Long noncoding RNAs in cell biology

Seminars in Cell and Developmental Biology

Volumn 22, Issue 4, 2011, Pages 366-376

  Clark, Michael B ^a   Mattick, John S ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Cytoplasm; Development; Localization; Neurons; Nucleus; Paraspeckles; Trafficking

Indexed keywords

BC1; BC200; G22; GOMAFU; KCNQ1OT1; LONG NONCODING RNA; MALAT1; NEAT1; PINC; RIBONUCLEOPROTEIN; UNCLASSIFIED DRUG; UNTRANSLATED RNA; VEGT; XLSIRTS;

ARABIDOPSIS; CELL CYCLE; CELL DIFFERENTIATION; CELL ORGANELLE; CELL STRUCTURE; CELLULAR DISTRIBUTION; CENTROMERE; CYTOLOGY; DENDRITE; DROSOPHILA; EMBRYO DEVELOPMENT; EMBRYONIC STEM CELL; EPILEPTIC DISCHARGE; EUKARYOTIC CELL; GENE CONTROL; GENE LOCATION; GENE SILENCING; HUMAN; MUSCLE DEVELOPMENT; NERVE CELL DIFFERENTIATION; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; QUALITY CONTROL; RETINA DEVELOPMENT; REVIEW; UPREGULATION; X CHROMOSOME; XENOPUS LAEVIS;

ANIMALIA; MAMMALIA;

EID: 79957580288     PISSN: 10849521     EISSN: 10963634     Source Type: Journal    
DOI: 10.1016/j.semcdb.2011.01.001     Document Type: Review

References (179)

1. Kapranov P., Cawley S.E., Drenkow J., Bekiranov S., Strausberg R.L., Fodor S.P., et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 2002, 296:916-919.
2. Okazaki Y., Furuno M., Kasukawa T., Adachi J., Bono H., Kondo S., et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420:563-573.
3. Stolc V., Gauhar Z., Mason C., Halasz G., van Batenburg M.F., Rifkin S.A., et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 2004, 306:655-660.
4. Cheng J., Kapranov P., Drenkow J., Dike S., Brubaker S., Patel S., et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005, 308:1149-1154.
5. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
6. Katayama S., Tomaru Y., Kasukawa T., Waki K., Nakanishi M., Nakamura M., et al. Antisense transcription in the mammalian transcriptome. Science 2005, 309:1564-1566.
7. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
8. He H., Wang J., Liu T., Liu X.S., Li T., Wang Y., et al. Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res 2007, 17:1471-1477.
9. He Y., Vogelstein B., Velculescu V.E., Papadopoulos N., Kinzler K.W. The antisense transcriptomes of human cells. Science 2008, 322:1855-1857.
10. Wilhelm B.T., Marguerat S., Watt S., Schubert F., Wood V., Goodhead I., et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453:1239-1243.
11. Lyle R., Watanabe D., te Vruchte D., Lerchner W., Smrzka O.W., Wutz A., et al. The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat Genet 2000, 25:19-21.
12. Furuno M., Pang K.C., Ninomiya N., Fukuda S., Frith M.C., Bult C., et al. Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet 2006, 2:e37.
13. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
14. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 2009, 106:11667-11672.
15. Marques A.C., Ponting C.P. Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol 2009, 10:R124.
16. Ørom U.A., Derrien T., Beringer M., Gumireddy K., Gardini A., Bussotti G., et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010, 143:46-58.
17. Mattick J.S. The genetic signatures of noncoding RNAs. PLoS Genet 2009, 5:e1000459.
18. Ravasi T., Suzuki H., Pang K.C., Katayama S., Furuno M., Okunishi R., et al. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res 2006, 16:11-19.
19. Dinger M.E., Amaral P.P., Mercer T.R., Pang K.C., Bruce S.J., Gardiner B.B., et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008, 18:1433-1445.
20. Pang K.C., Dinger M.E., Mercer T.R., Malquori L., Grimmond S.M., Chen W., et al. Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol 2009, 182:7738-7748.
21. Mercer T.R., Qureshi I.A., Gokhan S., Dinger M.E., Li G., Mattick J.S., et al. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 2010, 11:14.
22. Loewer S., Cabili M.N., Guttman M., Loh Y.H., Thomas K., Park I.H., et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet 2010, 42:1113-1117.
23. Cao X., Yeo G., Muotri A.R., Kuwabara T., Gage F.H. Noncoding RNAs in the mammalian central nervous system. Annu Rev Neurosci 2006, 29:77-103.
24. Mercer T.R., Dinger M.E., Sunkin S.M., Mehler M.F., Mattick J.S. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 2008, 105:716-721.
25. Mehler M.F., Mattick J.S. Non-coding RNAs in the nervous system. J Physiol 2006, 575:333-341.
26. Mehler M.F., Mattick J.S. Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol Rev 2007, 87:799-823.
27. Amaral P.P., Mattick J.S. Noncoding RNA in development. Mamm Genome 2008, 19:454-492.
28. Zhao J., Sun B.K., Erwin J.A., Song J.J., Lee J.T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008, 322:750-756.
29. Tian D., Sun S., Lee J.T. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 2010, 143:390-403.
30. Mohammad F., Pandey R.R., Nagano T., Chakalova L., Mondal T., Fraser P., et al. Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 2008, 28:3713-3728.
31. Sleutels F., Zwart R., Barlow D.P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 2002, 415:810-813.
32. Nagano T., Mitchell J.A., Sanz L.A., Pauler F.M., Ferguson-Smith A.C., Feil R., et al. The air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008, 322:1717-1720.
33. Pandey R.R., Mondal T., Mohammad F., Enroth S., Redrup L., Komorowski J., et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 2008, 32:232-246.
34. Rinn J.L., Kertesz M., Wang J.K., Squazzo S.L., Xu X., Brugmann S.A., et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129:1311-1323.
35. Yu W., Gius D., Onyango P., Muldoon-Jacobs K., Karp J., Feinberg A.P., et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008, 451:202-206.
36. Rodriguez-Campos A., Azorin F. RNA Is an integral component of chromatin that contributes to its structural organization. PLoS ONE 2007, 2:e1182.
37. Wang X., Arai S., Song X., Reichart D., Du K., Pascual G., et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 2008, 454:126-130.
38. Schwartz J.C., Younger S.T., Nguyen N.B., Hardy D.B., Monia B.P., Corey D.R., et al. Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol 2008, 15:842-848.
39. Tasheva E.S., Roufa D.J. Regulation of human RPS14 transcription by intronic antisense RNAs and ribosomal protein S14. Genes Dev 1995, 9:304-316.
40. Kino T., Hurt D.E., Ichijo T., Nader N., Chrousos G.P. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 2010, 3:ra8.
41. Yan M.D., Hong C.C., Lai G.M., Cheng A.L., Lin Y.W., Chuang S.E. Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Hum Mol Genet 2005, 14:1465-1474.
42. Beltran M., Puig I., Pena C., Garcia J.M., Alvarez A.B., Pena R., et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev 2008, 22:756-769.
43. Lin D., Pestova T.V., Hellen C.U., Tiedge H. Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism. Mol Cell Biol 2008, 28:3008-3019.
44. Young T.L., Matsuda T., Cepko C.L. The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol 2005, 15:501-512.
45. Kloc M., Wilk K., Vargas D., Shirato Y., Bilinski S., Etkin L.D. Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes. Development 2005, 132:3445-3457.
46. Sunwoo H., Dinger M.E., Wilusz J.E., Amaral P.P., Mattick J.S., Spector D.L. MEN e{open}/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 2009, 19:347-359.
47. Yochum G.S., Cleland R., McWeeney S., Goodman R.H. An antisense transcript induced by Wnt/beta-catenin signaling decreases E2F4. J Biol Chem 2007, 282:871-878.
48. Mourtada-Maarabouni M., Hedge V.L., Kirkham L., Farzaneh F., Williams G.T. Growth arrest in human T-cells is controlled by the non-coding RNA growth-arrest-specific transcript 5 (GAS5). J Cell Sci 2008, 121:939-946.
49. Willingham A.T., Orth A.P., Batalov S., Peters E.C., Wen B.G., Aza-Blanc P., et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005, 309:1570-1573.
50. Shamovsky I., Ivannikov M., Kandel E.S., Gershon D., Nudler E. RNA-mediated response to heat shock in mammalian cells. Nature 2006, 440:556-560.
51. Mattick J.S., Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2001, 2:986-991.
52. Mattick J.S. A new paradigm for developmental biology. J Exp Biol 2007, 210:1526-1547.
53. Mattick J.S., Amaral P.P., Dinger M.E., Mercer T.R., Mehler M.F. RNA regulation of epigenetic processes. Bioessays 2009, 31:51-59.
54. Mattick J.S., Taft R.J., Faulkner G.J. A global view of genomic information-moving beyond the gene and the master regulator. Trends Genet 2010, 26:21-28.
55. Zhao J., Ohsumi T.K., Kung J.T., Ogawa Y., Grau D.J., Sarma K., et al. Genome-wide identification of Polycomb-associated RNAs by RIP-seq. Mol Cell 2010, 40:939-953.
56. Huarte M., Guttman M., Feldser D., Garber M., Koziol M.J., Kenzelmann-Broz D., et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010, 142:409-419.
57. Fox A.H., Lam Y.W., Leung A.K., Lyon C.E., Andersen J., Mann M., et al. Paraspeckles: a novel nuclear domain. Curr Biol 2002, 12:13-25.
58. Sone M., Hayashi T., Tarui H., Agata K., Takeichi M., Nakagawa S. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 2007, 120:2498-2506.
59. Sunwoo H., Dinger M.E., Wilusz J.E., Amaral P.P., Mattick J.S., Spector D.L. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 2009, 19:347-359.
60. Kloc M., Etkin L.D. RNA localization mechanisms in oocytes. J Cell Sci 2005, 118:269-282.
61. Sossin W.S., DesGroseillers L. Intracellular trafficking of RNA in neurons. Traffic 2006, 7:1581-1589.
62. Lecuyer E., Yoshida H., Parthasarathy N., Alm C., Babak T., Cerovina T., et al. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 2007, 131:174-187.
63. Mili S., Moissoglu K., Macara I.G. Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions. Nature 2008, 453:115-119.
64. Saha S., Murthy S., Rangarajan P.N. Identification and characterization of a virus-inducible non-coding RNA in mouse brain. J Gen Virol 2006, 87:1991-1995.
65. Hutchinson J.N., Ensminger A.W., Clemson C.M., Lynch C.R., Lawrence J.B., Chess A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 2007, 8:39.
66. Bond C.S., Fox A.H., Paraspeckles: nuclear bodies built on long noncoding RNA. J Cell Biol 2009, 186:637-644.
67. Clemson C.M., Hutchinson J.N., Sara S.A., Ensminger A.W., Fox A.H., Chess A., et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 2009, 33:717-726.
68. Sasaki Y.T., Ideue T., Sano M., Mituyama T., Hirose T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci USA 2009, 106:2525-2530.
69. Chen L.L., Carmichael G.G. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell 2009, 35:467-478.
70. Prasanth K.V., Prasanth S.G., Xuan Z., Hearn S., Freier S.M., Bennett C.F., et al. Regulating gene expression through RNA nuclear retention. Cell 2005, 123:249-263.
71. Wilusz J.E., Freier S.M., Spector D.L. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008, 135:919-932.
72. Tripathi V., Ellis J.D., Shen Z., Song D.Y., Pan Q., Watt A.T., et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010, 39:925-938.
73. Tseng J.J., Hsieh Y.T., Hsu S.L., Chou M.M. Metastasis associated lung adenocarcinoma transcript 1 is up-regulated in placenta previa increta/percreta and strongly associated with trophoblast-like cell invasion in vitro. Mol Hum Reprod 2009, 15:725-731.
74. Bernard D., Prasanth K.V., Tripathi V., Colasse S., Nakamura T., Xuan Z., et al. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J 2010, 29:3082-3093.
75. Ji P., Diederichs S., Wang W., Boing S., Metzger R., Schneider P.M., et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 2003, 22:6087-6097.
76. Lin R., Maeda S., Liu C., Karin M., Edgington T.S. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 2007, 26:851-858.
77. Rapicavoli N.A., Poth E.M., Blackshaw S. The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 2010, 10:49.
78. Ishii N., Ozaki K., Sato H., Mizuno H., Saito S., Takahashi A., et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 2006, 51:1087-1099.
79. Blackshaw S., Harpavat S., Trimarchi J., Cai L., Huang H., Kuo W.P., et al. Genomic analysis of mouse retinal development. PLoS Biol 2004, 2:E247.
80. Ginger M.R., Shore A.N., Contreras A., Rijnkels M., Miller J., Gonzalez-Rimbau M.F., et al. A noncoding RNA is a potential marker of cell fate during mammary gland development. Proc Natl Acad Sci USA 2006, 103:5781-5786.
81. Sutcliffe J.G., Milner R.J., Gottesfeld J.M., Lerner R.A. Identifier sequences are transcribed specifically in brain. Nature 1984, 308:237-241.
82. DeChiara T.M., Brosius J. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc Natl Acad Sci USA 1987, 84:2624-2628.
83. Tiedge H., Fremeau R.T., Weinstock P.H., Arancio O., Brosius J. Dendritic location of neural BC1 RNA. Proc Natl Acad Sci USA 1991, 88:2093-2097.
84. Rozhdestvensky T.S., Kopylov A.M., Brosius J., Huttenhofer A. Neuronal BC1 RNA structure: evolutionary conversion of a tRNA(Ala) domain into an extended stem-loop structure. RNA 2001, 7:722-730.
85. Muslimov I.A., Iacoangeli A., Brosius J., Tiedge H. Spatial codes in dendritic BC1 RNA. J Cell Biol 2006, 175:427-439.
86. Muslimov I.A., Titmus M., Koenig E., Tiedge H. Transport of neuronal BC1 RNA in Mauthner axons. J Neurosci 2002, 22:4293-4301.
87. Cristofanilli M., Iacoangeli A., Muslimov I.A., Tiedge H. Neuronal BC1 RNA: microtubule-dependent dendritic delivery. J Mol Biol 2006, 356:1118-1123.
88. Centonze D., Rossi S., Napoli I., Mercaldo V., Lacoux C., Ferrari F., et al. The brain cytoplasmic RNA BC1 regulates dopamine D2 receptor-mediated transmission in the striatum. J Neurosci 2007, 27:8885-8892.
89. Zhong J., Chuang S.C., Bianchi R., Zhao W., Lee H., Fenton A.A., et al. BC1 regulation of metabotropic glutamate receptor-mediated neuronal excitability. J Neurosci 2009, 29:9977-9986.
90. Skryabin B.V., Sukonina V., Jordan U., Lewejohann L., Sachser N., Muslimov I., et al. Neuronal untranslated BC1 RNA: targeted gene elimination in mice. Mol Cell Biol 2003, 23:6435-6441.
91. Lewejohann L., Skryabin B.V., Sachser N., Prehn C., Heiduschka P., Thanos S., et al. Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice. Behav Brain Res 2004, 154:273-289.
92. Skryabin B.V., Kremerskothen J., Vassilacopoulou D., Disotell T.R., Kapitonov V.V., Jurka J., et al. The BC200 RNA gene and its neural expression are conserved in Anthropoidea (Primates). J Mol Evol 1998, 47:677-685.
93. Ludwig A., Rozhdestvensky T.S., Kuryshev V.Y., Schmitz J., Brosius J. An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J Mol Biol 2005, 350:200-214.
94. Watson J.B., Sutcliffe J.G. Primate brain-specific cytoplasmic transcript of the Alu repeat family. Mol Cell Biol 1987, 7:3324-3327.
95. Kuryshev V.Y., Skryabin B.V., Kremerskothen J., Jurka J., Brosius J. Birth of a gene: locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage. J Mol Biol 2001, 309:1049-1066.
96. Muddashetty R., Khanam T., Kondrashov A., Bundman M., Iacoangeli A., Kremerskothen J., et al. Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J Mol Biol 2002, 321:433-445.
97. Khanam T., Rozhdestvensky T.S., Bundman M., Galiveti C.R., Handel S., Sukonina V., et al. Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners. Nucleic Acids Res 2007, 35:529-539.
98. Kondrashov A.V., Kiefmann M., Ebnet K., Khanam T., Muddashetty R.S., 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 2005, 353:88-103.
99. Allen L., Kloc M., Etkin L.D. Identification and characterization of the Xlsirt cis-acting RNA localization element. Differentiation 2003, 71:311-321.
100. Wong L.H., Brettingham-Moore K.H., Chan L., Quach J.M., Anderson M.A., Northrop E.L., et al. Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere. Genome Res 2007, 17:1146-1160.
101. Hore T.A., Rapkins R.W., Graves J.A. Construction and evolution of imprinted loci in mammals. Trends Genet 2007, 23:440-448.
102. Schoenfelder S., Smits G., Fraser P., Reik W., Paro R. Non-coding transcripts in the H19 imprinting control region mediate gene silencing in transgenic Drosophila. EMBO Rep 2007, 8:1068-1073.
103. Thakur N., Tiwari V.K., Thomassin H., Pandey R.R., Kanduri M., Gondor A., et al. An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Mol Cell Biol 2004, 24:7855-7862.
104. Murakami K., Oshimura M., Kugoh H. Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1. J Hum Genet 2007, 52:926-933.
105. Terranova R., Yokobayashi S., Stadler M.B., Otte A.P., van Lohuizen M., Orkin S.H., et al. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell 2008, 15:1-12.
106. Redrup L., Branco M.R., Perdeaux E.R., Krueger C., Lewis A., Santos F., et al. The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 2009, 136:525-530.
107. Mohammad F., Mondal T., Guseva N., Pandey G.K., Kanduri C. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 2010, 137:2493-2499.
108. Zhang L.F., Huynh K.D., Lee J.T. Perinucleolar targeting of the inactive X during S phase: evidence for a role in the maintenance of silencing. Cell 2007, 129:693-706.
109. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007, 316:1484-1488.
110. Kloc M., Zearfoss N.R., Etkin L.D. Mechanisms of subcellular mRNA localization. Cell 2002, 108:533-544.
111. Czaplinski K., Singer R.H. Pathways for mRNA localization in the cytoplasm. Trends Biochem Sci 2006, 31:687-693.
112. Martin K.C., Ephrussi A. mRNA localization: gene expression in the spatial dimension. Cell 2009, 136:719-730.
113. Valencia P., Dias A.P., Reed R. Splicing promotes rapid and efficient mRNA export in mammalian cells. Proc Natl Acad Sci USA 2008, 105:3386-3391.
114. Kohler A., Hurt E. Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol 2007, 8:761-773.
115. Moore M.J., Proudfoot N.J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009, 136:688-700.
116. Yoh S.M., Cho H., Pickle L., Evans R.M., Jones K.A. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Genes Dev 2007, 21:160-174.
117. Huang Y., Carmichael G.G. The mouse histone H2a gene contains a small element that facilitates cytoplasmic accumulation of intronless gene transcripts and of unspliced HIV-1-related mRNAs. Proc Natl Acad Sci USA 1997, 94:10104-10109.
118. Erkmann J.A., Sanchez R., Treichel N., Marzluff W.F., Kutay U. Nuclear export of metazoan replication-dependent histone mRNAs is dependent on RNA length and is mediated by TAP. RNA 2005, 11:45-58.
119. Isken O., Maquat L.E. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev 2007, 21:1833-1856.
120. Kurihara Y., Matsui A., Hanada K., Kawashima M., Ishida J., Morosawa T., et al. Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci USA 2009, 106:2453-2458.
121. Tycowski K.T., Shu M.D., Steitz J.A. A mammalian gene with introns instead of exons generating stable RNA products. Nature 1996, 379:464-466.
122. Seidl C.I., Stricker S.H., Barlow D.P. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J 2006, 25:3565-3575.
123. Sawata M., Takeuchi H., Kubo T. Identification and analysis of the minimal promoter activity of a novel noncoding nuclear RNA gene, AncR-1, from the honeybee (Apis mellifera L.). RNA 2004, 10:1047-1058.
124. Yap K.L., Li S., Munoz-Cabello A.M., Raguz S., Zeng L., Mujtaba S., et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 2010, 38:662-674.
125. Ashe H.L., Monks J., Wijgerde M., Fraser P., Proudfoot N.J. Intergenic transcription and transinduction of the human beta-globin locus. Genes Dev 1997, 11:2494-2509.
126. Zhu X., Ling J., Zhang L., Pi W., Wu M., Tuan D. A facilitated tracking and transcription mechanism of long-range enhancer function. Nucleic Acids Res 2007, 35:5532-5544.
127. Tiedge H., Chen W., Brosius J. Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. J Neurosci 1993, 13:2382-2390.
128. Hardiman K.E., Brewster R., Khan S.M., Deo M., Bodmer R. The bereft gene, a potential target of the neural selector gene cut, contributes to bristle morphogenesis. Genetics 2002, 161:231-247.
129. Royo H., Basyuk E., Marty V., Marques M., Bertrand E., Cavaille J. Bsr, a nuclear-retained RNA with monoallelic expression. Mol Biol Cell 2007, 18:2817-2827.
130. Mondal T., Rasmussen M., Pandey G.K., Isaksson A., Kanduri C. Characterization of the RNA content of chromatin. Genome Res 2010, 20:899-907.
131. Martianov I., Ramadass A., Serra Barros A., Chow N., Akoulitchev A. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 2007, 445:666-670.
132. Shimada N., Kawata T. Evidence that noncoding RNA dutA is a multicopy suppressor of Dictyostelium discoideum STAT protein Dd-STATa. Eukaryot Cell 2007, 6:1030-1040.
133. Feng J., Bi C., Clark B.S., Mady R., Shah P., 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 2006, 20:1470-1484.
134. Brookheart R.T., Michel C.I., Listenberger L.L., Ory D.S., Schaffer J.E. The non-coding RNA gadd7 is a regulator of lipid-induced oxidative and endoplasmic reticulum stress. J Biol Chem 2009, 284:7446-7454.
135. Hollander M.C., Alamo I., Fornace A.J. A novel DNA damage-inducible transcript, gadd7, inhibits cell growth, but lacks a protein product. Nucleic Acids Res 1996, 24:1589-1593.
136. Crawford D.R., Schools G.P., Salmon S.L., Davies K.J. Hydrogen peroxide induces the expression of adapt15, a novel RNA associated with polysomes in hamster HA-1 cells. Arch Biochem Biophys 1996, 325:256-264.
137. Mourtada-Maarabouni M., Pickard M.R., Hedge V.L., Farzaneh F., Williams G.T. GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene 2009, 28:195-208.
138. Matouk I.J., DeGroot N., Mezan S., Ayesh S., Abu-lail R., Hochberg A., et al. The H19 non-coding RNA is essential for human tumor growth. PLoS ONE 2007, 2:e845.
139. Yoshimizu T., Miroglio A., Ripoche M.A., Gabory A., Vernucci M., Riccio A., et al. The H19 locus acts in vivo as a tumor suppressor. Proc Natl Acad Sci USA 2008, 105:12417-12422.
140. Ripoche M.A., Kress C., Poirier F., Dandolo L. Deletion of the H19 transcription unit reveals the existence of a putative imprinting control element. Genes Dev 1997, 11:1596-1604.
141. Brannan C.I., Dees E.C., Ingram R.S., Tilghman S.M. The product of the H19 gene may function as an RNA. Mol Cell Biol 1990, 10:28-36.
142. Gupta R.A., Shah N., Wang K.C., Kim J., Horlings H.M., Wong D.J., et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
143. Tsai M.C., Manor O., Wan Y., Mosammaparast N., Wang J.K., Lan F., et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.
144. Prasanth K.V., Rajendra T.K., Lal A.K., Lakhotia S.C. Omega speckles-a novel class of nuclear speckles containing hnRNPs associated with noncoding hsr-omega RNA in Drosophila. J Cell Sci 2000, 113(Pt 19):3485-3497.
145. Rajendra T.K., Prasanth K.V., Lakhotia S.C. Male sterility associated with overexpression of the noncoding hsromega gene in cyst cells of testis of Drosophila melanogaster. J Genet 2001, 80:97-110.
146. Panzitt K., Tschernatsch M.M., Guelly C., Moustafa T., Stradner M., Strohmaier H.M., et al. Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 2007, 132:330-342.
147. Wang J., Liu X., Wu H., Ni P., Gu Z., Qiao Y., et al. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 2010, 38:5366-5383.
148. Imamura T., Yamamoto S., Ohgane J., Hattori N., Tanaka S., Shiota K. Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochem Biophys Res Commun 2004, 322:593-600.
149. Sawata M., Yoshino D., Takeuchi H., Kamikouchi A., Ohashi K., Kubo T. Identification and punctate nuclear localization of a novel noncoding RNA, Ks-1, from the honeybee brain. RNA 2002, 8:772-785.
150. Li L., Feng T., Lian Y., Zhang G., Garen A., Song X. Role of human noncoding RNAs in the control of tumorigenesis. Proc Natl Acad Sci USA 2009, 106:12956-12961.
151. Zhou Y., Zhong Y., Wang Y., Zhang X., Batista D.L., Gejman R., et al. Activation of p53 by MEG3 non-coding RNA. J Biol Chem 2007, 282:24731-24742.
152. Zhang X., Rice K., Wang Y., Chen W., Zhong Y., Nakayama Y., et al. Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions. Endocrinology 2010, 151:939-947.
153. Watanabe Y., Yamamoto M. S. pombe mei2+ encodes an RNA-binding protein essential for premeiotic DNA synthesis and meiosis I, which cooperates with a novel RNA species meiRNA. Cell 1994, 78:487-498.
154. Yamashita A., Watanabe Y., Nukina N., Yamamoto M. RNA-assisted nuclear transport of the meiotic regulator Mei2p in fission yeast. Cell 1998, 95:115-123.
155. Sato M., Shinozaki-Yabana S., Yamashita A., Watanabe Y., Yamamoto M. The fission yeast meiotic regulator Mei2p undergoes nucleocytoplasmic shuttling. FEBS Lett 2001, 499:251-255.
156. Liu A.Y., Torchia B.S., Migeon B.R., Siliciano R.F. The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4+ T cells. Genomics 1997, 39:171-184.
157. Camblong J., Iglesias N., Fickentscher C., Dieppois G., Stutz F. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 2007, 131:706-717.
158. Mayer C., Schmitz K.M., Li J., Grummt I., Santoro R. Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell 2006, 22:351-361.
159. Santoro R., Schmitz K.M., Sandoval J., Grummt I. Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans. EMBO Rep 2010, 11:52-58.
160. Hatada I., Morita S., Obata Y., Sotomaru Y., Shimoda M., Kono T. Identification of a new imprinted gene, Rian, on mouse chromosome 12 by fluorescent differential display screening. J Biochem (Tokyo) 2001, 130:187-190.
161. Meller V.H., Wu K.H., Roman G., Kuroda M.I., Davis R.L. roX1 RNA paints the X chromosome of male Drosophila and is regulated by the dosage compensation system. Cell 1997, 88:445-457.
162. Meller V.H., Rattner B.P. The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complex. EMBO J 2002, 21:1084-1091.
163. Valgardsdottir R., Chiodi I., Giordano M., Cobianchi F., Riva S., Biamonti G. Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. Mol Biol Cell 2005, 16:2597-2604.
164. Valgardsdottir R., Chiodi I., Giordano M., Rossi A., Bazzini S., Ghigna C., et al. Transcription of Satellite III non-coding RNAs is a general stress response in human cells. Nucleic Acids Res 2008, 36:423-434.
165. Pelczar P., Filipowicz W. The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 5'-terminal oligopyrimidine gene family. Mol Cell Biol 1998, 18:4509-4518.
166. Bortolin M.L., Kiss T. Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding. RNA 1998, 4:445-454.
167. Makarova J.A., Kramerov D.A. Noncoding RNA of U87 host gene is associated with ribosomes and is relatively resistant to nonsense-mediated decay. Gene 2005, 363:51-60.
168. Lanz R.B., McKenna N.J., Onate S.A., Albrecht U., Wong J., Tsai S.Y., et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell 1999, 97:17-27.
169. Lanz R.B., Chua S.S., Barron N., Soder B.M., DeMayo F., O'Malley B.W. Steroid receptor RNA activator stimulates proliferation as well as apoptosis in vivo. Mol Cell Biol 2003, 23:7163-7176.
170. Leygue E. Steroid receptor RNA activator (SRA1): unusual bifaceted gene products with suspected relevance to breast cancer. Nucl Recept Signal 2007, 5:e006.
171. Zhao X., Patton J.R., Ghosh S.K., Fischel-Ghodsian N., Shen L., Spanjaard R.A. Pus3p- and Pus1p-dependent pseudouridylation of steroid receptor RNA activator controls a functional switch that regulates nuclear receptor signaling. Mol Endocrinol 2007, 21:686-699.
172. Abarrategui I., Krangel M.S. Noncoding transcription controls downstream promoters to regulate T-cell receptor alpha recombination. EMBO J 2007, 26:4380-4390.
173. Azzalin C.M., Reichenbach P., Khoriauli L., Giulotto E., Lingner J. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 2007, 318:798-801.
174. Schoeftner S., Blasco M.A. Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol 2008, 10:228-236.
175. Xu Y., Suzuki Y., Ito K., Komiyama M. Telomeric repeat-containing RNA structure in living cells. Proc Natl Acad Sci USA 2010, 107:14579-14584.
176. Lee J.T., Davidow L.S., Warshawsky D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 1999, 21:400-404.
177. Sado T., Wang Z., Sasaki H., Li E. Regulation of imprinted X-chromosome inactivation in mice by Tsix. Development 2001, 128:1275-1286.
178. Brown C.J., Hendrich B.D., Rupert J.L., Lafreniere R.G., Xing Y., Lawrence J., et al. The human XIST gene: analysis of a 17kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992, 71:527-542.
179. Chaumeil J., Le Baccon P., Wutz A., Heard E. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev 2006, 20:2223-2237.