Mechanisms of miRNA-mediated gene regulation from common downregulation to mRNA-specific upregulation

International Journal of Genomics

Volumn 2014, Issue , 2014, Pages

  Orang, Ayla Valinezhad ^a   Safaralizadeh, Reza ^a   Kazemzadeh Bavili, Mina ^a  

^a UNIVERSITY OF TABRIZ   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; RNA;

BIOGENESIS; CELLULAR STRESS RESPONSE; DOWN REGULATION; GENE CONTROL; GENE EXPRESSION; GENETIC ASSOCIATION; HUMAN; REVIEW; RNA STABILITY; UPREGULATION;

EID: 84907405309     PISSN: 2314436X     EISSN: 23144378     Source Type: Journal    
DOI: 10.1155/2014/970607     Document Type: Review

References (173)

1. R. C. Lee, R. L. Feinbaum, and V. Ambros, "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14," Cell, vol. 75, no. 5, pp. 843-854, 1993.
2. R. W. Carthew and E. J. Sontheimer, "Origins and mechanisms of miRNAs and siRNAs," Cell, vol. 136, no. 4, pp. 642-655, 2009.
3. M. Ghildiyal and P. D. Zamore, "Small silencing RNAs: an expanding universe," Nature Reviews Genetics, vol. 10, no. 2, pp. 94-108, 2009.
4. V. N. Kim, J. Han, and M. C. Siomi, "Biogenesis of small RNAs in animals," Nature Reviews Molecular Cell Biology, vol. 10, no. 2, pp. 126-139, 2009.
5. H. Siomi and M. C. Siomi, "On the road to reading the RNA-interference code," Nature, vol. 457, no. 7228, pp. 396-404, 2009.
6. V. Oliveira-Carvalho, V. O. Carvalho, M. M. Silva, G. V. Guimarães, and E. A. Bocchi, "MicroRNAs: a new paradigm in the treatment and diagnosis of heart failure?" Arquivos Brasileiros de Cardiologia, vol. 98, no. 4, pp. 362-369, 2012.
7. V. Ambros, "The functions of animal microRNAs," Nature, vol. 431, no. 7006, pp. 350-355, 2004.
8. R. J. Johnston Jr. and O. Hobert, "A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans," Nature, vol. 426, no. 6968, pp. 845-849, 2003.
9. Y. Zhao, E. Samal, and D. Srivastava, "Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis," Nature, vol. 436, no. 7048, pp. 214-220, 2005.
10. A. M. Cheng, M. W. Byrom, J. Shelton, and L. P. Ford, "Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis," Nucleic Acids Research, vol. 33, no. 4, pp. 1290-1297, 2005.
11. J. F. Chen, E. M. Mandel, J. M. Thomson et al., "The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation," Nature Genetics, vol. 38, no. 2, pp. 228-233, 2006.
12. S. D. Hatfield, H. R. Shcherbata, K. A. Fischer, K. Nakahara, R. W. Carthew, and H. Ruohola-Baker, "Stem cell division is regulated by the microRNA pathway," Nature, vol. 435, no. 7044, pp. 974-978, 2005.
13. C. M. Croce and G. A. Calin, "miRNAs, cancer, and stem cell division," Cell, vol. 122, no. 1, pp. 6-7, 2005.
14. I. Naguibneva, M. Ameyar-Zazoua, A. Polesskaya et al., "The microRNA miR-181 targets the homeobox protein Hox-A11 during mammalian myoblast differentiation," Nature Cell Biology, vol. 8, no. 3, pp. 278-284, 2006.
15. D. P. Bartel, "MicroRNAs: genomics, biogenesis, mechanism, and function," Cell, vol. 116, no. 2, pp. 281-297, 2004.
16. W. Filipowicz, "RNAi: the nuts and bolts of the RISC machine," Cell, vol. 122, no. 1, pp. 17-20, 2005.
17. F. Jamshidi-Adegani, L. Langroudi, A. Shafiee, A. Mohammadi-Sangcheshmeh, A. Ardeshirylajimi, and M. Barzegar, "Mir-302 cluster exhibits tumor suppressor properties on human unrestricted somatic stem cells," Tumour Biology, 2014.
18. K. Matsushima, H. Isomoto, N. Yamaguchi et al., "MiRNA-205 modulates cellular invasion and migration via regulating zinc finger E-box binding homeobox 2 expression in esophageal squamous cell carcinoma cells," Journal of Translational Medicine, vol. 9, article 30, 2011.
19. M. N. Poy, L. Eliasson, J. Krutzfeldt et al., "A pancreatic islet-specific microRNA regulates insulin secretion," Nature, vol. 432, no. 7014, pp. 226-230, 2004.
20. H. R. Mollaie, S. H. Monavari, S. A. Arabzadeh, M. Shamsi-Shahrabadi, M. Fazlalipour, and R. M. Afshar, "RNAi and miRNA in viral infections and cancers," Asian Pacific Journal of Cancer Prevention, vol. 14, no. 12, pp. 7045-7056, 2013.
21. D. Baek, J. Villén, C. Shin, F. D. Camargo, S. P. Gygi, and D. P. Bartel, "The impact of microRNAs on protein output," Nature, vol. 455, no. 7209, pp. 64-71, 2008.
22. A. V. Orang, R. Safaralizadeh, and M. A. Hosseinpour Feizi, "Insights into the diverse roles of miR-205 in human cancers," Asian Pacific Journal of Cancer Prevention, vol. 15, no. 2, pp. 577-83, 2014.
23. C. Thorns, C. Schurmann, N. Gebauer et al., "Global MicroRNA profiling of pancreatic neuroendocrine neoplasias," Anticancer Research, vol. 34, no. 5, pp. 2249-2254, 2014.
24. M. Li, J. Li, X. Ding, M. He, and S.-Y. Cheng, "microRNA and cancer," The AAPS Journal, vol. 12, no. 3, pp. 309-317, 2010.
25. R. Rupaimoole, H. Han, G. Lopez-Berestein, and A. K. Sood, "MicroRNA therapeutics: principles, expectations, and challenges," Chinese Journal of Cancer, vol. 30, no. 6, pp. 368-370, 2011.
26. B. P. Lewis, I.-H. Shih, M. W. Jones-Rhoades, D. P. Bartel, and C. B. Burge, "Prediction of mammalian microRNA targets," Cell, vol. 115, no. 7, pp. 787-798, 2003.
27. J. Brennecke, A. Stark, R. B. Russell, and S. M. Cohen, "Principles of microRNA-target recognition," PLoS Biology, vol. 3, no. 3, article e85, 2005.
28. Y. Watanabe, M. Tomita, and A. Kanai, "Computational methods for microRNA target prediction," Methods in Enzymology, vol. 427, pp. 65-86, 2007.
29. T. W. Nilsen, "Mechanisms of microRNA-mediated gene regulation in animal cells," Trends in Genetics, vol. 23, no. 5, pp. 243-249, 2007.
30. S. Vasudevan, "Posttranscriptional upregulation by microRNAs," Wiley Interdisciplinary Reviews: RNA, vol. 3, no. 3, pp. 311-330, 2012.
31. V. N. Kim and J. W. Nam, "Genomics of microRNA," Trends in Genetics : TIG, vol. 22, no. 3, pp. 165-173, 2006.
32. J. Krol, I. Loedige, and W. Filipowicz, "The widespread regulation of microRNA biogenesis, function and decay," Nature Reviews Genetics, vol. 11, no. 9, pp. 597-610, 2010.
33. N. Shomron and C. Levy, "MicroRNA-biogenesis and prem-RNA splicing crosstalk," Journal of Biomedicine and Biotechnology, vol. 2009, Article ID 594678, 6 pages, 2009.
34. H. Seitz, N. Youngson, S. Lin et al., "Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene," Nature Genetics, vol. 34, no. 3, pp. 261-262, 2003.
35. C. Sevignani, G. A. Calin, S. C. Nnadi et al., "MicroRNA genes are frequently located near mouse cancer susceptibility loci," Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 19, pp. 8017-8022, 2007.
36. K. Huppi, N. Volfovsky, T. Runfola et al., "The identification of microRNAs in a genomically unstable region of human chromosome 8q24," Molecular Cancer Research, vol. 6, no. 2, pp. 212-221, 2008.
37. G. A. Calin, C. Sevignani, C. D. Dumitru et al., "Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers," Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 9, pp. 2999-3004, 2004.
38. A. G. Hoss, V. K. Kartha, X. Dong et al., "MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis," PLoS Genetics, vol. 10, no. 2, Article ID e1004188, 2014.
39. A. Issabekova, O. Berillo, and M. Regnier, "Anatoly I. Interactions of intergenic microRNAs with mRNAs of genes involved in carcinogenesis," Bioinformation, vol. 8, no. 11, pp. 513-518, 2012.
40. I. Godnic, M. Zorc, D. Jevsinek Skok et al., "Genome-wide and species-wide in silico screening for intragenic MicroRNAs in human, mouse and chicken," PLoS ONE, vol. 8, no. 6, Article ID e65165, 2013.
41. F. Ozsolak, L. L. Poling, Z. Wang et al., "Chromatin structure analyses identify miRNA promoters," Genes & Development, vol. 22, no. 22, pp. 3172-3183, 2008.
42. B. C. Schanen and X. Li, "Transcriptional regulation of mammalian miRNA genes," Genomics, vol. 97, no. 1, pp. 1-6, 2011.
43. Y. Lee, M. Kim, J. Han et al., "MicroRNA genes are transcribed by RNA polymerase II," The EMBO Journal, vol. 23, no. 20, pp. 4051-4060, 2004.
44. G. M. Borchert, W. Lanier, and B. L. Davidson, "RNA polymerase III transcribes human microRNAs," Nature Structural & Molecular Biology, vol. 13, no. 12, pp. 1097-1101, 2006.
45. X. Liu, K. Fortin, and Z. Mourelatos, "MicroRNAs: biogenesis and molecular functions," Brain Pathology, vol. 18, no. 1, pp. 113-121, 2008.
46. V. N. Kim, "MicroRNA biogenesis: coordinated cropping and dicing," Nature Reviews Molecular Cell Biology, vol. 6, no. 5, pp. 376-385, 2005.
47. A. M. Denli, B. B. J. Tops, R. H. A. Plasterk, R. F. Ketting, and G. J. Hannon, "Processing of primary microRNAs by the Microprocessor complex," Nature, vol. 432, no. 7014, pp. 231-235, 2004.
48. R. I. Gregory, K. Yan, G. Amuthan et al., "The Microprocessor complex mediates the genesis of microRNAs," Nature, vol. 432, no. 7014, pp. 235-240, 2004.
49. A. Rodriguez, S. Griffiths-Jones, J. L. Ashurst, and A. Bradley, "Identification of mammalian microRNA host genes and transcription units," Genome Research, vol. 14, no. 10A, pp. 1902-1910, 2004.
50. E. Lund, S. Güttinger, A. Calado, J. E. Dahlberg, and U. Kutay, "Nuclear export of microRNA precursors," Science, vol. 303, no. 5654, pp. 95-98, 2004.
51. C. Gwizdek, B. Ossareh-Nazari, A. M. Brownawell et al., "Exportin-5 mediates nuclear export of minihelix-containing RNAs," The Journal of Biological Chemistry, vol. 278, no. 8, pp. 5505-5508, 2003.
52. Y. Zeng and B. R. Cullen, "Structural requirements for pre-microRNA binding and nuclear export by Exportin 5," Nucleic Acids Research, vol. 32, no. 16, pp. 4776-4785, 2004.
53. M. R. Ladomery, D. G. Maddocks, and I. D. Wilson, "MicroRNAs: their discovery, biogenesis, function and potential use as biomarkers in non-invasive prenatal diagnostics," International Journal of Molecular Epidemiology and Genetics, vol. 2, no. 3, pp. 253-260, 2011.
54. D. S. Schwarz and P. D. Zamore, "Why do miRNAs live in the miRNP?" Genes and Development, vol. 16, no. 9, pp. 1025-1031, 2002.
55. Y. Cai, X. Yu, S. Hu, and J. Yu, "A brief review on the mechanisms of miRNA regulation," Genomics, Proteomics & Bioinformatics, vol. 7, no. 4, pp. 147-154, 2009.
56. J. A. Steitz and S. Vasudevan, "miRNPs: versatile regulators of gene expression in vertebrate cells," Biochemical Society Transactions, vol. 37, part 5, pp. 931-935, 2009.
57. B. P. Lewis, C. B. Burge, and D. P. Bartel, "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets," Cell, vol. 120, no. 1, pp. 15-20, 2005.
58. I. Lee, S. S. Ajay, I. Y. Jong et al., "New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites," Genome Research, vol. 19, no. 7, pp. 1175-1183, 2009.
59. A. Brummer and J. Hausser, "MicroRNA binding sites in the coding region of mRNAs: extending the repertoire of posttranscriptional gene regulation," BioEssays, vol. 36, no. 6, pp. 617-626, 2014.
60. A. P. Carroll, G. J. Goodall, and B. Liu, "Understanding principles of miRNA target recognition and function through integrated biological and bioinformatics approaches," Wiley Interdisciplinary Reviews RNA, vol. 5, no. 3, pp. 361-379, 2014.
61. X. Wang, "Composition of seed sequence is a major determinant of microRNA targeting patterns," Bioinformatics, vol. 30, no. 10, pp. 1377-1383, 2014.
62. U. Ohler, S. Yekta, L. P. Lim, D. P. Bartel, and C. B. Burge, "Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification," RNA, vol. 10, no. 9, pp. 1309-1322, 2004.
63. W. H. Majoros and U. Ohler, "Spatial preferences of microRNA targets in 3′ untranslated regions," BMC Genomics, vol. 8, article 152, 2007.
64. P. Brodersen and O. Voinnet, "Revisiting the principles of microRNA target recognition and mode of action," Nature Reviews Molecular Cell Biology, vol. 10, no. 2, pp. 141-148, 2009.
65. E. J. Finnegan and M. A. Matzke, "The small RNA world," Journal of Cell Science, vol. 116, no. 23, pp. 4689-4693, 2003.
66. S. I. S. Grewal and S. C. R. Elgin, "Transcription and RNA interference in the formation of heterochromatin," Nature, vol. 447, no. 7143, pp. 399-406, 2007.
67. M. R. Fabian, N. Sonenberg, and W. Filipowicz, "Regulation of mRNA translation and stability by microRNAs," Annual Review of Biochemistry, vol. 79, pp. 351-379, 2010.
68. M. A. Valencia-Sanchez, J. Liu, G. J. Hannon, and R. Parker, "Control of translation and mRNA degradation by miRNAs and siRNAs," Genes and Development, vol. 20, no. 5, pp. 515-524, 2006.
69. N. L. Garneau, J. Wilusz, and C. J. Wilusz, "The highways and byways of mRNA decay," Nature Reviews Molecular Cell Biology, vol. 8, no. 2, pp. 113-126, 2007.
70. S. Bagga, J. Bracht, S. Hunter et al., "Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation," Cell, vol. 122, no. 4, pp. 553-563, 2005.
71. G. Mathonnet, M. R. Fabian, Y. V. Svitkin et al., "MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F," Science, vol. 317, no. 5845, pp. 1764-1767, 2007.
72. S. Iwasaki and Y. Tomari, "Argonaute-mediated translational repression (and activation)," Fly, vol. 3, no. 3, pp. 204-206, 2009.
73. A. Eulalio, E. Huntzinger, and E. Izaurralde, "Getting to the root of miRNA-mediated gene silencing," Cell, vol. 132, no. 1, pp. 9-14, 2008.
74. B. Wang, A. Yanez, and C. D. Novina, "MicroRNA-repressed mRNAs contain 40S but not 60S components," Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 14, pp. 5343-5348, 2008.
75. J. R. Lytle, T. A. Yario, and J. A. Steitz, "Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR," Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 23, pp. 9667-9672, 2007.
76. T. P. Chendrimada, K. J. Finn, X. Ji et al., "MicroRNA silencing through RISC recruitment of eIF6," Nature, vol. 447, no. 7146, pp. 823-828, 2007.
77. X. C. Ding and H. Großhans, "Repression of C. elegans microRNA targets at the initiation level of translation requires GW182 proteins," The EMBO Journal, vol. 28, no. 3, pp. 213-222, 2009.
78. R. S. Pillai, S. N. Bhattacharyya, and W. Filipowicz, "Repression of protein synthesis by miRNAs: how many mechanisms?" Trends in Cell Biology, vol. 17, no. 3, pp. 118-126, 2007.
79. T. Eystathioy, A. Jakymiw, E. K. L. Chan, B. Séraphin, N. Cougot, and M. J. Fritzler, "The GW182 protein colocalizes with mRNA degradation associated proteins hDcp1 and hLSm4 in cytoplasmic GW bodies," RNA, vol. 9, no. 10, pp. 1171-1173, 2003.
80. M. A. Andrei, D. Ingelfinger, R. Heintzmann, T. Achsel, R. Rivera-Pomar, and R. Lührmann, "A role for eIF4E and eIF4E-transporter in targeting mRNPs to mammalian processing bodies," RNA, vol. 11, no. 5, pp. 717-727, 2005.
81. G. L. Sen and H. M. Blau, "Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies," Nature Cell Biology, vol. 7, no. 6, pp. 633-636, 2005.
82. S. Vasudevan and J. A. Steitz, "AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2," Cell, vol. 128, no. 6, pp. 1105-1118, 2007.
83. K. R. Cordes, N. T. Sheehy, M. P. White et al., "MiR-145 and miR-143 regulate smooth muscle cell fate and plasticity," Nature, vol. 460, no. 7256, pp. 705-710, 2009.
84. E. Li, J. Zhang, T. Yuan, and B. Ma, "miR-145 inhibits osteosarcoma cells proliferation and invasion by targeting ROCK1," Tumour Biology, 2014.
85. C. C. Lin, L. Z. Liu, J. B. Addison, W. F. Wonderlin, A. V. Ivanov, and J. M. Ruppert, "A KLF4-miRNA-206 autoregulatory feedback loop can promote or inhibit protein translation depending upon cell context," Molecular and Cellular Biology, vol. 31, no. 12, pp. 2513-2527, 2011.
86. S. Vasudevan, Y. Tong, and J. A. Steitz, "Switching from repression to activation: microRNAs can up-regulate translation," Science, vol. 318, no. 5858, pp. 1931-1934, 2007.
87. L. C. Li, S. T. Okino, H. Zhao et al., "Small dsRNAs induce transcriptional activation in human cells," Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 46, pp. 17337-17342, 2006.
88. H. A. Coller, L. Sang, and J. M. Roberts, "A new description of cellular quiescence.," PLoS Biology, vol. 4, no. 3, article e83, 2006.
89. S. S. Truesdell, R. D. Mortensen, M. Seo et al., "MicroRNA-mediated mRNA translation activation in quiescent cells and oocytes involves recruitment of a nuclear microRNP," Scientific Reports, vol. 2, article 842, 2012.
90. Y. M. Fu, Z. X. Yu, V. J. Ferrans, and G. G. Meadows, "Tyrosine and phenylalanine restriction induces G0/G1 cell cycle arrest in murine melanoma in vitro and in vivo," Nutrition and Cancer, vol. 29, no. 2, pp. 104-113, 1997.
91. M. Küppers, C. Ittrich, D. Faust, and C. Dietrich, "The transcriptional programme of contact-inhibition," Journal of Cellular Biochemistry, vol. 110, no. 5, pp. 1234-1243, 2010.
92. N. Furuno, A. Kawasaki, and N. Sagata, "Expressionof cell-cycle regulators during Xenopus oogenesis," Gene Expression Patterns, vol. 3, no. 2, pp. 165-168, 2003.
93. R. S. Pillai, C. G. Artus, and W. Filipowicz, "Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis," RNA, vol. 10, no. 10, pp. 1518-1525, 2004.
94. A. Turchinovich and B. Burwinkel, "Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma," RNA Biology, vol. 9, no. 8, pp. 1066-1075, 2012.
95. Z. Yang, A. Jakymiw, M. R. Wood et al., "GW182 is critical for the stability of GW bodies expressed during the cell cycle and cell proliferation," Journal of Cell Science, vol. 117, part 23, pp. 5567-5578, 2004.
96. S. N. Bhattacharyya and W. Filipowicz, "Argonautes and company: sailing against the wind," Cell, vol. 128, no. 6, pp. 1027-1028, 2007.
97. M. J. Moore and N. J. Proudfoot, "Pre-mRNA processing reaches back to transcription and ahead to translation," Cell, vol. 136, no. 4, pp. 688-700, 2009.
98. L. Weinmann, J. Höck, T. Ivacevic et al., "Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs," Cell, vol. 136, no. 3, pp. 496-507, 2009.
99. E. Lund, M. D. Sheets, S. B. Imboden, and J. E. Dahlberg, "Limiting ago protein restricts RNAi and microRNA biogenesis during early development in Xenopus laevis," Genes & Development, vol. 25, no. 11, pp. 1121-1131, 2011.
100. R. D. Mortensen, M. Serra, J. A. Steitz, and S. Vasudevan, "Posttranscriptional activation of gene expression in Xenopus laevis oocytes by microRNA-protein complexes (microRNPs)," Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 20, pp. 8281-8286, 2011.
101. S. Vasudevan, Y. Tong, and J. A. Steitz, "Cell cycle control of microRNA-mediated translation regulation," Cell Cycle, vol. 7, no. 11, pp. 1545-1549, 2008.
102. S. Ceman, V. Brown, and S. T. Warren, "Isolation of an FMRP-associated messenger ribonucleoprotein particle and identification of nucleolin and the fragile X-related proteins as components of the complex," Molecular and Cellular Biology, vol. 19, no. 12, pp. 7925-7932, 1999.
103. H. H. Kim, Y. Kuwano, S. Srikantan, E. K. Lee, J. L. Martindale, and M. Gorospe, "HuR recruits let-7/RISC to repress c-Myc expression," Genes and Development, vol. 23, no. 15, pp. 1743-1748, 2009.
104. S. U. Mertens-Talcott, S. Chintharlapalli, X. Li, and S. Safe, "The oncogenic microRNA-27a targets genes that regulate specificity protein transcription factors and the G2-M checkpoint in MDA-MB-231 breast cancer cells," Cancer Research, vol. 67, no. 22, pp. 11001-11011, 2007.
105. C. L. Jopling, S. Schütz, and P. Sarnow, "Position-dependent function for a tandem microRNA miR-122-binding site located in the hepatitis C virus RNA genome," Cell Host and Microbe, vol. 4, no. 1, pp. 77-85, 2008.
106. J. Chang, E. Nicolas, D. Marks et al., "miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1," RNA Biology, vol. 1, no. 2, pp. 106-113, 2004.
107. M. Niepmann, "Activation of hepatitis C virus translation by a liver-specific microRNA," Cell Cycle, vol. 8, no. 10, pp. 1473-1477, 2009.
108. J. I. Henke, D. Goergen, J. Zheng et al., "microRNA-122 stimulates translation of hepatitis C virus RNA," The EMBO Journal, vol. 27, no. 24, pp. 3300-3310, 2008.
109. E. S. Machlin, P. Sarnow, and S. M. Sagan, "Masking the 5′ terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex," Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 8, pp. 3193-3198, 2011.
110. Y. Li, T. Masaki, D. Yamane, D. R. McGivern, and S. M. Lemon, "Competing and noncompeting activities of miR-122 and the 5′ exonuclease Xrn1 in regulation of hepatitis C virus replication," Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 5, pp. 1881-1886, 2013.
111. T. Shimakami, D. Yamane, R. K. Jangra et al., "Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex," Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 3, pp. 941-946, 2012.
112. K. D. Conrad and M. Niepmann, "The role of microRNAs in hepatitis C virus RNA replication," Archives of Virology, vol. 159, no. 5, pp. 849-862, 2014.
113. O. Meyuhas, "Synthesis of the translational apparatus is regulated at the translational level," European Journal of Biochemistry, vol. 267, no. 21, pp. 6321-6330, 2000.
114. S. Levy, D. Avni, N. Hariharan, R. P. Perry, and O. Meyuhas, "Oligopyrimidine tract at the 5′ end of mammalian ribosomal protein mRNAs is required for their translational control," Proceedings of the National Academy of Sciences of the United States of America, vol. 88, no. 8, pp. 3319-3323, 1991.
115. N. Terada, H. R. Patel, K. Takase, K. Kohno, A. C. Nairn, and E. W. Gelfand, "Rapamycin selectively inhibits translation of mRNAs encoding elongation factors and ribosomal proteins," Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 24, pp. 11477-11481, 1994.
116. T. R. Rao and L. I. Slobin, "Regulation of the utilization of mRNA for eucaryotic elongation factor Tu in Friend erythroleukemia cells," Molecular and Cellular Biology, vol. 7, no. 2, pp. 687-697, 1987.
117. D. Avni, S. Shama, F. Loreni, and O. Meyuhas, "Vertebrate mRNAs with a 5′-terminal pyrimidine tract are candidates for translational repression in quiescent cells: characterization of the translational cis-regulatory element," Molecular and Cellular Biology, vol. 14, no. 6, pp. 3822-3833, 1994.
118. M. G. Agrawal and L. H. Bowman, "Transcriptional and translational regulation of ribosomal protein formation during mouse myoblast differentiation," The Journal of Biological Chemistry, vol. 262, no. 10, pp. 4868-4875, 1987.
119. P. Landgraf, M. Rusu, R. Sheridan et al., "A mammalian microRNA expression atlas based on small RNA library sequencing," Cell, vol. 129, no. 7, pp. 1401-1414, 2007.
120. U. A. Ørom, F. C. Nielsen, and A. H. Lund, "MicroRNA-10a binds the 5′UTR of ribosomal protein mRNAs and enhances their translation," Molecular Cell, vol. 30, no. 4, pp. 460-471, 2008.
121. L. Wei, "Retinoids and receptor interacting protein 140 (RIP140) in gene regulation," Current Medicinal Chemistry, vol. 11, no. 12, pp. 1527-1532, 2004.
122. N. Tsai, Y. Lin, and L. Wei, "MicroRNA mir-346 targets the 5′-untranslated region of receptor-interacting protein 140 (RIP140) mRNA and up-regulates its protein expression," Biochemical Journal, vol. 424, no. 3, pp. 411-418, 2009.
123. A. M. Powelka, A. Seth, J. V. Virbasius et al., "Suppression of oxidative metabolism and mitochondrial biogenesis by the transcriptional corepressor RIP140 in mouse adipocytes," The Journal of Clinical Investigation, vol. 116, no. 1, pp. 125-136, 2006.
124. C. A. Chen and A. Shyu, "AU-rich elements: characterization and importance in mRNA degradation," Trends in Biochemical Sciences, vol. 20, no. 11, pp. 465-470, 1995.
125. C. J. Wilusz, M. Wormington, and S. W. Peltz, "The cap-to-tail guide to mRNA turnover," Nature Reviews Molecular Cell Biology, vol. 2, no. 4, pp. 237-246, 2001.
126. J. Lykke-Andersen and E. Wagner, "Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1," Genes and Development, vol. 19, no. 3, pp. 351-361, 2005.
127. Q. Jing, S. Huang, S. Guth et al., "Involvement of microRNA in AU-rich element-mediated mRNA instability," Cell, vol. 120, no. 5, pp. 623-634, 2005.
128. C. von Roretz and I. Gallouzi, "Decoding ARE-mediated decay: is microRNA part of the equation?" Journal of Cell Biology, vol. 181, no. 2, pp. 189-194, 2008.
129. F. Ma, X. Liu, D. Li et al., "MicroRNA-466l upregulates IL-10 expression in TLR-triggered macrophages by antagonizing RNA-binding protein tristetraprolin-mediated IL-10 mRNA degradation," Journal of Immunology, vol. 184, no. 11, pp. 6053-6059, 2010.
130. A. J. Murphy, P. M. Guyre, and P. A. Pioli, "Estradiol suppresses NF-κB activation through coordinated regulation of let-7a and miR-125b in primary human macrophages," The Journal of Immunology, vol. 184, no. 9, pp. 5029-5037, 2010.
131. A. M. Eiring, J. G. Harb, P. Neviani et al., "miR-328 functions as an RNA decoy to modulate hnRNP E2 regulation of mRNA translation in leukemic blasts," Cell, vol. 140, no. 5, pp. 652-665, 2010.
132. S. N. Bhattacharyya, R. Habermacher, U. Martine, E. I. Closs, and W. Filipowicz, "Relief of microRNA-mediated translational repression in human cells subjected to stress," Cell, vol. 125, no. 6, pp. 1111-1124, 2006.
133. S. I. Ashraf, A. L. McLoon, S. M. Sclarsic, and S. Kunes, "Synaptic protein synthesis associated with memory is regulated by the RISC pathway in Drosophila," Cell, vol. 124, no. 1, pp. 191-205, 2006.
134. S. N. Bhattacharyya, R. Habermacher, U. Martine, E. I. Closs, and W. Filipowicz, "Stress-induced Reversal of microRNA repression and mRNA P-body localization in human cells," Cold Spring Harbor Symposia on Quantitative Biology, vol. 71, pp. 513-521, 2006.
135. M. Ivan, A. L. Harris, F. Martelli, and R. Kulshreshtha, "Hypoxia response and microRNAs: no longer two separate worlds," Journal of Cellular and Molecular Medicine, vol. 12, no. 5a, pp. 1426-1431, 2008.
136. K. A. Padgett, R. Y. Lan, P. C. Leung et al., "Primary biliary cirrhosis is associated with altered hepatic microRNA expression," Journal of Autoimmunity, vol. 32, no. 3-4, pp. 246-253, 2009.
137. M. L. Chen, L. S. Liang, and X. K. Wang, "MiR-200c inhibits invasion and migration in human colon cancer cells SW480/620 by targeting ZEB1," Clinical and Experimental Metastasis, vol. 29, no. 5, pp. 457-469, 2012.
138. L. García-Segura, M. Pérez-Andrade, J. Miranda-Ríos, and C. Piso, "The emerging role of MicroRNAs in the regulation of gene expression by nutrients," Journal of Nutrigenetics and Nutrigenomics, vol. 6, no. 1, pp. 16-31, 2013.
139. E. van Rooij, L. B. Sutherland, X. Qi, J. A. Richardson, J. Hill, and E. N. Olson, "Control of stress-dependent cardiac growth and gene expression by a microRNA," Science, vol. 316, no. 5824, pp. 575-579, 2007.
140. G. T. Bommer, I. Gerin, Y. Feng et al., "p53-mediated activation of miRNA34 candidate tumor-suppressor genes," Current Biology, vol. 17, no. 15, pp. 1298-1307, 2007.
141. T.-C. Chang, E. A. Wentzel, O. A. Kent et al., "Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis," Molecular Cell, vol. 26, no. 5, pp. 745-752, 2007.
142. L. He, X. He, L. P. Lim et al., "A microRNA component of the p53 tumour suppressor network," Nature, vol. 447, no. 7148, pp. 1130-1134, 2007.
143. N. Raver-Shapira, E. Marciano, E. Meiri et al., "Transcriptional activation of miR-34a contributes to p53-mediated apoptosis," Molecular Cell, vol. 26, no. 5, pp. 731-743, 2007.
144. B. Wang, Y. F. Sun, N. Song et al., "MicroRNAs involving in cold, wounding and salt stresses in Triticum aestivum L," Plant Physiology and Biochemistry C, vol. 80, pp. 90-96, 2014.
145. M. Hatzoglou, J. Fernandez, I. Yaman, and E. Closs, "Regulation of cationic amino acid transport: the story of the CAT-1 transporter," Annual Review of Nutrition, vol. 24, pp. 377-399, 2004.
146. I. Yaman, J. Fernandez, B. Sarkar et al., "Nutritional control of mRNA stability is mediated by a conserved AU-rich element that binds the cytoplasmic shuttling protein HuR," Journal of Biological Chemistry, vol. 277, no. 44, pp. 41539-41546, 2002.
147. I. Yaman, J. Fernandez, H. Liu et al., "The zipper model of translational control: a small upstream ORF is the switch that controls structural remodeling of an mRNA leader," Cell, vol. 113, no. 4, pp. 519-531, 2003.
148. C. M. Brennan and J. A. Steitz, "HuR and mRNA stability," Cellular and Molecular Life Sciences, vol. 58, no. 2, pp. 266-277, 2001.
149. V. Katsanou, O. Papadaki, S. Milatos et al., "HuR as a negative posttranscriptional modulator in inflammation," Molecular Cell, vol. 19, no. 6, pp. 777-789, 2005.
150. A. Lal, T. Kawai, X. Yang, K. Mazan-Mamczarz, and M. Gorospe, "Antiapoptotic function of RNA-binding protein HuR effected through prothymosin α," The EMBO Journal, vol. 24, no. 10, pp. 1852-1862, 2005.
151. K. Mazan-Mamczarz, P. R. Hagner, S. Corl et al., "Posttranscriptional gene regulation by HuR promotes a more tumorigenic phenotype," Oncogene, vol. 27, no. 47, pp. 6151-6163, 2008.
152. S. S.-Y. Peng, C. A. Chen, N. Xu, and A. Shyu, "RNA stabilization by the AU-rich element binding protein, HuR, an ELAV protein," The EMBO Journal, vol. 17, no. 12, pp. 3461-3470, 1998.
153. X. C. Fan and J. A. Steitz, "Overexpression of HuR, a nuclear-cytoplasmic shuttling protein, increases the in vivo stability of ARE-containing mRNAs," The EMBO Journal, vol. 17, no. 12, pp. 3448-3460, 1998.
154. M. Kedde, M. J. Strasser, B. Boldajipour et al., "RNA-binding protein Dnd1 inhibits microRNA access to target mRNA," Cell, vol. 131, no. 7, pp. 1273-1286, 2007.
155. J. Yoon, K. Abdelmohsen, S. Srikantan et al., "LincRNA-p21 suppresses target mRNA translation," Molecular Cell, vol. 47, no. 4, pp. 648-655, 2012.
156. E. A. Gibb, E. A. Vucic, K. S. S. Enfield et al., "Human cancer long non-coding RNA transcriptomes," PLoS ONE, vol. 6, no. 10, Article ID e25915, 2011.
157. J. H. Yoon, K. Abdelmohsen, and M. Gorospe, "Posttranscriptional gene regulation by long noncoding RNA," Journal of Molecular Biology, vol. 425, no. 19, pp. 3723-3730, 2013.
158. Q. Zhang and K.-T. Jeang, "Long noncoding RNAs and viral infections," BioMedicine, vol. 3, no. 1, pp. 34-42, 2013.
159. T. Nagano and P. Fraser, "No-nonsense functions for long noncoding RNAs," Cell, vol. 145, no. 2, pp. 178-181, 2011.
160. S. Y. Ng and L. W. Stanton, "Long non-coding RNAs in stem-cell pluripotency," Wiley Interdisciplinary Reviews: RNA, vol. 41, no. 1, pp. 121-128, 2013.
161. S. Loewer, M. N. Cabili, M. Guttman et al., "Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells," Nature Genetics, vol. 42, no. 12, pp. 1113-1117, 2010.
162. Y. Wang, Z. Xu, J. Jiang et al., "Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal," Developmental Cell, vol. 25, no. 1, pp. 69-80, 2013.
163. E. C. Cheng and H. Lin, "Repressing the repressor: a lincRNA as a microRNA sponge in embryonic stem cell self-renewal," Developmental Cell, vol. 25, no. 1, pp. 1-2, 2013.
164. H. Zhu, F. Hu, R. Wang et al., "Arabidopsis argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development," Cell, vol. 145, no. 2, pp. 242-256, 2011.
165. T. Ghosh, K. Soni, V. Scaria, M. Halimani, C. Bhattacharjee, and B. Pillai, "MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic β-actin gene," Nucleic Acids Research, vol. 36, no. 19, pp. 6318-6332, 2008.
166. G. M. Schratt, F. Tuebing, E. A. Nigh et al., "A brain-specific microRNA regulates dendritic spine development," Nature, vol. 439, no. 7074, pp. 283-289, 2006.
167. S. Khudayberdiev, R. Fiore, and G. Schratt, "MicroRNA as modulators of neuronal responses," Communicative & Integrative Biology, vol. 2, no. 5, pp. 411-413, 2009.
168. V. Glorian, G. Maillot, S. Polès, J. S. Iacovoni, G. Favre, and S. Vagner, "HuR-dependent loading of miRNA RISC to the mRNA encoding the Ras-related small GTPase RhoB controls its translation during UV-induced apoptosis," Cell Death and Differentiation, vol. 18, no. 11, pp. 1692-1701, 2011.
169. S. Srikantan, K. Abdelmohsen, E. K. Lee et al., "Translational control of TOP2A Influences doxorubicin efficacy," Molecular and Cellular Biology, vol. 31, no. 18, pp. 3790-3801, 2011.
170. L. Poliseno, L. Salmena, J. Zhang, B. Carver, W. J. Haveman, and P. P. Pandolfi, "A coding-independent function of gene and pseudogene mRNAs regulates tumour biology," Nature, vol. 465, no. 7301, pp. 1033-1038, 2010.
171. S. Gehrke, Y. Imai, N. Sokol, and B. Lu, "Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression," Nature, vol. 466, no. 7306, pp. 637-641, 2010.
172. S. Chan, G. Ramaswamy, E. Choi, and F. J. Slack, "Identification of specific let-7 microRNA binding complexes in Caenorhabditis elegans," RNA, vol. 14, no. 10, pp. 2104-2114, 2008.
173. M. R. Jones, L. J. Quinton, M. T. Blahna et al., "Zcchc11-dependent uridylation of microRNA directs cytokine expression," Nature Cell Biology, vol. 11, no. 9, pp. 1157-1163, 2009.