鸡的小RNA文库构建和非编码RNA的规模筛选
|
摘要
非编码RNA在生命活动中起着非常重要的作用,如参与染色质结构的调节,转录和转录后加工的调控,蛋白质合成、转运和活性的调控等,但是已知的非编码RNA只占生物体内全部非编码RNA的很少一部分,绝大多数的非编码RNA还有待于被发现和进行功能研究。通过构建特殊的cDNA文库发现新的非编码RNA是一个比较有效的方法。本研究以鸡为模式生物,构建了富集小分子非编码RNA的文库,从中找到一大批新的非编码RNA,并利用Northern杂交实验验证了这些非编码RNA的存在。对这些新的非编码RNA进行的整体性的研究使我们对非编码RNA有了更深入的了解。首先,通过分析各种非编码RNA在鸡的不同组织和骨骼肌不同发育阶段中的表达,发现绝大多数非编码RNA在时空上具有不同的表达水平,说明这些非编码RNA在体内的产生和降解受到了严格的调控,提示它们在某些生命活动中具有重要的作用;同时发现鸡中许多的非编码RNA在小鼠和人类中并没有同源RNA分子的存在,基因组水平的比对也不能找到同源的序列,这说明生物体在进化中会产生相当多的物种特有的非编码RNA,这与蛋白质编码基因所具有的保守性相比具有显著的不同,这些非编码RNA可能在很大程度上决定了物种的独特性。
本实验还发现了一个只在鸡的骨骼肌和心肌中表达的非编码RNA——MuN121,Blast分析表明它定位于一个已知的蛋白质编码基因的内含子之中,Northern杂交结果显示MuN121和该宿主基因在RNA水平具有一致的表达谱。为了研究MuN121的产生是经独立转录而来还是从pre-mRNA加工而来,我们构建了野生型和该内含子5'端剪接供体位点突变的2种载体,转染293T细胞发现突变体不能产生ncRNA而野生型能产生。表明MuN121的产生依赖于pre-mRNA的成功剪接,MuN121和宿主基因受相同的转录机制的调控。
In the last several years, noncoding RNAs (ncRNAs) have been identified in cells of all three kingdoms. It has been identified that ncRNAs can regulate gene regulation at different levels, such as chromatin modification; transcriptional and post-transcriptional regulation; protein synthesis, translocation and activity controlling. However, there is still a large number of ncRNAs need to be identified. Here we use chicken as a model to construct an ncRNA enriched cDNA library and then systematicly study ncRNAs' expression, conservation and biological function. We found that expression of the majority of ncRNAs is spatio-temporal regulated, suggestting that these ncRNAs play important roles during development. RNA blotting and comparative genomics analysis found that many ncRNAs do not have homologue in mouse and human. These results indicate that ncRNAs may contribute largely to the specialties of cell lineage.
We also found a muscle specific expressed ncRNA, MuN121. Blast analysis found that it is encoded in the intron of a host gene. MuN121 and The host gene have identical expression pattern, we also found that MuN121 biogenesis is depend on successful splicing of the encoded intron. These results suggest that MuN121 is produced from the pre-mRNA of the host gene. MuN121 may play an important role in host gene regulation or in regulating the same pathway that the host gene is involved.
本实验还发现了一个只在鸡的骨骼肌和心肌中表达的非编码RNA——MuN121,Blast分析表明它定位于一个已知的蛋白质编码基因的内含子之中,Northern杂交结果显示MuN121和该宿主基因在RNA水平具有一致的表达谱。为了研究MuN121的产生是经独立转录而来还是从pre-mRNA加工而来,我们构建了野生型和该内含子5'端剪接供体位点突变的2种载体,转染293T细胞发现突变体不能产生ncRNA而野生型能产生。表明MuN121的产生依赖于pre-mRNA的成功剪接,MuN121和宿主基因受相同的转录机制的调控。
In the last several years, noncoding RNAs (ncRNAs) have been identified in cells of all three kingdoms. It has been identified that ncRNAs can regulate gene regulation at different levels, such as chromatin modification; transcriptional and post-transcriptional regulation; protein synthesis, translocation and activity controlling. However, there is still a large number of ncRNAs need to be identified. Here we use chicken as a model to construct an ncRNA enriched cDNA library and then systematicly study ncRNAs' expression, conservation and biological function. We found that expression of the majority of ncRNAs is spatio-temporal regulated, suggestting that these ncRNAs play important roles during development. RNA blotting and comparative genomics analysis found that many ncRNAs do not have homologue in mouse and human. These results indicate that ncRNAs may contribute largely to the specialties of cell lineage.
We also found a muscle specific expressed ncRNA, MuN121. Blast analysis found that it is encoded in the intron of a host gene. MuN121 and The host gene have identical expression pattern, we also found that MuN121 biogenesis is depend on successful splicing of the encoded intron. These results suggest that MuN121 is produced from the pre-mRNA of the host gene. MuN121 may play an important role in host gene regulation or in regulating the same pathway that the host gene is involved.
引文
1. Carninci P, Hayashizaki Y: Noncoding RNA transcription beyond annotated genes. Curr Opin Genet Dev 2007,17:139-144.
2. Castillo-Davis CI: The evolution of noncoding DNA: how much junk, how much func? Trends Genet 2005, 21:533-536.
3. Huttenhofer A: RNomics: identification and function of small non-protein-coding RNAs in model organisms. Cold Spring Harb Symp Quant Biol 2006,71:135-140.
4. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al.: The transcriptional landscape of the mammalian genome. Science 2005,309:1559-1563.
5. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al.: Antisense transcription in the mammalian transcriptome. Science 2005,309:1564-1566.
6. Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, et al.: Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 2005,3:e7.
7. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD: 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.
8. Costa FF: Non-coding RNAs: lost in translation? Gene 2007,386:1-10.
9. Niwa R, Slack FJ: The evolution of animal microRNA function. Curr Opin Genet Dev 2007, 17:145-150.
10. Caplen NJ, Mousses S: Short interfering RNA (siRNA)-mediated RNA interference (RNAi) in human cells. Ann N Y Acad Sci 2003,1002:56-62.
11. Lin H: piRNAs in the germ line. Science 2007,316:397.
12. Mattick JS, Makunin IV: Non-coding RNA. Hum Mol Genet 2006,15 Spec No 1.R17-29.
13. Mattick JS: Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2001, 2:986-991.
14. Cao X, Yeo G, Muotri AR, Kuwabara T, Gage FH: Noncoding RNAs in the Mammalian Central Nervous System. Annu Rev Neurosci 2006.
15. Costa FF: Non-coding RNAs: new players in eukaryotic biology. Gene 2005,357:83-94.
16. Zaratiegui M, Irvine DV, Martienssen RA: Noncoding RNAs and gene silencing. Cell 2007, 128:763-776.
17. Hutvagner G, Simard MJ: Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 2008,9:22-32.
18. Rogelj B, Giese KP: Expression and function of brain specific small RNAs. Rev Neurosci 2004, 15:185-198.
19. Arasu P, Wightman B, Ruvkun G: Temporal regulation of lin-14 by the antagonistic action of two other heterochronic genes, lin-4 and lin-28. Genes Dev 1991, 5:1825-1833.
20. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G: The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000,403:901-906.
21. Zhao T, Li G, Mi S, Li S, Hannon GJ, Wang XJ, Qi Y: A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 2007, 21:1190-1203.
22. Alvarez-Garcia I, Miska EA: MicroRNA functions in animal development and human disease. Development 2005, 132:4653-4662.
23. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004,116:281-297.
24. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, et al.: The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-419.
25. Basyuk E, Suavet F, Doglio A, Bordonne R, Bertrand E: Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res 2003,31:6593-6597.
26. Filipowicz W: RNAi: the nuts and bolts of the RISC machine. Cell 2005,122:17-20.
27. Tang G, Reinhart BJ, Bartel DP, Zamore PD: A biochemical framework for RNA silencing in plants. Genes Dev 2003,17:49-63.
28. Okamura K, Ishizuka A, Siomi H, Siomi MC: Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev 2004,18:1655-1666.
29. Eulalio A, Huntzinger E, Izaurralde E: GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay. Nat Struct Mol Biol 2008, 15:346-353.
30. Bhattacharyya SN, Habermacher R, Martine U, Closs El, Filipowicz W: Stress-induced reversal of microRNA repression and mRNA P-body localization in human cells. Cold Spring Harb Symp Quant Biol 2006, 71:513-521.
31. Vasudevan S, Tong Y, Steitz JA: Switching from repression to activation: microRNAs can up-regulate translation. Science 2007,318:1931-1934.
32. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E: Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005, 120:21-24.
33. Napoli C, Lemieux C, Jorgensen R: Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. Plant Cell 1990,2:279-289.
34. Romano N, Macino G: Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 1992, 6:3343-3353.
35. Sijen T, Kooter JM: Post-transcriptional gene-silencing: RNAs on the attack or on the defense? Bioessays 2000, 22:520-531.
36. Montgomery MK, Fire A: Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 1998,14:255-258.
37. Gilmore IR, Fox SP, Hollins AJ, Akhtar S: Delivery strategies for siRNA-mediated gene silencing. Curr Drug Deliv 2006, 3:147-145.
38. Hannon GJ: RNA interference. Nature 2002,418:244-251.
39. Cerutti H: RNA interference: traveling in the cell and gaining functions? Trends Genet 2003, 19:39-46.
40. Marx J: Interfering with gene expression. Science 2000, 288:1370-1372.
41. Wu L, Belasco JG: Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs. Mol Cell 2008, 29:1-7.
42. Tijsterman M, Plasterk RH: Dicers at RISC; the mechanism of RNAi. Cell 2004,117:1-3.
43. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J: Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 2000, 408:325-330.
44. Yuan WZ, Bodmer R, Zhu CB, Wang YQ, Li YQ, Wu XS: [The use of RNAi as a technique to study the functions of heart-related genes in Drosophila]. Yi Chuan Xue Bao 2002, 29:34-38.
45. Wilda M, Fuchs U, Wossmann W, Borkhardt A: Killing of leukemic cells with a BCR/ABL fusion gene by RNA interference (RNAi). Oncogene 2002, 21:5716-5724.
46. Jacque JM, Triques K, Stevenson M: Modulation of HIV-1 replication by RNA interference. Nature 2002,418:435-438.
47. Song E, Lee SK, Wang J, Ince N, Ouyang N, Min J, Chen J, Shankar P, Lieberman J: RNA interference targeting Fas protects mice from fulminant hepatitis. Nat Med 2003, 9:347-351.
48. Song E, Zhu P, Lee SK, Chowdhury D, Kussman S, Dykxhoorn DM, Feng Y, Palliser D, Weiner DB, Shankar P, et al.: Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors. Nat Biotechnol 2005,23:709-717.
49. Wassenegger M, Heimes S, Riedel L, Sanger HL: RNA-directed de novo methylation of genomic sequences in plants. Cell 1994, 76:567-576.
50. Pelissier T, Wassenegger M: A DNA target of 30 bp is sufficient for RNA-directed DNA methylation. Rna 2000, 6:55-65.
51. Lavrov SA, Kibanov MV: Noncoding RNAs and chromatin structure. Biochemistry (Mosc) 2007, 72:1422-1438.
52. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA: Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 2002, 297:1833-1837.
53. Reinhart BJ, Bartel DP: Small RNAs correspond to centromere heterochromatic repeats. Science 2002,297:1831.
54. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D: RNAi-mediated targeting of heterochromatin by the RITS complex. Science 2004,303:672-676.
55. Kawasaki H, Taira K: Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 2004, 431:211-217.
56. Ting AH, Schuebel KE, Herman JG, Baylin SB: Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet 2005, 37:906-910.
57. Ekwall K: The RITS complex-A direct link between small RNA and heterochromatin. Mol Cell 2004,13:304-305.
58. Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH: A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 2004,116:779-793.
59. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R: Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 2006, 103:17337-17342.
60. Sanchez-Herrero E, Akam M: Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila. Development 1989,107:321-329.
61. Hartwell LH, Hood L, Goldberg ML, Reynolds AE, Silver LM, Veres RC: genetics from genes to genomes edn second edition: McGRAW-HILL; 2004.
62. Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC: The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev 2005,19:2947-2952.
63. Lipshitz HD, Peattie DA, Hogness DS: Novel transcripts from the Ultrabithorax domain of the bithorax complex. Genes Dev 1987,1:307-322.
64. Sanchez-Eisner T, Gou D, Kremmer E, Sauer F: Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 2006,311:1118-1123.
65. Martens JA, Wu PY, Winston F: Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev 2005,19:2695-2704.
66. Hanyu-Nakamura K, Sonobe-Nojima H, Tanigawa A, Lasko P, Nakamura A: Drosophila Pgc protein inhibits P-TEFb recruitment to chroma tin in primordial germ cells. Nature 2008, 451:730-733.
67. Yik JH, Chen R, Nishimura R, Jennings JL, Link AJ, Zhou Q: Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol Cell 2003,12:971-982.
68. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA: B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 2004,11:822-829.
69. Allen TA, Von Kaenel S, Goodrich JA, Kugel JF: The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 2004,11:816-821.
70. Caretti G, Schiltz RL, Dilworth FJ, Di Padova M, Zhao P, Ogryzko V, Fuller-Pace FV, Hoffman EP, Tapscott SJ, Sartorelli V: The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell 2006,11:547-560.
71. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG: A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005,309:1570-1573.
72. Rabinovitz M: The phosphofructokinase-uncharged tRNA interaction in metabolic and cell cycle control: an interpretive review. Nucleic Acids Symp Ser 1995:182-189.
73. Taipale M, Akhtar A: Chromatin mechanisms in Drosophila dosage compensation. Prog Mol Subcell Biol 2005,38:123-149.
74. Royo H, Cavaille J: Non-coding RNAs in imprinted gene clusters. Biol Cell 2008,100:149-166.
75. Werner A: Natural antisense transcripts. RNA Biol 2005,2:53-62.
76. Edwards TE, Klein DJ, Ferre-D'Amare AR: Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr Opin Struct Biol 2007,17:273-279.
77. Nguyen HT, Frasch M: MicroRNAs in muscle differentiation: lessons from Drosophila and beyond. Curr Opin Genet Dev 2006,16:533-539.
78. Buckingham M: Myogenic progenitor cells and skeletal myogenesis in vertebrates. Curr Opin Genet Dev 2006,16:525-532.
79. Gierer A: Networks of gene regulation, neural development and the evolution of general capabilities, such as human empathy. Z Naturforsch [C] 1998, 53:716-722.
80. Callis TE, Chen JF, Wang DZ: MicroRNAs in skeletal and cardiac muscle development. DNA Cell Biol 2007, 26:219-225.
81. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ: The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 2006, 38:228-233.
82. Zhao Y, Samal E, Srivastava D: Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005, 436:214-220.
83. Xu C, Lu Y, Pan Z, Chu W, Luo X, Lin H, Xiao J, Shan H, Wang Z, Yang B: The muscle-specific microRNAs miR-1 and miR-133 produce opposing effects on apoptosis by targeting HSP60, HSP70 and caspase-9 in cardiomyocytes. J Cell Sci 2007,120:3045-3052.
84. Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A: Muscle-specific microRNA miR-206 promotes muscle differentiation. J Cell Biol 2006,174:677-687.
85. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F, et al.: A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 2006,38:813-818.
86. Zhao Y, Ransom JF, Li A, Vedantham V, von Drehle M, Muth AN, Tsuchihashi T, McManus MT, Schwartz RJ, Srivastava D: Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 2007,129:303-317.
87. Ivey KN, Muth A, Arnold J, King FW, Yeh RF, Fish JE, Hsiao EC, Schwartz RJ, Conklin BR, Bernstein HS, et al.: MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell 2008,2:219-229.
88. Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, Patton JG: Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nat Genet 2007,39:259-263.
89. Naguibneva I, Ameyar-Zazoua M, Polesskaya A, Ait-Si-Ali S, Groisman R, Souidi M, Cuvellier S, Harel-Bellan A: The microRNA miR-181 targets the homeobox protein Hox-All during mammalian myoblast differentiation. Nat Cell Biol 2006, 8:278-284.
90. Sun Q, Zhang Y, Yang G, Chen X, Zhang Y, Cao G, Wang J, Sun Y, Zhang P, Fan M, et al.: Transforming growth factor-beta-regulated miR-24 promotes skeletal muscle differentiation. Nucleic Acids Res 2008,36:2690-2699.
91. Wong CF, Tellam RL: MicroRNA-26a targets the histone methyltransferase Enhancer of Zeste homolog 2 during myogenesis. J Biol Chem 2008,283:9836-9843.
92. McCarthy JJ, Esser KA: MicroRNA-1 and microRNA-133a expression are decreased during skeletal muscle hypertrophy. J Appl Physiol 2007,102:306-313.
93. Catalucci D, Latronico MV, Condorelli G: MicroRNAs Control Gene Expression: Importance for Cardiac Development and Pathophysiology. Ann N Y Acad Sci 2008,1123:20-29.
94. Luo X, Lin H, Pan Z, Xiao J, Zhang Y, Lu Y, Yang B, Wang Z: Downregulation of MIRNA-1/MIRNA-133 contributes to re-expression of pacemaker channel genes HCN2 and HCN4 in hypertrophic heart. J Biol Chem 2008.
95. Care A, Catalucci D, Felicetti F, Bonci D, Addario A, Gallo P, Bang ML, Segnalini P, Gu Y, Dalton ND, et al.: MicroRNA-133 controls cardiac hypertrophy. Nat Med 2007,13:613-618.
96. Tatsuguchi M, Seok HY, Callis TE, Thomson JM, Chen JF, Newman M, Rojas M, Hammond SM, Wang DZ: Expression of microRNAs is dynamically regulated during cardiomyocyte hypertrophy. J Mol Cell Cardiol 2007, 42:1137-1141.
97. Sayed D, Hong C, Chen IY, Lypowy J, Abdellatif M: MicroRNAs play an essential role in the development of cardiac hypertrophy. Circ Res 2007,100:416-424.
98. Cheng Y, Ji R, Yue J, Yang J, Liu X, Chen H, Dean DB, Zhang C: MicroRNAs are aberrantly expressed in hypertrophic heart: do they play a role in cardiac hypertrophy? Am J Pathol 2007,170:1831-1840.
99. Yang B, Lin H, Xiao J, Lu Y, Luo X, Li B, Zhang Y, Xu C, Bai Y, Wang H, et al.: The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2. Nat Med 2001,13:486-491.
100. McCarthy JJ, Esser KA, Andrade FH: MicroRNA-206 is overexpressed in the diaphragm but not the hindlimb muscle of mdx mouse. Am J Physiol Cell Physiol 2007, 293.C451-457.
101. Shi XB, Xue L, Yang J, Ma AH, Zhao J, Xu M, Tepper CG, Evans CP, Kung HJ, deVere White RW: An androgen-regulated miRNA suppresses Bak1 expression and induces androgen-independent growth of prostate cancer cells. Proc Natl Acad Sci U S A 2007, 104:19983-19988.
102. Tavazoie SF, Alarcon C, Oskarsson T, Padua D, Wang Q, Bos PD, Gerald WL, Massague J: Endogenous human microRNAs that suppress breast cancer metastasis. Nature 2008, 451:147-152.
103. Ma L, Teruya-Feldstein J, Weinberg RA: Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 2007,449:682-688.
104. Yang H, Kong W, He L, Zhao JJ, O'Donnell JD, Wang J, Wenham RM, Coppola D, Kruk PA, Nicosia SV, et al.: MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res 2008, 68:425-433.
105. Meng F, Henson R, Wehbe-Janek H, Ghoshal K, Jacob ST, Patel T: MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer. Gastroenterology 2007,133:647-658.
106. Corney DC, Flesken-Nikitin A, Godwin AK, Wang W, Nikitin AY: MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Res 2007, 67:8433-8438.
107. He A, Zhu L, Gupta N, Chang Y, Fang F: Overexpression of micro ribonucleic acid 29, highly up-regulated in diabetic rats, leads to insulin resistance in 3T3-L1 adipocytes. Mol Endocrinol 2007, 21:2785-2794.
108. Klenov MS, Lavrov SA, Stolyarenko AD, Ryazansky SS, Aravin AA, Tuschl T, Gvozdev VA: Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res 2007,35:5430-5438.
109. Qiao D, Zeeman AM, Deng W, Looijenga LH, Lin H: Molecular characterization of hiwi, a human member of the piwi gene family whose overexpression is correlated to seminomas. Oncogene 2002,21:3988-3999.
110.Zalfa F,Giorgi M,Primerano B,Moro A,Di Penta A,Reis S,Oostra B,Bagni C:The fragile X syndrome protein FMRP associates with BC1 RNA and regulates the translation of specific mRNAs at synapses.Cell 2003,112:317-327.
111.Kondrashov AV,Kiefmann M,Ebnet K,Khanam T,Muddashetty RS,Brosius J:Inhibitory effect of naked neural BCI 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.
112.Anzai K,Kobayashi S,Kotake H,Murakami H,Korematsu K,Nonaka I:Neural BC1 RNA in mouse skeletal muscle is a denervation-induced RNA whose expression is developmentally regulated.Neurosci Lett 1996,216:81-84.
113.Murad JM,de Souza LR,De Lucca FL:PKR activation by a non-coding RNA expressed in lymphocytes of mice bearing B16 melanoma.Blood Cells Mol Dis 2006,37:128-133.
114.Rinn JL,Kertesz M,Wang JK,Squazzo SL,Xu X,Brugmann SA,Goodnough LH,Helms JA,Farnham PJ,Segal E,et al.:Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.Cell 2007,129:1311-1323.
115.Ruby JG,Jan C,Player C,Axtell MJ,Lee W,Nusbaum C,Ge H,Bartel DP:Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C.elegans.Cell 2006,127:1193-1207.
116.Storz G,Opdyke JA,Zhang A:Controlling mRNA stability and translation with small,noncoding RNAs.Curr Opin Microbiol 2004,7:140-144.
117.Lung B,Zemann A,Madej MJ,Schuelke M,Techritz S,Ruf S,Bock R,Huttenhofer A:Identification of small non-coding RNAs from mitochondria and chloroplasts.Nucleic Acids Res 2006,34:3842-3852.
118.Grivna ST,Pyhtila B,Lin H:MIWI associates with translational machinery and PIWI-interacting RNAs(piRNAs) in regulating spermatogenesis.Proc Natl Acad Sci U S A 2006,103:13415-13420.
119.Mrazek J,Kreutmayer SB,Grasser FA,Polacek N,Huttenhofer A:Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells.Nucleic Acids Res 2007,35:e73.
120.Huttenhofer A,Vogel J:Experimental approaches to identify non-coding RNAs.Nucleic Acids Res 2006,34:635-646.
121.Molnar A,Schwach F,Studholme DJ,Thuenemann EC,Baulcombe DC:miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii.Nature 2007,447:1126-1129.
122.Yoon S,De Micheli G:Computational identification of microRNAs and their targets.Birth Defects Res C Embryo Today 2006,78:118-128.
123.Berezikov E,Chung WJ,Willis J,Cuppen E,Lai EC:Mammalian mirtron genes.Mol Cell 2007,28:328-336.
124.Ruby JG,Jan CH,Bartel DP:Intronic microRNA precursors that bypass Drosha processing.Nature 2007,448:83-86.
125.Okamura K,Hagen JW,Duan H,Tyler DM,Lai EC:The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila.Cell 2007,130:89-100.
126.Mercer TR,Dinger ME,Sunkin SM,Mehler MF,Mattick JS:Specific expression of long noncoding RNAs in the mouse brain.Proc Natl Acad Sci USA 2008,105:716-721.
127. Rivas E, Eddy SR: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2:8.
128. Wei Deng, 1, Xiaopeng Zhu, 1, Geir Skogerb(?), 2, Yi Zhao, 2, Zhuo Fu, 1, et al.: Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression Genome Res 2006,16:20-29.
2. Castillo-Davis CI: The evolution of noncoding DNA: how much junk, how much func? Trends Genet 2005, 21:533-536.
3. Huttenhofer A: RNomics: identification and function of small non-protein-coding RNAs in model organisms. Cold Spring Harb Symp Quant Biol 2006,71:135-140.
4. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al.: The transcriptional landscape of the mammalian genome. Science 2005,309:1559-1563.
5. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al.: Antisense transcription in the mammalian transcriptome. Science 2005,309:1564-1566.
6. Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, et al.: Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 2005,3:e7.
7. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD: 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.
8. Costa FF: Non-coding RNAs: lost in translation? Gene 2007,386:1-10.
9. Niwa R, Slack FJ: The evolution of animal microRNA function. Curr Opin Genet Dev 2007, 17:145-150.
10. Caplen NJ, Mousses S: Short interfering RNA (siRNA)-mediated RNA interference (RNAi) in human cells. Ann N Y Acad Sci 2003,1002:56-62.
11. Lin H: piRNAs in the germ line. Science 2007,316:397.
12. Mattick JS, Makunin IV: Non-coding RNA. Hum Mol Genet 2006,15 Spec No 1.R17-29.
13. Mattick JS: Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2001, 2:986-991.
14. Cao X, Yeo G, Muotri AR, Kuwabara T, Gage FH: Noncoding RNAs in the Mammalian Central Nervous System. Annu Rev Neurosci 2006.
15. Costa FF: Non-coding RNAs: new players in eukaryotic biology. Gene 2005,357:83-94.
16. Zaratiegui M, Irvine DV, Martienssen RA: Noncoding RNAs and gene silencing. Cell 2007, 128:763-776.
17. Hutvagner G, Simard MJ: Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 2008,9:22-32.
18. Rogelj B, Giese KP: Expression and function of brain specific small RNAs. Rev Neurosci 2004, 15:185-198.
19. Arasu P, Wightman B, Ruvkun G: Temporal regulation of lin-14 by the antagonistic action of two other heterochronic genes, lin-4 and lin-28. Genes Dev 1991, 5:1825-1833.
20. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G: The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000,403:901-906.
21. Zhao T, Li G, Mi S, Li S, Hannon GJ, Wang XJ, Qi Y: A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 2007, 21:1190-1203.
22. Alvarez-Garcia I, Miska EA: MicroRNA functions in animal development and human disease. Development 2005, 132:4653-4662.
23. Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004,116:281-297.
24. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, et al.: The nuclear RNase III Drosha initiates microRNA processing. Nature 2003, 425:415-419.
25. Basyuk E, Suavet F, Doglio A, Bordonne R, Bertrand E: Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res 2003,31:6593-6597.
26. Filipowicz W: RNAi: the nuts and bolts of the RISC machine. Cell 2005,122:17-20.
27. Tang G, Reinhart BJ, Bartel DP, Zamore PD: A biochemical framework for RNA silencing in plants. Genes Dev 2003,17:49-63.
28. Okamura K, Ishizuka A, Siomi H, Siomi MC: Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev 2004,18:1655-1666.
29. Eulalio A, Huntzinger E, Izaurralde E: GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay. Nat Struct Mol Biol 2008, 15:346-353.
30. Bhattacharyya SN, Habermacher R, Martine U, Closs El, Filipowicz W: Stress-induced reversal of microRNA repression and mRNA P-body localization in human cells. Cold Spring Harb Symp Quant Biol 2006, 71:513-521.
31. Vasudevan S, Tong Y, Steitz JA: Switching from repression to activation: microRNAs can up-regulate translation. Science 2007,318:1931-1934.
32. Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E: Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005, 120:21-24.
33. Napoli C, Lemieux C, Jorgensen R: Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. Plant Cell 1990,2:279-289.
34. Romano N, Macino G: Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 1992, 6:3343-3353.
35. Sijen T, Kooter JM: Post-transcriptional gene-silencing: RNAs on the attack or on the defense? Bioessays 2000, 22:520-531.
36. Montgomery MK, Fire A: Double-stranded RNA as a mediator in sequence-specific genetic silencing and co-suppression. Trends Genet 1998,14:255-258.
37. Gilmore IR, Fox SP, Hollins AJ, Akhtar S: Delivery strategies for siRNA-mediated gene silencing. Curr Drug Deliv 2006, 3:147-145.
38. Hannon GJ: RNA interference. Nature 2002,418:244-251.
39. Cerutti H: RNA interference: traveling in the cell and gaining functions? Trends Genet 2003, 19:39-46.
40. Marx J: Interfering with gene expression. Science 2000, 288:1370-1372.
41. Wu L, Belasco JG: Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs. Mol Cell 2008, 29:1-7.
42. Tijsterman M, Plasterk RH: Dicers at RISC; the mechanism of RNAi. Cell 2004,117:1-3.
43. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J: Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 2000, 408:325-330.
44. Yuan WZ, Bodmer R, Zhu CB, Wang YQ, Li YQ, Wu XS: [The use of RNAi as a technique to study the functions of heart-related genes in Drosophila]. Yi Chuan Xue Bao 2002, 29:34-38.
45. Wilda M, Fuchs U, Wossmann W, Borkhardt A: Killing of leukemic cells with a BCR/ABL fusion gene by RNA interference (RNAi). Oncogene 2002, 21:5716-5724.
46. Jacque JM, Triques K, Stevenson M: Modulation of HIV-1 replication by RNA interference. Nature 2002,418:435-438.
47. Song E, Lee SK, Wang J, Ince N, Ouyang N, Min J, Chen J, Shankar P, Lieberman J: RNA interference targeting Fas protects mice from fulminant hepatitis. Nat Med 2003, 9:347-351.
48. Song E, Zhu P, Lee SK, Chowdhury D, Kussman S, Dykxhoorn DM, Feng Y, Palliser D, Weiner DB, Shankar P, et al.: Antibody mediated in vivo delivery of small interfering RNAs via cell-surface receptors. Nat Biotechnol 2005,23:709-717.
49. Wassenegger M, Heimes S, Riedel L, Sanger HL: RNA-directed de novo methylation of genomic sequences in plants. Cell 1994, 76:567-576.
50. Pelissier T, Wassenegger M: A DNA target of 30 bp is sufficient for RNA-directed DNA methylation. Rna 2000, 6:55-65.
51. Lavrov SA, Kibanov MV: Noncoding RNAs and chromatin structure. Biochemistry (Mosc) 2007, 72:1422-1438.
52. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA: Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 2002, 297:1833-1837.
53. Reinhart BJ, Bartel DP: Small RNAs correspond to centromere heterochromatic repeats. Science 2002,297:1831.
54. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D: RNAi-mediated targeting of heterochromatin by the RITS complex. Science 2004,303:672-676.
55. Kawasaki H, Taira K: Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 2004, 431:211-217.
56. Ting AH, Schuebel KE, Herman JG, Baylin SB: Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat Genet 2005, 37:906-910.
57. Ekwall K: The RITS complex-A direct link between small RNA and heterochromatin. Mol Cell 2004,13:304-305.
58. Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH: A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 2004,116:779-793.
59. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R: Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 2006, 103:17337-17342.
60. Sanchez-Herrero E, Akam M: Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila. Development 1989,107:321-329.
61. Hartwell LH, Hood L, Goldberg ML, Reynolds AE, Silver LM, Veres RC: genetics from genes to genomes edn second edition: McGRAW-HILL; 2004.
62. Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC: The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev 2005,19:2947-2952.
63. Lipshitz HD, Peattie DA, Hogness DS: Novel transcripts from the Ultrabithorax domain of the bithorax complex. Genes Dev 1987,1:307-322.
64. Sanchez-Eisner T, Gou D, Kremmer E, Sauer F: Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 2006,311:1118-1123.
65. Martens JA, Wu PY, Winston F: Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae. Genes Dev 2005,19:2695-2704.
66. Hanyu-Nakamura K, Sonobe-Nojima H, Tanigawa A, Lasko P, Nakamura A: Drosophila Pgc protein inhibits P-TEFb recruitment to chroma tin in primordial germ cells. Nature 2008, 451:730-733.
67. Yik JH, Chen R, Nishimura R, Jennings JL, Link AJ, Zhou Q: Inhibition of P-TEFb (CDK9/Cyclin T) kinase and RNA polymerase II transcription by the coordinated actions of HEXIM1 and 7SK snRNA. Mol Cell 2003,12:971-982.
68. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA: B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 2004,11:822-829.
69. Allen TA, Von Kaenel S, Goodrich JA, Kugel JF: The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 2004,11:816-821.
70. Caretti G, Schiltz RL, Dilworth FJ, Di Padova M, Zhao P, Ogryzko V, Fuller-Pace FV, Hoffman EP, Tapscott SJ, Sartorelli V: The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell 2006,11:547-560.
71. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG: A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science 2005,309:1570-1573.
72. Rabinovitz M: The phosphofructokinase-uncharged tRNA interaction in metabolic and cell cycle control: an interpretive review. Nucleic Acids Symp Ser 1995:182-189.
73. Taipale M, Akhtar A: Chromatin mechanisms in Drosophila dosage compensation. Prog Mol Subcell Biol 2005,38:123-149.
74. Royo H, Cavaille J: Non-coding RNAs in imprinted gene clusters. Biol Cell 2008,100:149-166.
75. Werner A: Natural antisense transcripts. RNA Biol 2005,2:53-62.
76. Edwards TE, Klein DJ, Ferre-D'Amare AR: Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr Opin Struct Biol 2007,17:273-279.
77. Nguyen HT, Frasch M: MicroRNAs in muscle differentiation: lessons from Drosophila and beyond. Curr Opin Genet Dev 2006,16:533-539.
78. Buckingham M: Myogenic progenitor cells and skeletal myogenesis in vertebrates. Curr Opin Genet Dev 2006,16:525-532.
79. Gierer A: Networks of gene regulation, neural development and the evolution of general capabilities, such as human empathy. Z Naturforsch [C] 1998, 53:716-722.
80. Callis TE, Chen JF, Wang DZ: MicroRNAs in skeletal and cardiac muscle development. DNA Cell Biol 2007, 26:219-225.
81. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM, Conlon FL, Wang DZ: The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat Genet 2006, 38:228-233.
82. Zhao Y, Samal E, Srivastava D: Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 2005, 436:214-220.
83. Xu C, Lu Y, Pan Z, Chu W, Luo X, Lin H, Xiao J, Shan H, Wang Z, Yang B: The muscle-specific microRNAs miR-1 and miR-133 produce opposing effects on apoptosis by targeting HSP60, HSP70 and caspase-9 in cardiomyocytes. J Cell Sci 2007,120:3045-3052.
84. Kim HK, Lee YS, Sivaprasad U, Malhotra A, Dutta A: Muscle-specific microRNA miR-206 promotes muscle differentiation. J Cell Biol 2006,174:677-687.
85. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F, et al.: A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 2006,38:813-818.
86. Zhao Y, Ransom JF, Li A, Vedantham V, von Drehle M, Muth AN, Tsuchihashi T, McManus MT, Schwartz RJ, Srivastava D: Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 2007,129:303-317.
87. Ivey KN, Muth A, Arnold J, King FW, Yeh RF, Fish JE, Hsiao EC, Schwartz RJ, Conklin BR, Bernstein HS, et al.: MicroRNA regulation of cell lineages in mouse and human embryonic stem cells. Cell Stem Cell 2008,2:219-229.
88. Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, Patton JG: Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nat Genet 2007,39:259-263.
89. Naguibneva I, Ameyar-Zazoua M, Polesskaya A, Ait-Si-Ali S, Groisman R, Souidi M, Cuvellier S, Harel-Bellan A: The microRNA miR-181 targets the homeobox protein Hox-All during mammalian myoblast differentiation. Nat Cell Biol 2006, 8:278-284.
90. Sun Q, Zhang Y, Yang G, Chen X, Zhang Y, Cao G, Wang J, Sun Y, Zhang P, Fan M, et al.: Transforming growth factor-beta-regulated miR-24 promotes skeletal muscle differentiation. Nucleic Acids Res 2008,36:2690-2699.
91. Wong CF, Tellam RL: MicroRNA-26a targets the histone methyltransferase Enhancer of Zeste homolog 2 during myogenesis. J Biol Chem 2008,283:9836-9843.
92. McCarthy JJ, Esser KA: MicroRNA-1 and microRNA-133a expression are decreased during skeletal muscle hypertrophy. J Appl Physiol 2007,102:306-313.
93. Catalucci D, Latronico MV, Condorelli G: MicroRNAs Control Gene Expression: Importance for Cardiac Development and Pathophysiology. Ann N Y Acad Sci 2008,1123:20-29.
94. Luo X, Lin H, Pan Z, Xiao J, Zhang Y, Lu Y, Yang B, Wang Z: Downregulation of MIRNA-1/MIRNA-133 contributes to re-expression of pacemaker channel genes HCN2 and HCN4 in hypertrophic heart. J Biol Chem 2008.
95. Care A, Catalucci D, Felicetti F, Bonci D, Addario A, Gallo P, Bang ML, Segnalini P, Gu Y, Dalton ND, et al.: MicroRNA-133 controls cardiac hypertrophy. Nat Med 2007,13:613-618.
96. Tatsuguchi M, Seok HY, Callis TE, Thomson JM, Chen JF, Newman M, Rojas M, Hammond SM, Wang DZ: Expression of microRNAs is dynamically regulated during cardiomyocyte hypertrophy. J Mol Cell Cardiol 2007, 42:1137-1141.
97. Sayed D, Hong C, Chen IY, Lypowy J, Abdellatif M: MicroRNAs play an essential role in the development of cardiac hypertrophy. Circ Res 2007,100:416-424.
98. Cheng Y, Ji R, Yue J, Yang J, Liu X, Chen H, Dean DB, Zhang C: MicroRNAs are aberrantly expressed in hypertrophic heart: do they play a role in cardiac hypertrophy? Am J Pathol 2007,170:1831-1840.
99. Yang B, Lin H, Xiao J, Lu Y, Luo X, Li B, Zhang Y, Xu C, Bai Y, Wang H, et al.: The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2. Nat Med 2001,13:486-491.
100. McCarthy JJ, Esser KA, Andrade FH: MicroRNA-206 is overexpressed in the diaphragm but not the hindlimb muscle of mdx mouse. Am J Physiol Cell Physiol 2007, 293.C451-457.
101. Shi XB, Xue L, Yang J, Ma AH, Zhao J, Xu M, Tepper CG, Evans CP, Kung HJ, deVere White RW: An androgen-regulated miRNA suppresses Bak1 expression and induces androgen-independent growth of prostate cancer cells. Proc Natl Acad Sci U S A 2007, 104:19983-19988.
102. Tavazoie SF, Alarcon C, Oskarsson T, Padua D, Wang Q, Bos PD, Gerald WL, Massague J: Endogenous human microRNAs that suppress breast cancer metastasis. Nature 2008, 451:147-152.
103. Ma L, Teruya-Feldstein J, Weinberg RA: Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 2007,449:682-688.
104. Yang H, Kong W, He L, Zhao JJ, O'Donnell JD, Wang J, Wenham RM, Coppola D, Kruk PA, Nicosia SV, et al.: MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res 2008, 68:425-433.
105. Meng F, Henson R, Wehbe-Janek H, Ghoshal K, Jacob ST, Patel T: MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer. Gastroenterology 2007,133:647-658.
106. Corney DC, Flesken-Nikitin A, Godwin AK, Wang W, Nikitin AY: MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Res 2007, 67:8433-8438.
107. He A, Zhu L, Gupta N, Chang Y, Fang F: Overexpression of micro ribonucleic acid 29, highly up-regulated in diabetic rats, leads to insulin resistance in 3T3-L1 adipocytes. Mol Endocrinol 2007, 21:2785-2794.
108. Klenov MS, Lavrov SA, Stolyarenko AD, Ryazansky SS, Aravin AA, Tuschl T, Gvozdev VA: Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res 2007,35:5430-5438.
109. Qiao D, Zeeman AM, Deng W, Looijenga LH, Lin H: Molecular characterization of hiwi, a human member of the piwi gene family whose overexpression is correlated to seminomas. Oncogene 2002,21:3988-3999.
110.Zalfa F,Giorgi M,Primerano B,Moro A,Di Penta A,Reis S,Oostra B,Bagni C:The fragile X syndrome protein FMRP associates with BC1 RNA and regulates the translation of specific mRNAs at synapses.Cell 2003,112:317-327.
111.Kondrashov AV,Kiefmann M,Ebnet K,Khanam T,Muddashetty RS,Brosius J:Inhibitory effect of naked neural BCI 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.
112.Anzai K,Kobayashi S,Kotake H,Murakami H,Korematsu K,Nonaka I:Neural BC1 RNA in mouse skeletal muscle is a denervation-induced RNA whose expression is developmentally regulated.Neurosci Lett 1996,216:81-84.
113.Murad JM,de Souza LR,De Lucca FL:PKR activation by a non-coding RNA expressed in lymphocytes of mice bearing B16 melanoma.Blood Cells Mol Dis 2006,37:128-133.
114.Rinn JL,Kertesz M,Wang JK,Squazzo SL,Xu X,Brugmann SA,Goodnough LH,Helms JA,Farnham PJ,Segal E,et al.:Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.Cell 2007,129:1311-1323.
115.Ruby JG,Jan C,Player C,Axtell MJ,Lee W,Nusbaum C,Ge H,Bartel DP:Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C.elegans.Cell 2006,127:1193-1207.
116.Storz G,Opdyke JA,Zhang A:Controlling mRNA stability and translation with small,noncoding RNAs.Curr Opin Microbiol 2004,7:140-144.
117.Lung B,Zemann A,Madej MJ,Schuelke M,Techritz S,Ruf S,Bock R,Huttenhofer A:Identification of small non-coding RNAs from mitochondria and chloroplasts.Nucleic Acids Res 2006,34:3842-3852.
118.Grivna ST,Pyhtila B,Lin H:MIWI associates with translational machinery and PIWI-interacting RNAs(piRNAs) in regulating spermatogenesis.Proc Natl Acad Sci U S A 2006,103:13415-13420.
119.Mrazek J,Kreutmayer SB,Grasser FA,Polacek N,Huttenhofer A:Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells.Nucleic Acids Res 2007,35:e73.
120.Huttenhofer A,Vogel J:Experimental approaches to identify non-coding RNAs.Nucleic Acids Res 2006,34:635-646.
121.Molnar A,Schwach F,Studholme DJ,Thuenemann EC,Baulcombe DC:miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii.Nature 2007,447:1126-1129.
122.Yoon S,De Micheli G:Computational identification of microRNAs and their targets.Birth Defects Res C Embryo Today 2006,78:118-128.
123.Berezikov E,Chung WJ,Willis J,Cuppen E,Lai EC:Mammalian mirtron genes.Mol Cell 2007,28:328-336.
124.Ruby JG,Jan CH,Bartel DP:Intronic microRNA precursors that bypass Drosha processing.Nature 2007,448:83-86.
125.Okamura K,Hagen JW,Duan H,Tyler DM,Lai EC:The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila.Cell 2007,130:89-100.
126.Mercer TR,Dinger ME,Sunkin SM,Mehler MF,Mattick JS:Specific expression of long noncoding RNAs in the mouse brain.Proc Natl Acad Sci USA 2008,105:716-721.
127. Rivas E, Eddy SR: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2:8.
128. Wei Deng, 1, Xiaopeng Zhu, 1, Geir Skogerb(?), 2, Yi Zhao, 2, Zhuo Fu, 1, et al.: Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression Genome Res 2006,16:20-29.