Non-coding RNAs in the development of sensory organs and related diseases

Cellular and Molecular Life Sciences

Volumn 70, Issue 21, 2013, Pages 4141-4155

  Conte, Ivan ^a   Banfi, Sandro ^a,b   Bovolenta, Paola ^c,d  

^a TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^b SECOND UNIVERSITY OF NAPLES   (Italy)

^c CENTRO DE BIOLOGÍA MOLECULAR SEVERO OCHOA   (Spain)

^d INSTITUTO DE SALUD CARLOS III   (Spain)

Author keywords

Eye; Inner ear; Long non coding RNA; MicroRNA; Olfactory system

Indexed keywords

APOPTOTIC PROTEASE ACTIVATING FACTOR 1; CASPASE 9; LONG UNTRANSLATED RNA; MICRORNA; MICRORNA 124; MICRORNA 133B; MICRORNA 135B; MICRORNA 182; MICRORNA 183; MICRORNA 204; MICRORNA 218; MICRORNA 24A; MICRORNA 7A; MICRORNA 96; NOTCH RECEPTOR; ROUNDABOUT RECEPTOR; SEMAPHORIN 3A; T BOX TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DLX5; TRANSCRIPTION FACTOR HMX3; TRANSCRIPTION FACTOR LHX2; TRANSCRIPTION FACTOR MEIS2; TRANSCRIPTION FACTOR OTX1; TRANSCRIPTION FACTOR PAX2; TRANSCRIPTION FACTOR PAX6; TRANSCRIPTION FACTOR PITX3; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARTICLE; BALANCE DISORDER; CHROMATIN ASSEMBLY AND DISASSEMBLY; DISEASE ASSOCIATION; EYE DEVELOPMENT; EYE DISEASE; HUMAN; INNER EAR; INNER EAR DEVELOPMENT; INNER EAR DISEASE; NONHUMAN; OLFACTORY DEVELOPMENT; ORGANOGENESIS; PATHOGENESIS; PROTEIN EXPRESSION; RNA INTERFERENCE; SIGNAL TRANSDUCTION; SMELLING DISORDER; TRANSCRIPTION REGULATION; VERTEBRATE;

ANIMALS; CELL LINEAGE; CELL PROLIFERATION; CHROMATIN; EAR DISEASES; EAR, INNER; EYE; EYE DISEASES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME; HUMANS; OLFACTORY PATHWAYS; PHENOTYPE; RNA, UNTRANSLATED; TIME FACTORS;

VERTEBRATA;

EID: 84887057344     PISSN: 1420682X     EISSN: 14209071     Source Type: Journal    
DOI: 10.1007/s00018-013-1335-z     Document Type: Article

References (191)

1. Jalali S, Jayaraj GG, Scaria V (2012) Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol Direct 7:25
2. Carninci P, Hayashizaki Y (2007) Noncoding RNA transcription beyond annotated genes. Curr Opin Genet Dev 17(2):139-144
3. Qureshi IA, Mehler MF (2012) Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 13(8):528-541
4. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, Schierup MH, Jensen TH (2008) RNA exosome depletion reveals transcription upstream of active human promoters. Science 322(5909):1851-1854
5. Jacquier A (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet 10(12):833-844
6. Rosa A, Brivanlou AH (2009) MicroRNAs in early vertebrate development. Cell Cycle 8(21):3513-3520
7. Harfe BD (2005) MicroRNAs in vertebrate development. Curr Opin Genet Dev 15(4):410-415
8. Pauli A, Rinn JL, Schier AF (2011) Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 12(2):136-149
9. Bushati N, Cohen SM (2007) microRNA functions. Annu Rev Cell Dev Biol 23:175-205
10. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843-854
11. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403(6772):901-906
12. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408(6808):86-89
13. Winter J, Jung S, Keller S, Gregory RI, Diederichs S (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11(3):228-234
14. Guo H, Ingolia NT, Weissman JS, Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466(7308):835-840. doi: 10.1038/nature09267
15. Bazzini AA, Lee MT, Giraldez AJ (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336(6078):233-237.doi: 10.1126/science.1215704
16. Djuranovic S, Nahvi A, Green R (2012) miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336(6078):237-240
17. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5(7):522-531
18. Lee I, Ajay SS, Yook JI, Kim HS, Hong SH, Kim NH, Dhanasekaran SM, Chinnaiyan AM, Athey BD (2009) New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites. Genome Res 19(7):1175-1183
19. Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455(7216):1124-1128
20. Lytle JR, Yario TA, Steitz JA (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc Natl Acad Sci USA 104(23):9667-9672
21. Gonzalez S, Pisano DG, Serrano M (2008) Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs. Cell Cycle 7(16):2601-2608
22. Chitnis NS, Pytel D, Bobrovnikova-Marjon E, Pant D, Zheng H, Maas NL, Frederick B, Kushner JA, Chodosh LA, Koumenis C, Fuchs SY, Diehl JA (2012) miR-211 Is a prosurvival microRNA that regulates chop expression in a PERK-dependent manner. Mol Cell 48(3):353-364
23. Chen X, Liang H, Zhang J, Zen K, Zhang CY (2012) Horizontal transfer of microRNAs: molecular mechanisms and clinical applications. Protein Cell 3(1):28-37
24. Fabbri M, Paone A, Calore F, Galli R, Gaudio E, Santhanam R, Lovat F, Fadda P, Mao C, Nuovo GJ, Zanesi N, Crawford M, Ozer GH, Wernicke D, Alder H, Caligiuri MA, Nana-Sinkam P, Perrotti D, Croce CM (2012) MicroRNAs bind to Toll-like receptors to induce prometastatic inflammatory response. Proc Natl Acad Sci USA 109(31):E2110-E2116
25. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, 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 SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, 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 KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, 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 SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, 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, Hayashizaki Y (2005) The transcriptional landscape of the mammalian genome. Science 309(5740):1559-1563
26. Dinger ME, Pang KC, Mercer TR, Mattick JS (2008) Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol 4(11):e1000176
27. Frith MC, Bailey TL, Kasukawa T, Mignone F, Kummerfeld SK, Madera M, Sunkara S, Furuno M, Bult CJ, Quackenbush J, Kai C, Kawai J, Carninci P, Hayashizaki Y, Pesole G, Mattick JS (2006) Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol 3(1):40-48
28. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830):1484-1488
29. Saxena A, Carninci P (2011) Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays 33(11):830-839
30. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL (2004) Genomic analysis of mouse retinal development. PLoS Biol 2(9):E247
31. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311-1323
32. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC, Mattick JS (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18(9):1433-1445
33. Ravasi T, Suzuki H, Pang KC, Katayama S, Furuno M, Okunishi R, Fukuda S, Ru K, Frith MC, Gongora MM, Grimmond SM, Hume DA, Hayashizaki Y, Mattick JS (2006) Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 16(1):11-19
34. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 105(2):716-721
35. Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, Lawrence JB (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 33(6):717-726
36. Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A (2007) A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC genomics 8:39
37. Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S (2007) The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 120(Pt 15):2498-2506
38. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19(3):347-359
39. Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J (2005) A new frontier for molecular medicine: noncoding RNAs. Biochim Biophys Acta 1756(1):65-75
40. Prasanth KV, Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev 21(1):11-42
41. Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G, Cui Q (2012) LncRNAdisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 41:D983-D986. doi: 10.1093/nar/gks1099
42. Rackham O, Shearwood AM, Mercer TR, Davies SM, Mattick JS, Filipovska A (2011) Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA 17(12):2085-2093
43. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322(5902):750-756
44. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291):1071-1076
45. Hung T, Chang HY (2010) Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol 7(5):582-585
46. Mohammad F, Mondal T, Guseva N, Pandey GK, Kanduri C (2010) Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 137(15):2493-2499
47. Bertani S, Sauer S, Bolotin E, Sauer F (2011) The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol Cell 43(6):1040-1046
48. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 309(5740):1570-1573
49. Moran VA, Perera RJ, Khalil AM (2012) Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res 40(14):6391-6400
50. Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470(7333):284-288
51. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G 3rd, Kenny PJ, Wahlestedt C (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase. Nat Med 14(7):723-730
52. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491(7424):454-457
53. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465(7301):1033-1038
54. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, Garcia JA, Paz-Ares J (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39(8):1033-1037
55. Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, Karreth F, Poliseno L, Provero P, Di Cunto F, Lieberman J, Rigoutsos I, Pandolfi PP (2011) Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147(2):344-357
56. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147(2):358-369
57. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146(3):353-358
58. Bond AM, Vangompel MJ, Sametsky EA, Clark MF, Savage JC, Disterhoft JF, Kohtz JD (2009) Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat Neurosci 12(8):1020-1027
59. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA (2013) Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152(3):570-583
60. Alsina B, Giraldez F, Pujades C (2009) Patterning and cell fate in ear development. Int J Dev Biol 53(8-10):1503-1513
61. Cole LK, Le Roux I, Nunes F, Laufer E, Lewis J, Wu DK (2000) Sensory organ generation in the chicken inner ear: contributions of bone morphogenetic protein 4, serrate1, and lunatic fringe. J Comp Neurol 424(3):509-520
62. Lleras-Forero L, Streit A (2012) Development of the sensory nervous system in the vertebrate head: the importance of being on time. Curr Opin Genet Dev 22(4):315-322
63. Groves AK, Fekete DM (2012) Shaping sound in space: the regulation of inner ear patterning. Development 139(2):245-257
64. Wu DK, Kelley MW (2012) Molecular mechanisms of inner ear development. Cold Spring Harb Perspect Biol 4(8):a008409
65. Brigande JV, Kiernan AE, Gao X, Iten LE, Fekete DM (2000) Molecular genetics of pattern formation in the inner ear: do compartment boundaries play a role? Proc Natl Acad Sci USA 97(22):11700-11706
66. Cantos R, Cole LK, Acampora D, Simeone A, Wu DK (2000) Patterning of the mammalian cochlea. Proc Natl Acad Sci USA 97(22):11707-11713
67. Patel M, Hu BH (2012) MicroRNAs in inner ear biology and pathogenesis. Hear Res 287(1-2):6-14
68. Weston MD, Pierce ML, Rocha-Sanchez S, Beisel KW, Soukup GA (2006) MicroRNA gene expression in the mouse inner ear. Brain Res 1111(1):95-104
69. Hirai M, Maeda Y, Fukushima K, Sugaya A, Kataoka Y, Nishizaki K (2011) Expression analysis of microRNAs in murine cochlear explants. NeuroReport 22(13):652-654
70. Elkan-Miller T, Ulitsky I, Hertzano R, Rudnicki A, Dror AA, Lenz DR, Elkon R, Irmler M, Beckers J, Shamir R, Avraham KB (2011) Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear. PLoS ONE 6(4):e18195
71. Friedman LM, Dror AA, Mor E, Tenne T, Toren G, Satoh T, Biesemeier DJ, Shomron N, Fekete DM, Hornstein E, Avraham KB (2009) MicroRNAs are essential for development and function of inner ear hair cells in vertebrates. Proc Natl Acad Sci USA 106(19):7915-7920
72. Hertzano R, Elkon R (2012) High throughput gene expression analysis of the inner ear. Hear Res 288(1-2):77-88
73. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH (2005) MicroRNA expression in zebrafish embryonic development. Science 309(5732):310-311
74. Wang XR, Zhang XM, Zhen J, Zhang PX, Xu G, Jiang H (2010) MicroRNA expression in the embryonic mouse inner ear. NeuroReport 21(9):611-617
75. Ohyama T, Groves AK (2004) Generation of Pax2-Cre mice by modification of a Pax2 bacterial artificial chromosome. Genesis 38(4):195-199
76. Soukup GA, Fritzsch B, Pierce ML, Weston MD, Jahan I, McManus MT, Harfe BD (2009) Residual microRNA expression dictates the extent of inner ear development in conditional Dicer knockout mice. Dev Biol 328(2):328-341
77. Weston MD, Pierce ML, Jensen-Smith HC, Fritzsch B, Rocha-Sanchez S, Beisel KW, Soukup GA (2011) MicroRNA-183 family expression in hair cell development and requirement of microRNAs for hair cell maintenance and survival. Dev Dyn 240(4):808-819
78. Kersigo J, D'Angelo A, Gray BD, Soukup GA, Fritzsch B (2011) The role of sensory organs and the forebrain for the development of the craniofacial shape as revealed by Foxg1-cre-mediated microRNA loss. Genesis 49(4):326-341
79. Bohne BA, Yohman L, Gruner MM (1987) Cochlear damage following interrupted exposure to high-frequency noise. Hear Res 29(2-3):251-264
80. Fechter LD, Liu Y, Pearce TA (1997) Cochlear protection from carbon monoxide exposure by free radical blockers in the guinea pig. Toxicol Appl Pharmacol 142(1):47-55
81. Hu BH, Henderson D, Nicotera TM (2002) Involvement of apoptosis in progression of cochlear lesion following exposure to intense noise. Hear Res 166(1-2):62-71
82. Sha SH, Taylor R, Forge A, Schacht J (2001) Differential vulnerability of basal and apical hair cells is based on intrinsic susceptibility to free radicals. Hear Res 155(1-2):1-8
83. Sacheli R, Nguyen L, Borgs L, Vandenbosch R, Bodson M, Lefebvre P, Malgrange B (2009) Expression patterns of miR-96, miR-182, and miR-183 in the development inner ear. Gene Expr Patterns 9(5):364-370
84. Xu S, Witmer PD, Lumayag S, Kovacs B, Valle D (2007) MicroRNA (miRNA) transcriptome of mouse retina and identification of a sensory organ-specific miRNA cluster. J Biol Chem 282(34):25053-25066
85. Jalvy-Delvaille S, Maurel M, Majo V, Pierre N, Chabas S, Combe C, Rosenbaum J, Sagliocco F, Grosset CF (2012) Molecular basis of differential target regulation by miR-96 and miR-182: the Glypican-3 as a model. Nucleic Acids Res 40(3):1356-1365
86. Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP (2009) An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet 41(5):614-618
87. Li H, Kloosterman W, Fekete DM (2010) MicroRNA-183 family members regulate sensorineural fates in the inner ear. J Neurosci 30(9):3254-3263
88. Wang XR, Zhang XM, Du J, Jiang H (2012) MicroRNA-182 regulates otocyst-derived cell differentiation and targets T-box1 gene. Hear Res 286(1-2):55-63
89. Gu C, Li X, Tan Q, Wang Z, Chen L, Liu Y (2013) MiR-183 family regulates chloride intracellular channel 5 expression in inner ear hair cells. Toxicol In Vitro 27(1):486-491
90. Hertzano R, Elkon R, Kurima K, Morrisson A, Chan SL, Sallin M, Biedlingmaier A, Darling DS, Griffith AJ, Eisenman DJ, Strome SE (2011) Cell type-specific transcriptome analysis reveals a major role for Zeb1 and miR-200b in mouse inner ear morphogenesis. PLoS Genet 7(9):e1002309
91. Frucht CS, Santos-Sacchi J, Navaratnam DS (2011) MicroRNA181a plays a key role in hair cell regeneration in the avian auditory epithelium. Neurosci Lett 493(1-2):44-48
92. Mencia A, Modamio-Hoybjor S, Redshaw N, Morin M, Mayo-Merino F, Olavarrieta L, Aguirre LA, del Castillo I, Steel KP, Dalmay T, Moreno F, Moreno-Pelayo MA (2009) Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet 41(5):609-613
93. Solda G, Robusto M, Primignani P, Castorina P, Benzoni E, Cesarani A, Ambrosetti U, Asselta R, Duga S (2012) A novel mutation within the MIR96 gene causes non-syndromic inherited hearing loss in an Italian family by altering pre-miRNA processing. Hum Mol Genet 21(3):577-585
94. Cioffi JA, Yue WY, Mendolia-Loffredo S, Hansen KR, Wackym PA, Hansen MR (2010) MicroRNA-21 overexpression contributes to vestibular schwannoma cell proliferation and survival. Otol Neurotol 31(9):1455-1462
95. Friedland DR, Eernisse R, Erbe C, Gupta N, Cioffi JA (2009) Cholesteatoma growth and proliferation: posttranscriptional regulation by microRNA-21. Otol Neurotol 30(7):998-1005
96. Roberts KA, Abraira VE, Tucker AF, Goodrich LV, Andrews NC (2012) Mutation of Rubie, a novel long non-coding RNA located upstream of Bmp4, causes vestibular malformation in mice. PLoS ONE 7(1):e29495
97. Esteve P, Bovolenta P (2006) Secreted inducers in vertebrate eye development: more functions for old morphogens. Curr Opin Neurobiol 16(1):13-19
98. Martinez-Morales JR, Rodrigo I, Bovolenta P (2004) Eye development: a view from the retina pigmented epithelium. Bioessays: News Rev Mol Cell Dev Biol 26(7):766-777
99. Beccari L, Marco-Ferreres R, Bovolenta P (2013) The logic of gene regulatory networks in early vertebrate forebrain patterning. Mech Dev 130:95-111
100. Bassett EA, Wallace VA (2012) Cell fate determination in the vertebrate retina. Trends Neurosci 35(9):565-573
101. Shaham O, Menuchin Y, Farhy C, Ashery-Padan R (2012) Pax6: a multi-level regulator of ocular development. Prog Retin Eye Res 31(5):351-376
102. Fuhrmann S (2010) Eye morphogenesis and patterning of the optic vesicle. Curr Top Dev Biol 93:61-84
103. Frederikse PH, Donnelly R, Partyka LM (2006) MiRNA and Dicer in the mammalian lens: expression of brain-specific miRNAs in the lens. Histochem Cell Biol 126(1):1-8
104. Karali M, Peluso I, Gennarino VA, Bilio M, Verde R, Lago G, Dolle P, Banfi S (2010) miRNeye: a microRNA expression atlas of the mouse eye. BMC Genomics 11:715
105. Karali M, Peluso I, Marigo V, Banfi S (2007) Identification and characterization of microRNAs expressed in the mouse eye. Invest Ophthalmol Vis Sci 48(2):509-515
106. Ryan DG, Oliveira-Fernandes M, Lavker RM (2006) MicroRNAs of the mammalian eye display distinct and overlapping tissue specificity. Mol Vis 12:1175-1184
107. Makarev E, Spence JR, Del Rio-Tsonis K, Tsonis PA (2006) Identification of microRNAs and other small RNAs from the adult newt eye. Mol Vis 12:1386-1391. doi: v12/a156
108. Wu C, Lin H, Wang Q, Chen W, Luo H, Zhang H (2012) Discrepant expression of microRNAs in transparent and cataractous human lenses. Invest Ophthalmol Vis Sci 53(7):3906-3912
109. Yan N, Ma K, Ma J, Chen W, Wang Y, Cao G, Man-Kit Lam D, Liu X (2010) Profiling microRNAs differentially expressed in rabbit retina. Adv Exp Med Biol 664:203-209
110. Hackler L Jr, Wan J, Swaroop A, Qian J, Zack DJ (2010) MicroRNA profile of the developing mouse retina. Invest Ophthalmol Vis Sci 51(4):1823-1831
111. Arora A, Guduric-Fuchs J, Harwood L, Dellett M, Cogliati T, Simpson DA (2010) Prediction of microRNAs affecting mRNA expression during retinal development. BMC Dev Biol 10:1
112. Arora A, McKay GJ, Simpson DA (2007) Prediction and verification of miRNA expression in human and rat retinas. Invest Ophthalmol Vis Sci 48(9):3962-3967
113. Li Y, Piatigorsky J (2009) Targeted deletion of Dicer disrupts lens morphogenesis, corneal epithelium stratification, and whole eye development. Dev Dyn 238(9):2388-2400
114. Pinter R, Hindges R (2010) Perturbations of microRNA function in mouse dicer mutants produce retinal defects and lead to aberrant axon pathfinding at the optic chiasm. PLoS ONE 5(4):e10021
115. Iida A, Shinoe T, Baba Y, Mano H, Watanabe S (2011) Dicer plays essential roles for retinal development by regulation of survival and differentiation. Invest Ophthalmol Vis Sci 52(6):3008-3017
116. Georgi SA, Reh TA (2010) Dicer is required for the transition from early to late progenitor state in the developing mouse retina. J Neurosci 30(11):4048-4061
117. Damiani D, Alexander JJ, O'Rourke JR, McManus M, Jadhav AP, Cepko CL, Hauswirth WW, Harfe BD, Strettoi E (2008) Dicer inactivation leads to progressive functional and structural degeneration of the mouse retina. J Neurosci 28(19):4878-4887
118. Decembrini S, Andreazzoli M, Barsacchi G, Cremisi F (2008) Dicer inactivation causes heterochronic retinogenesis in Xenopus laevis. Int J Dev Biol 52(8):1099-1103
119. Davis N, Mor E, Ashery-Padan R (2011) Roles for Dicer1 in the patterning and differentiation of the optic cup neuroepithelium. Development 138(1):127-138
120. Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, Kariko K, Yoo JW, Lee DK, Hadziahmetovic M, Song Y, Misra S, Chaudhuri G, Buaas FW, Braun RE, Hinton DR, Zhang Q, Grossniklaus HE, Provis JM, Madigan MC, Milam AH, Justice NL, Albuquerque RJ, Blandford AD, Bogdanovich S, Hirano Y, Witta J, Fuchs E, Littman DR, Ambati BK, Rudin CM, Chong MM, Provost P, Kugel JF, Goodrich JA, Dunaief JL, Baffi JZ, Ambati J (2011) DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature 471(7338):325-330
121. Qiu R, Liu Y, Wu JY, Liu K, Mo W, He R (2009) Misexpression of miR-196a induces eye anomaly in Xenopus laevis. Brain Res Bull 79(1):26-31
122. Walker JC, Harland RM (2009) microRNA-24a is required to repress apoptosis in the developing neural retina. Genes Dev 23(9):1046-1051
123. Qiu R, Liu K, Liu Y, Mo W, Flynt AS, Patton JG, Kar A, Wu JY, He R (2009) The role of miR-124a in early development of the Xenopus eye. Mech Dev 126(10):804-816
124. Liu K, Liu Y, Mo W, Qiu R, Wang X, Wu JY, He R (2011) MiR-124 regulates early neurogenesis in the optic vesicle and forebrain, targeting NeuroD1. Nucleic Acids Res 39(7):2869-2879
125. Baudet ML, Zivraj KH, Abreu-Goodger C, Muldal A, Armisen J, Blenkiron C, Goldstein LD, Miska EA, Holt CE (2012) miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones. Nat Neurosci 15(1):29-38
126. Decembrini S, Bressan D, Vignali R, Pitto L, Mariotti S, Rainaldi G, Wang X, Evangelista M, Barsacchi G, Cremisi F (2009) MicroRNAs couple cell fate and developmental timing in retina. Proc Natl Acad Sci USA 106(50):21179-21184
127. Conte I, Carrella S, Avellino R, Karali M, Marco-Ferreres R, Bovolenta P, Banfi S (2010) miR-204 is required for lens and retinal development via Meis2 targeting. Proc Natl Acad Sci USA 107(35):15491-15496
128. Wang FE, Zhang C, Maminishkis A, Dong L, Zhi C, Li R, Zhao J, Majerciak V, Gaur AB, Chen S, Miller SS (2010) MicroRNA-204/211 alters epithelial physiology. FASEB J 24(5):1552-1571
129. Adijanto J, Castorino JJ, Wang ZX, Maminishkis A, Grunwald GB, Philp NJ (2012) Microphthalmia-associated transcription factor (MITF) promotes differentiation of human retinal pigment epithelium (RPE) by regulating microRNAs-204/211 expression. J Biol Chem 287(24):20491-20503
130. Zhu Q, Sun W, Okano K, Chen Y, Zhang N, Maeda T, Palczewski K (2011) Sponge transgenic mouse model reveals important roles for the microRNA-183 (miR-183)/96/182 cluster in postmitotic photoreceptors of the retina. J Biol Chem 286(36):31749-31760
131. Lumayag S, Haldin CE, Corbett NJ, Wahlin KJ, Cowan C, Turturro S, Larsen PE, Kovacs B, Witmer PD, Valle D, Zack DJ, Nicholson DA, Xu S (2013) Inactivation of the microRNA-183/96/182 cluster results in syndromic retinal degeneration. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1212655110
132. Jin ZB, Hirokawa G, Gui L, Takahashi R, Osakada F, Hiura Y, Takahashi M, Yasuhara O, Iwai N (2009) Targeted deletion of miR-182, an abundant retinal microRNA. Mol Vis 15:523-533
133. Sanuki R, Onishi A, Koike C, Muramatsu R, Watanabe S, Muranishi Y, Irie S, Uneo S, Koyasu T, Matsui R, Cherasse Y, Urade Y, Watanabe D, Kondo M, Yamashita T, Furukawa T (2011) miR-124a is required for hippocampal axogenesis and retinal cone survival through Lhx2 suppression. Nat Neurosci 14(9):1125-1134
134. Ramachandran R, Fausett BV, Goldman D (2010) Ascl1a regulates Muller glia dedifferentiation and retinal regeneration through a Lin-28-dependent, let-7 microRNA signalling pathway. Nat Cell Biol 12(11):1101-1107
135. Li Y, Li C, Chen Z, He J, Tao Z, Yin ZQ (2012) A microRNA, mir133b, suppresses melanopsin expression mediated by failure dopaminergic amacrine cells in RCS rats. Cell Signal 24(3):685-698
136. Shen J, Yang X, Xie B, Chen Y, Swaim M, Hackett SF, Campochiaro PA (2008) MicroRNAs regulate ocular neovascularization. Mol Ther 16(7):1208-1216
137. Small EM, Sutherland LB, Rajagopalan KN, Wang S, Olson EN (2010) MicroRNA-218 regulates vascular patterning by modulation of Slit-Robo signaling. Circ Res 107(11):1336-1344
138. Krol J, Busskamp V, Markiewicz I, Stadler MB, Ribi S, Richter J, Duebel J, Bicker S, Fehling HJ, Schubeler D, Oertner TG, Schratt G, Bibel M, Roska B, Filipowicz W (2010) Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs. Cell 141(4):618-631
139. Silva VA, Polesskaya A, Sousa TA, Correa VM, Andre ND, Reis RI, Kettelhut IC, Harel-Bellan A, De Lucca FL (2011) Expression and cellular localization of microRNA-29b and RAX, an activator of the RNA-dependent protein kinase (PKR), in the retina of streptozotocin-induced diabetic rats. Mol Vis 17:2228-2240
140. Loscher CJ, Hokamp K, Kenna PF, Ivens AC, Humphries P, Palfi A, Farrar GJ (2007) Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa. Genome Biol 8(11):R248
141. Loscher CJ, Hokamp K, Wilson JH, Li T, Humphries P, Farrar GJ, Palfi A (2008) A common microRNA signature in mouse models of retinal degeneration. Exp Eye Res 87(6):529-534
142. Ishida W, Fukuda K, Higuchi T, Kajisako M, Sakamoto S, Fukushima A (2011) Dynamic changes of microRNAs in the eye during the development of experimental autoimmune uveoretinitis. Invest Ophthalmol Vis Sci 52(1):611-617
143. Kovacs B, Lumayag S, Cowan C, Xu S (2011) MicroRNAs in early diabetic retinopathy in streptozotocin-induced diabetic rats. Invest Ophthalmol Vis Sci 52(7):4402-4409
144. Peng CH, Liu JH, Woung LC, Lin TJ, Chiou SH, Tseng PC, Du WY, Cheng CK, Hu CC, Chien KH, Chen SJ (2012) MicroRNAs and cataracts: correlation among let-7 expression, age and the severity of lens opacity. Br J Ophthalmol 96(5):747-751
145. Hughes AE, Bradley DT, Campbell M, Lechner J, Dash DP, Simpson DA, Willoughby CE (2011) Mutation altering the miR-184 seed region causes familial keratoconus with cataract. Am J Hum Genet 89(5):628-633
146. Hoffmann A, Huang Y, Suetsugu-Maki R, Ringelberg CS, Tomlinson CR, Del Rio-Tsonis K, Tsonis PA (2012) Implication of the miR-184 and miR-204 competitive RNA network in control of mouse secondary cataract. Mol Med 18:528-538
147. Georgiadis A, Tschernutter M, Bainbridge JW, Robbie SJ, McIntosh J, Nathwani AC, Smith AJ, Ali RR (2010) AAV-mediated knockdown of peripherin-2 in vivo using miRNA-based hairpins. Gene Ther 17(4):486-493
148. Karali M, Manfredi A, Puppo A, Marrocco E, Gargiulo A, Allocca M, Corte MD, Rossi S, Giunti M, Bacci ML, Simonelli F, Surace EM, Banfi S, Auricchio A (2011) MicroRNA-restricted transgene expression in the retina. PLoS ONE 6(7):e22166
149. Pihlmann M, Askou AL, Aagaard L, Bruun GH, Svalgaard JD, Holm-Nielsen MH, Dagnaes-Hansen F, Bek T, Mikkelsen JG, Jensen TG, Corydon TJ (2012) Adeno-associated virus-delivered polycistronic microRNA-clusters for knockdown of vascular endothelial growth factor in vivo. J Gene Med 14(5):328-338
150. Bai Y, Bai X, Wang Z, Zhang X, Ruan C, Miao J (2011) MicroRNA-126 inhibits ischemia-induced retinal neovascularization via regulating angiogenic growth factors. Exp Mol Pathol 91(1):471-477
151. McArthur K, Feng B, Wu Y, Chen S, Chakrabarti S (2011) MicroRNA-200b regulates vascular endothelial growth factor-mediated alterations in diabetic retinopathy. Diabetes 60(4):1314-1323
152. Chen KC, Hsi E, Hu CY, Chou WW, Liang CL, Juo SH (2012) MicroRNA-328 may influence myopia development by mediating the PAX6 gene. Invest Ophthalmol Vis Sci 53(6):2732-2739
153. Rapicavoli NA, Blackshaw S (2009) New meaning in the message: noncoding RNAs and their role in retinal development. Dev Dyn 238(9):2103-2114
154. Geng X, Lavado A, Lagutin OV, Liu W, Oliver G (2007) Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Gene Expr Patterns 7(3):252-257
155. Rapicavoli NA, Poth EM, Zhu H, Blackshaw S (2011) The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev 6:32
156. Meola N, Pizzo M, Alfano G, Surace EM, Banfi S (2012) The long noncoding RNA Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina. RNA 18(1):111-123
157. Alfano G, Vitiello C, Caccioppoli C, Caramico T, Carola A, Szego MJ, McInnes RR, Auricchio A, Banfi S (2005) Natural antisense transcripts associated with genes involved in eye development. Hum Mol Genet 14(7):913-923
158. Young TL, Matsuda T, Cepko CL (2005) The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol 15(6):501-512
159. Rapicavoli NA, Poth EM, Blackshaw S (2010) The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 10:49
160. Sheik Mohamed J, Gaughwin PM, Lim B, Robson P, Lipovich L (2010) Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 16(2):324-337
161. Tsuiji H, Yoshimoto R, Hasegawa Y, Furuno M, Yoshida M, Nakagawa S (2011) Competition between a noncoding exon and introns: gomafu contains tandem UACUAAC repeats and associates with splicing factor-1. Genes Cells: Devoted Mol Cell Mech 16(5):479-490
162. Mori K, Yoshihara Y (1995) Molecular recognition and olfactory processing in the mammalian olfactory system. Prog Neurobiol 45(6):585-619
163. Yoshihara Y, Mori K (1997) Basic principles and molecular mechanisms of olfactory axon pathfinding. Cell Tissue Res 290(2):457-463
164. Mori K, von Campenhause H, Yoshihara Y (2000) Zonal organization of the mammalian main and accessory olfactory systems. Philos Trans R Soc Lond B Biol Sci 355(1404):1801-1812
165. Brunjes PC, Greer CA (2003) Progress and directions in olfactory development. Neuron 38(3):371-374
166. Nicolay DJ, Doucette JR, Nazarali AJ (2006) Transcriptional regulation of neurogenesis in the olfactory epithelium. Cell Mol Neurobiol 26(4-6):803-821
167. Lopez-Mascaraque L, de Castro F (2002) The olfactory bulb as an independent developmental domain. Cell Death Differ 9(12):1279-1286
168. Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, Wittbrodt J, Antin PB, Plasterk RH (2006) Differences in vertebrate microRNA expression. Proc Natl Acad Sci USA 103(39):14385-14389
169. Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE, Hentze MW, Muckenthaler MU (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12(5):913-920
170. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20):e179
171. Choi PS, Zakhary L, Choi WY, Caron S, Alvarez-Saavedra E, Miska EA, McManus M, Harfe B, Giraldez AJ, Horvitz HR, Schier AF, Dulac C (2008) Members of the miRNA-200 family regulate olfactory neurogenesis. Neuron 57(1):41-55
172. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12(9):735-739
173. Bak M, Silahtaroglu A, Moller M, Christensen M, Rath MF, Skryabin B, Tommerup N, Kauppinen S (2008) MicroRNA expression in the adult mouse central nervous system. RNA 14(3):432-444
174. Obernosterer G, Martinez J, Alenius M (2007) Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat Protoc 2(6):1508-1514
175. Korpal M, Lee ES, Hu G, Kang Y (2008) The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2. J Biol Chem 283(22):14910-14914
176. Akerblom M, Sachdeva R, Barde I, Verp S, Gentner B, Trono D, Jakobsson J (2012) MicroRNA-124 is a subventricular zone neuronal fate determinant. J Neurosci 32(26):8879-8889
177. Pathania M, Torres-Reveron J, Yan L, Kimura T, Lin TV, Gordon V, Teng ZQ, Zhao X, Fulga TA, Van Vactor D, Bordey A (2012) miR-132 enhances dendritic morphogenesis, spine density, synaptic integration, and survival of newborn olfactory bulb neurons. PLoS One 7(5):e38174
178. de Chevigny A, Core N, Follert P, Gaudin M, Barbry P, Beclin C, Cremer H (2012) miR-7a regulation of Pax6 controls spatial origin of forebrain dopaminergic neurons. Nat Neurosci 15(8):1120-1126
179. Meola N, Gennarino VA, Banfi S (2009) microRNAs and genetic diseases. Pathogenetics 2(1):7
180. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigo R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775-1789
181. Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10:135-151
182. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294(5543):853-858
183. Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297(5589):2056-2060
184. Kim VN (2006) Small RNAs just got bigger: piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev 20(15):1993-1997
185. Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS (2009) Tiny RNAs associated with transcription start sites in animals. Nat Genet 41(5):572-578
186. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143(1):46-58
187. Kiss T (2002) Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 109(2):145-148
188. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA (2008) Divergent transcription from active promoters. Science 322(5909):1849-1851
189. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R, Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik SE, Shimizu M, Tili E, Rossi S, Taccioli C, Pichiorri F, Liu X, Zupo S, Herlea V, Gramantieri L, Lanza G, Alder H, Rassenti L, Volinia S, Schmittgen TD, Kipps TJ, Negrini M, Croce CM (2007) Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12(3):215-229
190. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C (2005) Antisense transcription in the mammalian transcriptome. Science 309(5740):1564-1566
191. Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142(3):409-419