacho-Montero C, et al. 2005. Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader-Willi syndrome mouse models. Mamm. Genome 16:424-31
35. Doudna JA, Batey RT. 2004. Structural insights into the signal recognition particle. Annu. Rev. Biochem. 73:539-57
36. Eddy SR. 2001. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2:919-29
37. Esnault C, Maestre J, Heidmann T. 2000. Human LINE retrotransposons generate processed pseudogenes. Nat. Genet. 24:363-67
38. Fedor MJ, Williamson JR. 2005. The catalytic diversity of RNAs. Nat. Rev. Mol. Cell Biol. 6:399-412
39. Filipowicz W. 2000. Imprinted expression of small nucleolar RNAs in brain: time for RNomics. Proc. Natl. Acad. Sci. USA 97:14035-37
40. Filipowicz W. 2005. RNAi: the nuts and bolts of the RISC machine. Cell 122:17-20
41. Frank O, Giehl M, Zheng C, Hehlmann R, Leib-Mosch C, Seifarth W. 2005. Human endogenous retrovirus expression profiles in samples from brains of patients with schizophrenia and bipolar disorders. J. Virol. 79:10890-901
42. Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, et al. 2005. MicroRNAs regulate brain morphogenesis in zebrafish. Science 308:833-38
43. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33:D121-24
44. Grimes JA, Nielsen SJ, Battaglioli E, Miska EA, Speh JC, et al. 2000. The co-repressor mSin3A is a functional component of the REST-CoREST repressor complex. J. Biol. Chem. 275:9461-67
45. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-57
46. Han JS, Szak ST, Boeke JD. 2004. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature 429:268-74
47. Hartmann E, Hartmann RK. 2003. The enigma of ribonuclease P evolution. Trends Genet. 19:561-69
48. He L, Hannon GJ. 2004. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5:522-31
49. Huang Y, Myers SJ, Dingledine R. 1999. Transcriptional repression by REST: recruitment of Sin3A and histone deacetylase to neuronal genes. Nat. Neurosci. 2:867-72
50. Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, et al. 2001. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J. 20:2943-53
51. Huttenhofer A, Schattner P, Polacek N. 2005. Non-coding RNAs: hope or hype? Trends Genet. 21:289-97
52. Jin P, Zarnescu DC, Ceman S, Nakamoto M, Mowrey J, et al. 2004. Biochemical and genetic interaction between the fragile X mental retardation protein and the microRNA pathway. Nat. Neurosci. 7:113-17
53. John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. 2004. Human microRNA targets. PLoS Biol. 2:1862-79
54. Johnston RJ Jr, Robert O. 2003. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426:845-49
55. Johnston RJ Jr, Chang S, Etchberger JF, Ortiz CO, Hoben O. 2005. From the cover: microRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl. Acad. Sci. USA 102:12449-54
56. Kajikawa M, Okada N. 2002. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111:433-14
57. Karlsson H, Bachmann S, Schroder J, McArthur J, Torrey EF, Yolken RH. 2001. Retroviral RNA identified in the cerebrospinal fluids and brains of individuals with schizophrenia. Proc. Natl. Acad. Sci. USA 98:4634-39
58. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, et al. 2005. Antisense transcription in the mammalian transcriptome. Science 309:1564-66
59. Kazazian HH. 2001. Retrotransposon insertions in germ cells and somatic cells. Dev. Biol. (Basel) 106:307-13; discussion pp. 13-4, 17-29
60. Kelleher RJ 3rd, Govindarajan A, Tonegawa S. 2004. Translational regulatory mechanisms in persistent forms of synaptic plasticity. Neuron 44:59-73
61. Killian JK, Nolan CM, Wylie AA, Li T, Vu TH, et al. 2001. Divergent evolution in M6P/IGF2R imprinting from the Jurassic to the Quaternary. Hum. Mol. Genet. 10:1721-28
62. Kim HS, Takenaka O, Crow TJ. 1999. Cloning and nucleotide sequence of retroposons specific to hominoid primates derived from an endogenous retrovirus (HERV-K). AIDS Res. Hum. Retroviruses 15:595-601
63. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, et al. 2004. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc. Natl. Acad. Sci. USA 101:360-65
64. Kim VN. 2005. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6:376-85
65. Kishore S, Stamm S. (December 15, 2005)The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science; 10.1126/science. 1118265
66. Kiss T. 2001. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 20:3617-22
67. Krichevsky AM, King KS, Donahue CP, Khrapko K, Kosik KS. 2003. A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9:1274-81
68. Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH. 2004. A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116:779-93
69. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. 2002. Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12:735-39
70. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G. 2004. In search of antisense. Trends Biochem. Sci. 29:88-94
71. Lerner MR, Steitz JA. 1981. Snurps and scyrps. Cell 25:298-300
72. Lewejohann L, Skryabin BV, Sachser N, Prehn C, Heiduschka P, et al. 2004. Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice. Behav. Brain. Res. 154:273-89
73. Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA rargets. Cell 120:15-20
74. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769-73
75. Lipscombe D. 2005. Neuronal proteins custom designed by alternative splicing. Curr. Opin. Neurobiol. 15:358-63
76. Lisman J, Schulman H, Cline H. 2002. The molecular basis of CaMKII function in synaptic and behavioural memory. Nat. Rev. Neurosci. 3:175-90
77. Lunyak W, Burgess R, Prefontaine GG, Nelson C, Sze SH, et al. 2002. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science 298:1747-52
78. Lutz SM, Vincent BJ, Kazazian HH Jr, Batzer MA, Moran JV. 2003. Allelic heterogeneity in LINE-1 retrotransposition activity. Am. J. Hum. Genet. 73:1431-37
79. Lyle R, Watanabe D, te Vruchte D, Lerchner W, Smrzka OW, et al. 2000. The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat. Genet. 25:19-21
80. Martignetti JA, Brosius J. 1993. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. Proc. Natl. Acad. Sci. USA 90:11563-67
81. Mattick JS, Makunin IV. 2005. Small regulatory RNAs in mammals. Hum. Mol. Genet. 15:R121-32
82. Michels AA, Fraldi A, Li Q, Adamson TE, Bonnet F, et al. 2004. Binding of the 7SK snRNA turns the HEXIM1 protein into a P-TEFb (CDK9/cyclin T) inhibitor. EMBO J. 23:2608-19
83. Miki Y, Nishisho I, Horii A, Miyoshi Y, Utsunomiya J, et al. 1992. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 52:643-45
84. Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, et al. 2004. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5:R68
85. Moran JV, Holmes SE, Naas TP, DeBerardinis RJ, Boeke JD, Kazazian HH Jr. 1996. High frequency retrotransposition in cultured mammalian cells. Cell 87:917-27
86. Morrish TA, Gilbert N, Myers JS, Vincent BJ, Stamato TD, et al. 2002. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31:159-65
87. Muddashetty RS, Khanam T, Kondrashov A, Bundman M, Iacoangeli A, et al. 2002. Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J. Mol. Biol. 321:433-45
88. Muotri AR, Chu VT, Marchetto MC, Deng W, Moran JV, Gage FH. 2005. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 435:903-10
89. Muslimov IA, Banker G, Brosius J, Tiedge H. 1998. Activity-dependent regulation of dendritic BC1 RNA in hippocampal neurons in culture. J. Cell Biol. 141:1601-11
90. Nakamura A, Okazaki Y, Sugimoto J, Oda T, Jinno Y. 2003. Human endogenous retroviruses with transcriptional potential in the brain. J. Hum. Genet. 48:575-81
91. Nguyen VT, Kiss T, Michels AA, Bensaude O. 2001. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 414:322-25
92. Olsen PH, Ambros V. 1999. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216:671-80
93. Ostertag EM, DeBerardinis RJ, Goodier JL, Zhang Y, Yang N, et al. 2002. A mouse model of human L1 retrotransposition. Nat. Genet. 32:655-60
94. Ostertag EM, Kazazian HH Jr. 2001a. Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35:501-38
95. Ostertag EM, Kazazian HH Jr. 2001b. Twin priming: a proposed mechanism for the creation of inversions in L1 retrotransposition. Genome Res. 11:2059-65
96. Ostertag EM, Prak ET, DeBerardinis RJ, Moran JV, Kazazian HH Jr. 2000. Determination of L1 retrotransposition kinetics in cultured cells. Nucleic Acids Res. 28:1418-23
97. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, et al. 2004. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet. 36:40-45
98. Pang KC, Stephen S, Engstrom PG, Tajul-Arifin K, Chen W, et al. 2005. RNAdb - a comprehensive mammalian noncoding RNA database. Nucleic Acids Res. 33:D125-30
99. Pasquinelli AE, Hunter S, Bracht JU. 2005. MicroRNAs: a developing story. Curr. Opin. Genet. Dev. 15:200-5
100. Patel AA, Steitz JA. 2003. Splicing double: insights from the second spliceosome. Nat. Rev. Mol. Cell Biol. 4:960-70
101. Paul MS, Bass BL. 1998. Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J. 17:1120-27
102. Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N. 1996. Requirement for Xist in X chromosome inactivation. Nature 379:131-37
103. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, et al. 2005. Inhibition of translational initiation by Let-7 microRNA in human cells. Science 309:1573-76
104. Prak ET, Dodson AW, Farkash EA, Kazazian HH Jr. 2003. Tracking an embryonic L1 retrotransposition event. Proc. Natl. Acad. Sci. USA 100:1832-37
105. Ranum LP, Day JW. 2004. Pathogenic RNA repeats: an expanding role in genetic disease. Trends Genet. 20:506-12
106. Rivas E, Eddy SR. 2001. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2:8
107. Rogelj B, Hartmann CE, Yeo CH, Hunt SP, Giese KP. 2003. Contextual fear conditioning regulates the expression of brain-specific small nucleolar RNAs in hippocampus. Eur. J. Neurosci. 18:3089-96
108. Salter MW, Kalia LV. 2004. Src kinases: a hub for NMDA receptor regulation. Nat. Rev. Neurosci. 5:317-28
109. Schadt EE, Edwards SW, GuhaThakurta D, Holder D, Ying L, et al. 2004. A comprehensive transcript index of the human genome generated using microarrays and computational approaches. Genome Biol. 5:R73
110. Schmid CW. 1998. Does SINE evolution preclude Alu function? Nucleic Acids Res. 26:4541-50
111. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, et al. 2000. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18:1262-68
112. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V. 2004. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 5:R13
113. Shabalina SA, Spiridonov NA. 2004. The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol. 5:105
114. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, et al. 2004. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119:941-53
115. Skryabin BV, Kremerskothen J, Vassilacopoulou D, Disotell TR, Kapitonov VV, et al. 1998. The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates). J. Mol. Evol. 47:677-85
116. Sleutels F, Zwart R, Barlow DP. 2002. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415:810-13
117. Smirnova L, Grafe A, Seiler A, Schumacher S, Nitsch R, Wulczyn FG. 2005. Regulation of miRNA expression during neural cell specification. Eur. J. Neurosci. 21:1469-77
118. Sontheimer EJ, Carthew RW. 2005. Silence from within: endogenous siRNAs and miRNAs. Cell 122:9-12
119. Stole V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, et al. 2004. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306:655-60
120. Stole V, Samanta MP, Tongprasit W, Sethi H, Liang S, et al. 2005. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl. Acad. Sci. USA 102:4453-58
121. Storz G. 2002. An expanding universe of noncoding RNAs. Science 296:1260-63
122. Storz G, Altuvia S, Wassarman KM. 2005. An abundance of RNA regulators. Annu. Rev. Biochem. 74:199-217
123. Sun YM, Greenway DJ, Johnson R, Street M, Belyaev ND, et al. 2005. Distinct profiles of REST interactions with its target genes at different stages of neuronal development. Mol. Biol. Cell 16:5630-38
124. Sutcliffe JG, Milner RJ, Bloom FE, Lerner RA. 1982. Common 82-nucleotide sequence unique to brain RNA. Proc. Natl. Acad. Sci. USA 79:4942-46
125. Sweatt JD. 2004. Mitogen-activated protein kinases in synaptic plasticity and memory. Curr. Opin. Neurobiol. 14:311-17
126. Thomson JM, Parker J, Perou CM, Hammond SM. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1:47-53
127. Tiedge H, Chen W, Brosius J. 1993. Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. J. Neurosci. 13:2382-90
128. Vitali P, Basyuk E, Le Meur E, Bertrand E, Muscatelli F, et al. 2005. ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs. J. Cell Biol. 169:745-53
129. Walter P, Blobel G. 1982. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature 299:691-98
130. Wang H, Iacoangeli A, Popp S, Muslimov IA, Imataka H, et al. 2002. Dendritic BC1 RNA: functional role in regulation of translation initiation. J. Neurosci. 22:10232-41
131. Wang Q, O'Brien PJ, Chen CX, Cho DS, Murray JM, Nishikura K. 2000. Altered G protein-coupling functions of RNA editing isoform and splicing variant serotonin2C receptors. J. Neurochem. 74:1290-300
132. Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF. 2005. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat. Biotechnol. 23:1383-90
133. Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S. 2001. Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15:1637-51
134. Watson JB, Sutcliffe JG. 1987. Primate brain-specific cytoplasmic transcript of the Alu repeat family. Mol. Cell Biol. 7:3324-27
135. Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, et al. 2001. Human L1 retrotransposition: cis preference versus trans complementation. Mol. Cell Biol. 21:1429-39
136. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, et al. 2005. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309:1570-73
137. Winder DG, Sweatt JD. 2001. Roles of serine/threonine phosphatases in hippocampal synaptic plasticity. Nat. Rev. Neurosci. 2:461-74
138. Yamada K, Lim J, Dale JM, Chen H, Shinn P, et al. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842-46
139. Yang Z, Zhu Q, Luo K, Zhou Q. 2001. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414:317-22
140. Yeo M, Lee SK, Lee B, Ruiz EC, Pfaff SL, Gill GN. 2005. Small CTD phosphatases function in silencing neuronal gene expression. Science 307:596-600
141. Yi-Brunozzi HY, Easterwood LM, Kamilar GM, Beal PA. 1999. Synthetic substrate analogs for the RNA-editing adenosine deaminase ADAR-2. Nucleic Acids Res. 27:2912-17
142. Yokota H, Iwasaki T, Takahashi M, Oishi M. 1989. A tissue-specific change in repetitive DNA in rats. Proc. Natl. Acad. Sci. USA 86:9233-37
143. Yolken RH, Karlsson H, Yee F, Johnston-Wilson NL, Torrey EF. 2000. Endogenous retroviruses and schizophrenia. Brain Res. Brain Res. Rev. 31:193-99
144. Zalfa F, Giorgi M, Primerano B, Moro A, Di Penta A, et al. 2003. The fragile X syndrome protein FMRP associates with BC1 RNA and regulates the translation of specific mRNAs at synapses. Cell 112:317-27
145. Zamore PD, Haley B. 2005. Ribo-gnome: the big world of small RNAs. Science 309:1519-24
146. Zhang YQ, Broadie K. 2005. Fathoming fragile X in fruit flies. Trends Genet. 21:37-45
147. Zieve GW. 1981. Two groups of small stable RNAs. Cell 25:296-97
148. Zuccato C, Tartari M, Crotti A, Goffredo D, Valenza M, et al. 2003. Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes. Nat. Genet. 35:76-83
149. Zwieb C, van Nues RW, Rosenblad MA, Brown JD, Samuelsson T. 2005. A nomenclature for all signal recognition particle RNAs. RNA 11:7-13