Regulatory RNAs in brain function and disorders

Brain Research

Volumn 1338, Issue , 2010, Pages 36-47

  Iacoangeli, Anna ^a   Bianchi, Riccardo ^a,b   Tiedge, Henri ^a,b  

^a SUNY Downstate Medical Center   (United States)

^b SUNY DOWNSTATE MEDICAL CENTER   (United States)

Author keywords

Brain disorders; Neurons; Non protein coding RNA; Regulatory RNA

Indexed keywords

BRAIN SPECIFIC CYTOPLASMIC REGULATORY RNA; MESSENGER RNA; REGULATORY RNA; RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

BRAIN DISEASE; BRAIN FUNCTION; DEGENERATIVE DISEASE; EPILEPSY; GENE EXPRESSION REGULATION; GENE SILENCING; GENOME IMPRINTING; HUMAN; NERVE CELL DIFFERENTIATION; NERVE CELL PLASTICITY; NONHUMAN; PRIORITY JOURNAL; REGULATOR GENE; REVIEW; STIMULATION; TRINUCLEOTIDE REPEAT;

ANIMALS; BRAIN; BRAIN DISEASES; GENE EXPRESSION REGULATION; HUMANS; RNA, UNTRANSLATED;

EID: 77952583729     PISSN: 00068993     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.brainres.2010.03.042     Document Type: Review

References (175)

1. Abraham M., Dror O., Nussinov R., and Wolfson H.J. Analysis and classification of RNA tertiary structures. RNA 14 (2008) 2274-2289
2. Acampora D., Merlo G.R., Paleari L., Zerega B., Postiglione M.P., Mantero S., Bober E., Barbieri O., Simeone A., and Levi G. Craniofacial, vestibular and bone defects in mice lacking the distal-less-related gene Dlx5. Development 126 (1999) 3795-3809
3. Amaral P.P., and Mattick J.S. Noncoding RNA in development. Mamm. Genome 19 (2008) 454-492
4. Anderson S.A., Qiu M., Bulfone A., Eisenstat D.D., Meneses J., Pedersen R., and Rubenstein J.L. Mutations of the homeobox genes Dlx-1 and Dlx-2 disrupt the striatal subventricular zone and differentiation of late born striatal neurons. Neuron 19 (1997) 27-37
5. Artero R., Prokop A., Paricio N., Begemann G., Pueyo I., Mlodzik M., Perez-Alonso M., and Baylies M.K. The muscleblind gene participates in the organization of Z-bands and epidermal attachments of Drosophila muscles and is regulated by Dmef2. Dev. Biol. 195 (1998) 131-143
6. Barlow D.P., and Bartolomei M.S. Genomic imprinting in mammals, Vol. (2007), CSH Press
7. Batten F.E., and Gibb H.P. Two cases of myotonia Atrophica, showing a peculiar distribution of muscular atrophy. Proc. R. Soc. Med. 2 (1909) 32-33
8. Begemann G., Paricio N., Artero R., Kiss I., Perez-Alonso M., and Mlodzik M. muscleblind, a gene required for photoreceptor differentiation in Drosophila, encodes novel nuclear Cys3His-type zinc-finger-containing proteins. Development 124 (1997) 4321-4331
9. Beniaminov A., Westhof E., and Krol A. Distinctive structures between chimpanzee and human in a brain noncoding RNA. RNA 14 (2008) 1270-1275
10. Bernstein E., and Allis C.D. RNA meets chromatin. Genes Dev. 19 (2005) 1635-1655
11. Bianchi R., Chuang S.C., Zhao W., Young S.R., and Wong R.K. Cellular plasticity for group I mGluR-mediated epileptogenesis. J. Neurosci. 29 (2009) 3497-3507
12. Bilen J., Liu N., and Bonini N.M. A new role for microRNA pathways: modulation of degeneration induced by pathogenic human disease proteins. Cell Cycle 5 (2006) 2835-2838
13. Bilen J., Liu N., Burnett B.G., Pittman R.N., and Bonini N.M. MicroRNA pathways modulate polyglutamine-induced neurodegeneration. Mol. Cell 24 (2006) 157-163
14. Bolton P.F., Veltman M.W., Weisblatt E., Holmes J.R., Thomas N.S., Youings S.A., Thompson R.J., Roberts S.E., Dennis N.R., Browne C.E., Goodson S., Moore V., and Brown J. Chromosome 15q11-13 abnormalities and other medical conditions in individuals with autism spectrum disorders. Psychiatr. Genet. 14 (2004) 131-137
15. Bond A.M., Vangompel M.J., Sametsky E.A., Clark M.F., Savage J.C., Disterhoft J.F., and Kohtz J.D. Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat. Neurosci. 12 (2009) 1020-1027
16. Brook J.D., McCurrach M.E., Harley H.G., Buckler A.J., Church D., Aburatani H., Hunter K., Stanton V.P., Thirion J.P., Hudson T., et al. 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 (1992) 799-808
17. Brosius J., and Tiedge H. RNomenclature. RNA Biol. 1 (2004) 81-83
18. Brouwer J.R., Willemsen R., and Oostra B.A. The FMR1 gene and fragile X-associated tremor/ataxia syndrome. Am. J. Med. Genet. B Neuropsychiatr. Genet. (2008)
19. Brown C.J., Hendrich B.D., Rupert J.L., Lafreniere R.G., Xing Y., Lawrence J., and Willard H.F. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71 (1992) 527-542
20. 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
21. Carango P., Noble J.E., Marks H.G., and Funanage V.L. Absence of myotonic dystrophy protein kinase (DMPK) mRNA as a result of a triplet repeat expansion in myotonic dystrophy. Genomics 18 (1993) 340-348
22. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J., Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schonbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., and Hayashizaki Y. The transcriptional landscape of the mammalian genome. Science 309 (2005) 1559-1563
23. Cassidy S.B., Dykens E., and Williams C.A. Prader-Willi and Angelman syndromes: sister imprinted disorders. Am. J. Med. Genet. 97 (2000) 136-146
24. Cavaille J., Buiting K., Kiefmann M., Lalande M., Brannan C.I., Horsthemke B., Bachellerie J.P., Brosius J., and Huttenhofer A. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl. Acad. Sci. USA 97 (2000) 14311-14316
25. Cavaille J., Seitz H., Paulsen M., Ferguson-Smith A.C., and Bachellerie J.P. 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 (2002) 1527-1538
26. Chang S., Wen S., Chen D., and Jin P. Small regulatory RNAs in neurodevelopmental disorders. Hum. Mol. Genet. 18 (2009) R18-R26
27. Chekulaeva M., and Filipowicz W. Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Curr. Opin. Cell Biol. 21 (2009) 452-460
28. Chen W.L., Lin J.W., Huang H.J., Wang S.M., Su M.T., Lee-Chen G.J., Chen C.M., and Hsieh-Li H.M. SCA8 mRNA expression suggests an antisense regulation of KLHL1 and correlates to SCA8 pathology. Brain Res. 1233 (2008) 176-184
29. Cheng H.Y., Papp J.W., Varlamova O., Dziema H., Russell B., Curfman J.P., Nakazawa T., Shimizu K., Okamura H., Impey S., and Obrietan K. microRNA modulation of circadian-clock period and entrainment. Neuron 54 (2007) 813-829
30. Cho D.H., and Tapscott S.J. Myotonic dystrophy: emerging mechanisms for DM1 and DM2. Biochim. Biophys. Acta 1772 (2007) 195-204
31. Chuang S.C., Bianchi R., and Wong R.K. Group I mGluR activation turns on a voltage-gated inward current in hippocampal pyramidal cells. J. Neurophysiol. 83 (2000) 2844-2853
32. Chuang S.C., Bianchi R., Kim D., Shin H.S., and Wong R.K. Group I metabotropic glutamate receptors elicit epileptiform discharges in the hippocampus through PLCbeta1 signaling. J. Neurosci. 21 (2001) 6387-6394
33. Cobos I., Calcagnotto M.E., Vilaythong A.J., Thwin M.T., Noebels J.L., Baraban S.C., and Rubenstein J.L. Mice lacking Dlx1 show subtype-specific loss of interneurons, reduced inhibition and epilepsy. Nat. Neurosci. 8 (2005) 1059-1068
34. Consortium I.M.G.S.o.A. Further characterization of the autism susceptibility locus AUTS1 on chromosome 7q. Hum. Mol. Genet. 10 (2001) 973-982
35. Cook Jr. E.H., Lindgren V., Leventhal B.L., Courchesne R., Lincoln A., Shulman C., Lord C., and Courchesne E. Autism or atypical autism in maternally but not paternally derived proximal 15q duplication. Am. J. Hum. Genet. 60 (1997) 928-934
36. Costa F.F. Non-coding RNAs: new players in eukaryotic biology. Gene 357 (2005) 83-94
37. Costa F.F. Non-coding RNAs: lost in translation?. Gene 386 (2007) 1-10
38. da Rocha S.T., Edwards C.A., Ito M., Ogata T., and Ferguson-Smith A.C. Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends Genet. 24 (2008) 306-316
39. Daughters R.S., Tuttle D.L., Gao W., Ikeda Y., Moseley M.L., Ebner T.J., Swanson M.S., and Ranum L.P. RNA gain-of-function in spinocerebellar ataxia type 8. PLoS Genet. 5 (2009) e1000600
40. de Smith A.J., Purmann C., Walters R.G., Ellis R.J., Holder S.E., Van Haelst M.M., Brady A.F., Fairbrother U.L., Dattani M., Keogh J.M., Henning E., Yeo G.S., O'Rahilly S., Froguel P., Farooqi I.S., and Blakemore A.I. A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism. Hum. Mol. Genet. 18 (2009) 3257-3265
41. DeChiara T.M., and Brosius J. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc. Natl. Acad. Sci. USA 84 (1987) 2624-2628
42. Descheemaeker M.J., Govers V., Vermeulen P., and Fryns J.P. Pervasive developmental disorders in Prader-Willi syndrome: the Leuven experience in 59 subjects and controls. Am. J. Med. Genet. 140 (2006) 1136-1142
43. Dick K.A., Margolis J.M., Day J.W., and Ranum L.P. Dominant non-coding repeat expansions in human disease. Genome Dyn. 1 (2006) 67-83
44. Ding F., Li H.H., Zhang S., Solomon N.M., Camper S.A., Cohen P., and Francke U. SnoRNA Snord116 (Pwcr1/MBII-85) deletion causes growth deficiency and hyperphagia in mice. PLoS ONE 3 (2008) e1709
45. Ding F., Sharma S., Chalasani P., Demidov V.V., Broude N.E., and Dokholyan N.V. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA 14 (2008) 1164-1173
46. Doe C.M., Relkovic D., Garfield A.S., Dalley J.W., Theobald D.E., Humby T., Wilkinson L.S., and Isles A.R. Loss of the imprinted snoRNA mbii-52 leads to increased 5htr2c pre-RNA editing and altered 5HT2CR-mediated behaviour. Hum. Mol. Genet. 18 (2009) 2140-2148
47. Eacker S.M., Dawson T.M., and Dawson V.L. Understanding microRNAs in neurodegeneration. Nat. Rev. Neurosci. 10 (2009) 837-841
48. Eddy S.R. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2 (2001) 919-929
49. Erdmann V.A., Szymanski M., Hochberg A., Groot N., and Barciszewski J. Non-coding, mRNA-like RNAs database Y2K. Nucleic Acids Res. 28 (2000) 197-200
50. Erdmann V.A., Barciszewska M.Z., Hochberg A., de Groot N., and Barciszewski J. Regulatory RNAs. Cell. Mol. Life Sci. 58 (2001) 960-977
51. 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
52. Fardaei M., Larkin K., Brook J.D., and Hamshere M.G. In vivo co-localisation of MBNL protein with DMPK expanded-repeat transcripts. Nucleic Acids Res. 29 (2001) 2766-2771
53. Feng J., Bi C., Clark B.S., Mady R., Shah P., and Kohtz J.D. The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev. 20 (2006) 1470-1484
54. Fineberg S.K., Kosik K.S., and Davidson B.L. MicroRNAs potentiate neural development. Neuron 64 (2009) 303-309
55. Frellsen J., Moltke I., Thiim M., Mardia K.V., Ferkinghoff-Borg J., and Hamelryck T. A probabilistic model of RNA conformational space. PLoS Comput. Biol. 5 (2009) e1000406
56. French P.J., Bliss T.V., and O'Connor V. Ntab, a novel non-coding RNA abundantly expressed in rat brain. Neuroscience 108 (2001) 207-215
57. Fridman C., and Koiffmann C.P. Origin of uniparental disomy 15 in patients with Prader-Willi or Angelman syndrome. Am. J. Med. Genet. 94 (2000) 249-253
58. Fu Y.H., Pizzuti A., Fenwick Jr. R.G., King J., Rajnarayan S., Dunne P.W., Dubel J., Nasser G.A., Ashizawa T., de Jong P., et al. An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science 255 (1992) 1256-1258
59. Fu Y.H., Friedman D.L., Richards S., Pearlman J.A., Gibbs R.A., Pizzuti A., Ashizawa T., Perryman M.B., Scarlato G., Fenwick Jr. R.G., et al. Decreased expression of myotonin-protein kinase messenger RNA and protein in adult form of myotonic dystrophy. Science 260 (1993) 235-238
60. Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., Wilkinson A.C., Finn R.D., Griffiths-Jones S., Eddy S.R., and Bateman A. Rfam: updates to the RNA families database. Nucleic Acids Res. 37 (2009) D136-D140
61. Gillberg C. Chromosomal disorders and autism. J. Autism Dev. Disord. 28 (1998) 415-425
62. Greco C.M., Hagerman R.J., Tassone F., Chudley A.E., Del Bigio M.R., Jacquemont S., Leehey M., and Hagerman P.J. Neuronal intranuclear inclusions in a new cerebellar tremor/ataxia syndrome among fragile X carriers. Brain 125 (2002) 1760-1771
63. Greer P.L., Hanayama R., Bloodgood B.L., Mardinly A.R., Lipton D.M., Flavell S.W., Kim T.K., Griffith E.C., Waldon Z., Maehr R., Ploegh H.L., Chowdhury S., Worley P.F., Steen J., and Greenberg M.E. The Angelman syndrome protein Ube3A regulates synapse development by ubiquitinating Arc. Cell 140 (2010) 704-716
64. Griffiths-Jones S. Annotating noncoding RNA genes. Annu. Rev. Genomics Hum. Genet. 8 (2007) 279-298
65. Griffiths-Jones S., Saini H.K., van Dongen S., and Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36 (2008) D154-D158
66. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., Huarte M., Zuk O., Carey B.W., Cassady J.P., Cabili M.N., Jaenisch R., Mikkelsen T.S., Jacks T., Hacohen N., Bernstein B.E., Kellis M., Regev A., Rinn J.L., and Lander E.S. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458 (2009) 223-227
67. Hagan J.P., O'Neill B.L., Stewart C.L., Kozlov S.V., and Croce C.M. At least ten genes define the imprinted Dlk1-Dio3 cluster on mouse chromosome 12qF1. PLoS ONE 4 (2009) e4352
68. Hagerman P.J., and Hagerman R.J. The fragile-X premutation: a maturing perspective. Am. J. Hum. Genet. 74 (2004) 805-816
69. Hagerman R.J., Leehey M., Heinrichs W., Tassone F., Wilson R., Hills J., Grigsby J., Gage B., and Hagerman P.J. Intention tremor, parkinsonism, and generalized brain atrophy in male carriers of fragile X. Neurology 57 (2001) 127-130
70. Hashem V., Galloway J.N., Mori M., Willemsen R., Oostra B.A., Paylor R., and Nelson D.L. Ectopic expression of CGG containing mRNA is neurotoxic in mammals. Hum. Mol. Genet. 18 (2009) 2443-2451
71. Herzing L.B., Kim S.J., Cook Jr. E.H., and Ledbetter D.H. The human aminophospholipid-transporting ATPase gene ATP10C maps adjacent to UBE3A and exhibits similar imprinted expression. Am. J. Hum. Genet. 68 (2001) 1501-1505
72. Hofmann-Radvanyi H., Lavedan C., Rabes J.P., Savoy D., Duros C., Johnson K., and Junien C. Myotonic dystrophy: absence of CTG enlarged transcript in congenital forms, and low expression of the normal allele. Hum. Mol. Genet. 2 (1993) 1263-1266
73. Hu J.F., Oruganti H., Vu T.H., and Hoffman A.R. Tissue-specific imprinting of the mouse insulin-like growth factor II receptor gene correlates with differential allele-specific DNA methylation. Mol. Endocrinol. 12 (1998) 220-232
74. Ito H., Kawakami H., Wate R., Matsumoto S., Imai T., Hirano A., and Kusaka H. Clinicopathologic investigation of a family with expanded SCA8 CTA/CTG repeats. Neurology 67 (2006) 1479-1481
75. Iwahashi C.K., Yasui D.H., An H.J., Greco C.M., Tassone F., Nannen K., Babineau B., Lebrilla C.B., Hagerman R.J., and Hagerman P.J. Protein composition of the intranuclear inclusions of FXTAS. Brain 129 (2006) 256-271
76. Jiang Y.H., Armstrong D., Albrecht U., Atkins C.M., Noebels J.L., Eichele G., Sweatt J.D., and Beaudet A.L. Mutation of the Angelman ubiquitin ligase in mice causes increased cytoplasmic p53 and deficits of contextual learning and long-term potentiation. Neuron 21 (1998) 799-811
77. Jin P., Duan R., Qurashi A., Qin Y., Tian D., Rosser T.C., Liu H., Feng Y., and Warren S.T. Pur alpha binds to rCGG repeats and modulates repeat-mediated neurodegeneration in a Drosophila model of fragile X tremor/ataxia syndrome. Neuron 55 (2007) 556-564
78. Kagami M., Nishimura G., Okuyama T., Hayashidani M., Takeuchi T., Tanaka S., Ishino F., Kurosawa K., and Ogata T. Segmental and full paternal isodisomy for chromosome 14 in three patients: narrowing the critical region and implication for the clinical features. Am. J. Med. Genet. 138A (2005) 127-132
79. Kagami M., Sekita Y., Nishimura G., Irie M., Kato F., Okada M., Yamamori S., Kishimoto H., Nakayama M., Tanaka Y., Matsuoka K., Takahashi T., Noguchi M., Masumoto K., Utsunomiya T., Kouzan H., Komatsu Y., Ohashi H., Kurosawa K., Kosaki K., Ferguson-Smith A.C., Ishino F., and Ogata T. Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. Nat. Genet. 40 (2008) 237-242
80. Kaliman P., and Llagostera E. Myotonic dystrophy protein kinase (DMPK) and its role in the pathogenesis of myotonic dystrophy 1. Cell. Signal. 20 (2008) 1935-1941
81. Kanadia R.N., Johnstone K.A., Mankodi A., Lungu C., Thornton C.A., Esson D., Timmers A.M., Hauswirth W.W., and Swanson M.S. A muscleblind knockout model for myotonic dystrophy. Science 302 (2003) 1978-1980
82. Kanber D., Giltay J., Wieczorek D., Zogel C., Hochstenbach R., Caliebe A., Kuechler A., Horsthemke B., and Buiting K. A paternal deletion of MKRN3, MAGEL2 and NDN does not result in Prader-Willi syndrome. Eur. J. Hum. Genet. 17 (2009) 582-590
83. Kantor B., Shemer R., and Razin A. The Prader-Willi/Angelman imprinted domain and its control center. Cytogenet. Genome Res. 113 (2006) 300-305
84. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermuller J., Hofacker I.L., Bell I., Cheung E., Drenkow J., Dumais E., Patel S., Helt G., Ganesh M., Ghosh S., Piccolboni A., Sementchenko V., Tammana H., and Gingeras T.R. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316 (2007) 1484-1488
85. Kavanaugh L.A., and Dietrich F.S. Non-coding RNA prediction and verification in Saccharomyces cerevisiae. PLoS Genet. 5 (2009) e1000321
86. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., Thomas K., Presser A., Bernstein B.E., van Oudenaarden A., Regev A., Lander E.S., and Rinn J.L. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106 (2009) 11667-11672
87. Kishino T., Lalande M., and Wagstaff J. UBE3A/E6-AP mutations cause Angelman syndrome. Nat. Genet. 15 (1997) 70-73
88. Kishore S., and Stamm S. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311 (2006) 230-232
89. Kloc A., Zaratiegui M., Nora E., and Martienssen R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 18 (2008) 490-495
90. Kocerha J., Faghihi M.A., Lopez-Toledano M.A., Huang J., Ramsey A.J., Caron M.G., Sales N., Willoughby D., Elmen J., Hansen H.F., Orum H., Kauppinen S., Kenny P.J., and Wahlestedt C. MicroRNA-219 modulates NMDA receptor-mediated neurobehavioral dysfunction. Proc. Natl. Acad. Sci. USA 106 (2009) 3507-3512
91. Kocerha J., Kauppinen S., and Wahlestedt C. microRNAs in CNS disorders. Neuromolecular Med. (2009)
92. Koerner M.V., Pauler F.M., Huang R., and Barlow D.P. The function of non-coding RNAs in genomic imprinting. Development 136 (2009) 1771-1783
93. Kohtz J.D., and Fishell G. Developmental regulation of EVF-1, a novel non-coding RNA transcribed upstream of the mouse Dlx6 gene. Gene Expr. Patterns 4 (2004) 407-412
94. Kohtz J.D., Baker D.P., Corte G., and Fishell G. Regionalization within the mammalian telencephalon is mediated by changes in responsiveness to Sonic Hedgehog. Development 125 (1998) 5079-5089
95. Kondrashov A.V., Kiefmann M., Ebnet K., Khanam T., Muddashetty R.S., and Brosius J. Inhibitory effect of naked neural BC1 RNA or BC200 RNA on eukaryotic in vitro translation systems is reversed by poly(A)-binding protein (PABP). J. Mol. Biol. 353 (2005) 88-103
96. Koob M.D., Moseley M.L., Schut L.J., Benzow K.A., Bird T.D., Day J.W., and Ranum L.P. An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8). Nat. Genet. 21 (1999) 379-384
97. Kosik K.S. The neuronal microRNA system. Nat. Rev. Neurosci. 7 (2006) 911-920
98. Krichevsky A.M., King K.S., Donahue C.P., Khrapko K., and Kosik K.S. A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9 (2003) 1274-1281
99. Krichevsky A.M., Sonntag K.C., Isacson O., and Kosik K.S. Specific microRNAs modulate embryonic stem cell-derived neurogenesis. Stem Cells 24 (2006) 857-864
100. Landers M., Calciano M.A., Colosi D., Glatt-Deeley H., Wagstaff J., and Lalande M. Maternal disruption of Ube3a leads to increased expression of Ube3a-ATS in trans. Nucleic Acids Res. 33 (2005) 3976-3984
101. Latos P.A., and Barlow D.P. Regulation of imprinted expression by macro non-coding RNAs. RNA Biol. 6 (2009)
102. Le Meur E., Watrin F., Landers M., Sturny R., Lalande M., and Muscatelli F. Dynamic developmental regulation of the large non-coding RNA associated with the mouse 7C imprinted chromosomal region. Dev. Biol. 286 (2005) 587-600
103. Lee R.C., and Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294 (2001) 862-864
104. Lee R.C., Feinbaum R.L., and Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 (1993) 843-854
105. Leehey M.A., Berry-Kravis E., Goetz C.G., Zhang L., Hall D.A., Li L., Rice C.D., Lara R., Cogswell J., Reynolds A., Gane L., Jacquemont S., Tassone F., Grigsby J., Hagerman R.J., and Hagerman P.J. FMR1 CGG repeat length predicts motor dysfunction in premutation carriers. Neurology 70 (2008) 1397-1402
106. 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
107. Lin D., Pestova T.V., Hellen C.U., and Tiedge H. Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism. Mol. Cell. Biol. 28 (2008) 3008-3019
108. Liquori C.L., Ricker K., Moseley M.L., Jacobsen J.F., Kress W., Naylor S.L., Day J.W., and Ranum L.P. Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science 293 (2001) 864-867
109. Lukiw W.J. Micro-RNA speciation in fetal, adult and Alzheimer's disease hippocampus. NeuroReport 18 (2007) 297-300
110. Lyle R., Watanabe D., te Vruchte D., Lerchner W., Smrzka O.W., Wutz A., Schageman J., Hahner L., Davies C., and Barlow D.P. The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat. Genet. 25 (2000) 19-21
111. Mathews D.H., and Turner D.H. Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol. 16 (2006) 270-278
112. Matsuura T., Sutcliffe J.S., Fang P., Galjaard R.J., Jiang Y.H., Benton C.S., Rommens J.M., and Beaudet A.L. De novo truncating mutations in E6-AP ubiquitin-protein ligase gene (UBE3A) in Angelman syndrome. Nat. Genet. 15 (1997) 74-77
113. Mattick J.S. The genetic signatures of noncoding RNAs. PLoS Genet. 5 (2009) e1000459
114. Mattick J.S., and Makunin I.V. Non-coding RNA. Hum. Mol. Genet. 15 Spec No 1 (2006) R17-R29
115. Meguro M., Kashiwagi A., Mitsuya K., Nakao M., Kondo I., Saitoh S., and Oshimura M. A novel maternally expressed gene, ATP10C, encodes a putative aminophospholipid translocase associated with Angelman syndrome. Nat. Genet. 28 (2001) 19-20
116. Mehler M.F., and Mattick J.S. Non-coding RNAs in the nervous system. J. Physiol. 575 (2006) 333-341
117. 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
118. Mercer T.R., Dinger M.E., Mariani J., Kosik K.S., Mehler M.F., and Mattick J.S. Noncoding RNAs in long-term memory formation. Neuroscientist 14 (2008) 434-445
119. 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. USA 105 (2008) 716-721
120. Merlin L.R., and Wong R.K. Role of group I metabotropic glutamate receptors in the patterning of epileptiform activities in vitro. J. Neurophysiol. 78 (1997) 539-544
121. Merlin L.R., Bergold P.J., and Wong R.K. Requirement of protein synthesis for group I mGluR-mediated induction of epileptiform discharges. J. Neurophysiol. 80 (1998) 989-993
122. Miller J.W., Urbinati C.R., Teng-Umnuay P., Stenberg M.G., Byrne B.J., Thornton C.A., and Swanson M.S. Recruitment of human muscleblind proteins to (CUG)(n) expansions associated with myotonic dystrophy. EMBO J. 19 (2000) 4439-4448
123. Milner R.J., Bloom F.E., Lai C., Lerner R.A., and Sutcliffe J.G. Brain-specific genes have identifier sequences in their introns. Proc. Natl. Acad. Sci. USA 81 (1984) 713-717
124. Muslimov I.A., Santi E., Homel P., Perini S., Higgins D., and Tiedge H. RNA transport in dendrites: a cis-acting targeting element is contained within neuronal BC1 RNA. J. Neurosci. 17 (1997) 4722-4733
125. Mutsuddi M., Marshall C.M., Benzow K.A., Koob M.D., and Rebay I. The spinocerebellar ataxia 8 noncoding RNA causes neurodegeneration and associates with staufen in Drosophila. Curr. Biol. 14 (2004) 302-308
126. Nakatani J., Tamada K., Hatanaka F., Ise S., Ohta H., Inoue K., Tomonaga S., Watanabe Y., Chung Y.J., Banerjee R., Iwamoto K., Kato T., Okazawa M., Yamauchi K., Tanda K., Takao K., Miyakawa T., Bradley A., and Takumi T. Abnormal behavior in a chromosome-engineered mouse model for human 15q11-13 duplication seen in autism. Cell 137 (2009) 1235-1246
127. Napierala M., and Krzyzosiak W.J. CUG repeats present in myotonin kinase RNA form metastable "slippery" hairpins. J. Biol. Chem. 272 (1997) 31079-31085
128. Nemes J.P., Benzow K.A., Moseley M.L., Ranum L.P., and Koob M.D. The SCA8 transcript is an antisense RNA to a brain-specific transcript encoding a novel actin-binding protein (KLHL1). Hum. Mol. Genet. 9 (2000) 1543-1551
129. O'Neill M.J. The influence of non-coding RNAs on allele-specific gene expression in mammals. Hum. Mol. Genet. 14 Spec No 1 (2005) R113-R120
130. Onoa B., and Tinoco Jr. I. RNA folding and unfolding. Curr. Opin. Struct. Biol. 14 (2004) 374-379
131. Pauler F.M., Koerner M.V., and Barlow D.P. Silencing by imprinted noncoding RNAs: is transcription the answer?. Trends Genet. 23 (2007) 284-292
132. Perkins D.O., Jeffries C., and Sullivan P. Expanding the 'central dogma': the regulatory role of nonprotein coding genes and implications for the genetic liability to schizophrenia. Mol. Psychiatry 10 (2005) 69-78
133. Perkins D.O., Jeffries C.D., Jarskog L.F., Thomson J.M., Woods K., Newman M.A., Parker J.S., Jin J., and Hammond S.M. microRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder. Genome Biol. 8 (2007) R27
134. 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
135. Ponting C.P., Oliver P.L., and Reik W. Evolution and functions of long noncoding RNAs. Cell 136 (2009) 629-641
136. Qureshi I.A., and Mehler M.F. Regulation of non-coding RNA networks in the nervous system-What's the REST of the story?. Neurosci. Lett. (2009)
137. Ranum L.P., and Cooper T.A. RNA-mediated neuromuscular disorders. Annu. Rev. Neurosci. 29 (2006) 259-277
138. Royo H., and Cavaille J. Non-coding RNAs in imprinted gene clusters. Biol. Cell 100 (2008) 149-166
139. Runte M., Huttenhofer A., Gross S., Kiefmann M., Horsthemke B., and Buiting K. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum. Mol. Genet. 10 (2001) 2687-2700
140. Sahoo T., del Gaudio D., German J.R., Shinawi M., Peters S.U., Person R.E., Garnica A., Cheung S.W., and Beaudet A.L. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat. Genet. 40 (2008) 719-721
141. Satterlee J.S., Barbee S., Jin P., Krichevsky A., Salama S., Schratt G., and Wu D.Y. Noncoding RNAs in the brain. J. Neurosci. 27 (2007) 11856-11859
142. Schratt G. microRNAs at the synapse. Nat. Rev. Neurosci. 10 (2009) 842-849
143. Shamovsky I., and Nudler E. Gene control by large noncoding RNAs. Sci. STKE (2006) pe40
144. Sharma S., Ding F., and Dokholyan N.V. iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics 24 (2008) 1951-1952
145. Skryabin B.V., Gubar L.V., Seeger B., Pfeiffer J., Handel S., Robeck T., Karpova E., Rozhdestvensky T.S., and Brosius J. Deletion of the MBII-85 snoRNA gene cluster in mice results in postnatal growth retardation. PLoS Genet. 3 (2007) e235
146. Sleutels F., and Barlow D.P. Investigation of elements sufficient to imprint the mouse air promoter. Mol. Cell. Biol. 21 (2001) 5008-5017
147. Soong B.W., and Paulson H.L. Spinocerebellar ataxias: an update. Curr. Opin. Neurol. 20 (2007) 438-446
148. St George-Hyslop P., and Haass C. Regulatory RNA goes awry in Alzheimer's disease. Nat. Med. 14 (2008) 711-712
149. Sutcliffe J.G., Milner R.J., Bloom F.E., and Lerner R.A. Common 82-nucleotide sequence unique to brain RNA. Proc. Natl. Acad. Sci. USA 79 (1982) 4942-4946
150. Sutcliffe J.G., Milner R.J., Gottesfeld J.M., and Lerner R.A. Identifier sequences are transcribed specifically in brain. Nature 308 (1984) 237-241
151. Szell M., Bata-Csorgo Z., and Kemeny L. The enigmatic world of mRNA-like ncRNAs: their role in human evolution and in human diseases. Semin. Cancer Biol. 18 (2008) 141-148
152. Takahashi N., Okamoto A., Kobayashi R., Shirai M., Obata Y., Ogawa H., Sotomaru Y., and Kono T. Deletion of Gtl2, imprinted non-coding RNA, with its differentially methylated region induces lethal parent-origin-dependent defects in mice. Hum. Mol. Genet. 18 (2009) 1879-1888
153. Taniura H., Sng J.C., and Yoneda Y. Histone modifications in the brain. Neurochem. Int. 51 (2007) 85-91
154. Tiedge H., Fremeau Jr. R.T., Weinstock P.H., Arancio O., and Brosius J. Dendritic location of neural BC1 RNA. Proc. Natl. Acad. Sci. USA 88 (1991) 2093-2097
155. Tiedge H., Chen W., and Brosius J. Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. J. Neurosci. 13 (1993) 2382-2390
156. Timchenko L.T., Miller J.W., Timchenko N.A., DeVore D.R., Datar K.V., Lin L., Roberts R., Caskey C.T., and Swanson M.S. Identification of a (CUG)n triplet repeat RNA-binding protein and its expression in myotonic dystrophy. Nucleic Acids Res. 24 (1996) 4407-4414
157. Tran D.H., Satou K., and Ho T.B. Finding microRNA regulatory modules in human genome using rule induction. BMC Bioinform. 9 Suppl 12 (2008) S5
158. Valencia-Sanchez M.A., Liu J., Hannon G.J., and Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20 (2006) 515-524
159. Veltman M.W., Thompson R.J., Roberts S.E., Thomas N.S., Whittington J., and Bolton P.F. Prader-Willi syndrome-a study comparing deletion and uniparental disomy cases with reference to autism spectrum disorders. Eur. Child Adolesc. Psychiatry 13 (2004) 42-50
160. Verona R.I., Mann M.R., and Bartolomei M.S. Genomic imprinting: intricacies of epigenetic regulation in clusters. Annu. Rev. Cell Dev. Biol. 19 (2003) 237-259
161. Vitali P., Basyuk E., Le Meur E., Bertrand E., Muscatelli F., Cavaille J., and Huttenhofer A. ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNAs. J. Cell Biol. 169 (2005) 745-753
162. Voss B., Georg J., Schon V., Ude S., and Hess W.R. Biocomputational prediction of non-coding RNAs in model cyanobacteria. BMC Genomics 10 (2009) 123
163. Wang H., Iacoangeli A., Popp S., Muslimov I.A., Imataka H., Sonenberg N., Lomakin I.B., and Tiedge H. Dendritic BC1 RNA: functional role in regulation of translation initiation. J. Neurosci. 22 (2002) 10232-10241
164. Wang H., Iacoangeli A., Lin D., Williams K., Denman R.B., Hellen C.U.T., and Tiedge H. Dendritic BC1 RNA in translational control mechanisms. J. Cell Biol. 171 (2005) 811-821
165. Wassink T.H., and Piven J. The molecular genetics of autism. Curr. Psychiatry Rep. 2 (2000) 170-175
166. Weinberg M.S., and Wood M.J. Short non-coding RNA biology and neurodegenerative disorders: novel disease targets and therapeutics. Hum. Mol. Genet. 18 (2009) R27-R39
167. Wheeler T.M., Krym M.C., and Thornton C.A. Ribonuclear foci at the neuromuscular junction in myotonic dystrophy type 1. Neuromuscul. Disord. 17 (2007) 242-247
168. Wong R.K., Bianchi R., Taylor G.W., and Merlin L.R. Role of metabotropic glutamate receptors in epilepsy. Adv. Neurol. 79 (1999) 685-698
169. Wutz A., and Gribnau J. X inactivation Xplained. Curr. Opin. Genet. Dev. 17 (2007) 387-393
170. Xu X., Ji Y., and Stormo G.D. RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics 23 (2007) 1883-1891
171. Yamasaki Y., Kayashima T., Soejima H., Kinoshita A., Yoshiura K., Matsumoto N., Ohta T., Urano T., Masuzaki H., Ishimaru T., Mukai T., Niikawa N., and Kishino T. Neuron-specific relaxation of Igf2r imprinting is associated with neuron-specific histone modifications and lack of its antisense transcript Air. Hum. Mol. Genet. 14 (2005) 2511-2520
172. Yoon S., and De Micheli G. Prediction and analysis of human microRNA regulatory modules. Conf. Proc. IEEE Eng. Med. Biol. Soc. 5 (2005) 4799-4802
173. Yoon S., and De Micheli G. Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 21 Suppl 2 (2005) ii93-ii100
174. Zhao W., Bianchi R., Wang M., and Wong R.K. Extracellular signal-regulated kinase 1/2 is required for the induction of group I metabotropic glutamate receptor-mediated epileptiform discharges. J. Neurosci. 24 (2004) 76-84
175. Zhong J., Chuang S.C., Bianchi R., Zhao W., Lee H., Fenton A.A., Wong R.K., and Tiedge H. BC1 regulation of metabotropic glutamate receptor-mediated neuronal excitability. J. Neurosci. 29 (2009) 9977-9986