MicroRNA target identification: Lessons from HypoxamiRs

Antioxidants and Redox Signaling

Volumn 21, Issue 8, 2014, Pages 1249-1268

  Bertero, Thomas ^a,b   Robbe Sermesant, Karine ^a,b   Le Brigand, Kevin ^a,b   Ponzio, Gilles ^a,b   Pottier, Nicolas ^c   Rezzonico, Roger ^a,b   Mazure, Nathalie M ^b,d   Barbry, Pascal ^a,b   Mari, Bernard ^a,b  

^a CNRS   (France)

^b UNIVERSITÉ CÔTE D'AZUR   (France)

^c UFR3S Pharmacie   (France)

^d UNIVERSITY OF NICE SOPHIA ANTIPOLIS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

3' UNTRANSLATED REGION; APOPTOSIS; BIOINFORMATICS; CANCER CELL; CELL CYCLE REGULATION; CELL PROLIFERATION; CELL SURVIVAL; COMPUTER MODEL; DNA DAMAGE; ENDOTHELIUM CELL; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE TARGETING; GENETIC IDENTIFICATION; HOMOLOGOUS RECOMBINATION; HUMAN; HYPOXIA; MITOCHONDRIAL RESPIRATION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEOMICS; REVIEW; ANIMAL; COMPUTER PROGRAM; DNA SEQUENCE; FEEDBACK SYSTEM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; RNA INTERFERENCE;

ANIMALS; BASE SEQUENCE; FEEDBACK, PHYSIOLOGICAL; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS; PROTEOMICS; RNA INTERFERENCE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84904404403     PISSN: 15230864     EISSN: 15577716     Source Type: Journal    
DOI: 10.1089/ars.2013.5648     Document Type: Review

References (208)

1. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, and Hatzigeorgiou AG. Lost in translation: An assessment and perspective for computational microRNA target identification. Bioinformatics 25: 3049-3055, 2009
2. Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, and Hatzigeorgiou AG. The DIANA-mir-ExTra web server: From gene expression Data to microRNA function. PLoS One 5: E9171, 2010
3. Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, and Hatzigeorgiou AG. miRGen 2.0: A database of microRNA genomic information and regulation. Nucleic Acids Res 38: D137-D141, 2010
4. Antonov AV, Dietmann S, Wong P, Lutter D, and Mewes HW. GeneSet2miRNA: Finding the signature of cooperative miRNA activities in the gene lists. Nucleic Acids Res 37: W323-W328, 2009
5. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, and Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100: 3889-3894, 2003
6. Babar IA, Czochor J, Steinmetz A, Weidhaas JB, Glazer PM, and Slack FJ. Inhibition of hypoxia-induced miR-155 radiosensitizes hypoxic lung cancer cells. Cancer Biol Ther 12: 908-914, 2011
7. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, and Bartel DP. The impact of microRNAs on protein output. Nature 455: 64-71, 2008
8. Bartel DP. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297, 2004
9. Bartel DP. MicroRNAs: Target recognition and regulatory functions. Cell 136: 215-233, 2009
10. Bartonicek N and Enright AJ. SylArray: A web server for automated detection of miRNA effects from expression Data. Bioinformatics 26: 2900-2901, 2010
11. Bazzini AA, Lee MT, and Giraldez AJ. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336: 233-237, 2012
12. Beitzinger M, Peters L, Zhu JY, Kremmer E, and Meister G. Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol 4: 76-84, 2007
13. Bertero T, Gastaldi C, Bourget-Ponzio I, Imbert V, Loubat A, Selva E, Busca R, Mari B, Hofman P, Barbry P, Meneguzzi G, Ponzio G, and Rezzonico R. miR-483-3p controls proliferation in wounded epithelial cells. FASEB J 25: 3092-3105, 2011
14. Bertero T, Gastaldi C, Bourget-Ponzio I, Mari B, Meneguzzi G, Barbry P, Ponzio G, and Rezzonico R. CDC25A targeting by miR-483-3p decreases CCND-CDK4/6 assembly and contributes to cell cycle arrest. Cell Death Differ 20: 800-811, 2013
15. Bertero T, Grosso S, Robbe-Sermesant K, Lebrigand K, Henaoui IS, Puissegur MP, Fourre S, Zaragosi LE, Mazure NM, Ponzio G, Cardinaud B, Barbry P, Rezzonico R, and Mari B. Seed-Milarity" confers to hsa-miR-210 and hsamiR-147b similar functional activity. PLoS One 7: E44919, 2012
16. Betel D, Wilson M, Gabow A, Marks DS, and Sander C. The microRNA.org resource: Targets and expression. Nucleic Acids Res 36: D149-D153, 2008
17. Biswas S, Roy S, Banerjee J, Hussain SR, Khanna S, Meenakshisundaram G, Kuppusamy P, Friedman A, and Sen CK. Hypoxia inducible microRNA 210 attenuates keratinocyte proliferation and impairs closure in a murine model of ischemic wounds. Proc Natl Acad Sci U S A 107: 6976-6981, 2010
18. Blais JD, Addison CL, Edge R, Falls T, Zhao H, Wary K, Koumenis C, Harding HP, Ron D, Holcik M, and Bell JC. Perk-dependent translational regulation promotes tumor cell adaptation and angiogenesis in response to hypoxic stress. Mol Cell Biol 26: 9517-9532, 2006
19. Blais JD, Filipenko V, Bi M, Harding HP, Ron D, Koumenis C, Wouters BG, and Bell JC. Activating transcription factor 4 is translationally regulated by hypoxic stress. Mol Cell Biol 24: 7469-7482, 2004
20. Bracken CP, Gregory PA, Kolesnikoff N, Bert AG, Wang J, Shannon MF, and Goodall GJ. A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res 68: 7846-7854, 2008
21. Braunstein S, Karpisheva K, Pola C, Goldberg J, Hochman T, Yee H, Cangiarella J, Arju R, Formenti SC, and Schneider RJ. A hypoxia-controlled cap-dependent to cap-independent translation switch in breast cancer. Mol Cell 28: 501-512, 2007
22. Brennecke J, Stark A, Russell RB, and Cohen SM. Principles of microRNA-Target recognition. PLoS Biol 3: E85, 2005
23. Brest P, Lassalle S, Hofman V, Bordone O, Gavric-Tanga V, Bonnetaud C, Moreilhon C, Rios G, Santini J, Barbry P, Svanborg C, Mograbi B, Mari B, and Hofman P. MiR-129-5p is required for histone deacetylase inhibitor-induced cell death in thyroid cancer cells. Endocr Relat Cancer 18: 711-719, 2011
24. Brodersen P and Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10: 141-148, 2009
25. Brugarolas J, Lei K, Hurley RL, Manning BD, Reiling JH, Hafen E, Witters LA, Ellisen LW, and Kaelin WG, Jr. Regulation of mTOR function in response to hypoxia by REDD1 and the TSC1/TSC2 tumor suppressor complex. Genes Dev 18: 2893-2904, 2004
26. Bruning U, Cerone L, Neufeld Z, Fitzpatrick SF, Cheong A, Scholz CC, Simpson DA, Leonard MO, Tambuwala MM, Cummins EP, and Taylor CT. MicroRNA-155 promotes resolution of hypoxia-inducible factor 1alpha activity during prolonged hypoxia. Mol Cell Biol 31: 4087-4096, 2011
27. Buffa FM, Camps C, Winchester L, Snell CE, Gee HE, Sheldon H, Taylor M, Harris AL, and Ragoussis J. micro-RNA-Associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer. Cancer Res 71: 5635-5645, 2011
28. Cascio S, D'Andrea A, Ferla R, Surmacz E, Gulotta E, Amodeo V, Bazan V, Gebbia N, and Russo A. miR-20b modulates VEGF expression by targeting HIF-1 alpha and STAT3 in MCF-7 breast cancer cells. J Cell Physiol 224: 242-249, 2010
29. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, and Bozzoni I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147: 358-369, 2011
30. Chan SY and Loscalzo J. MicroRNA-210: A unique and pleiotropic hypoxamir. Cell Cycle 9: 1072-1083, 2010
31. Chan SY, Zhang YY, Hemann C, Mahoney CE, Zweier JL, and Loscalzo J. MicroRNA-210 controls mitochondrial metabolism during hypoxia by repressing the iron-sulfur cluster assembly proteins ISCU1/2. Cell Metab 10: 273-284, 2009
32. Chan YC, Banerjee J, Choi SY, and Sen CK. miR-210: The master hypoxamir. Microcirculation 19: 215-223, 2012
33. Chen Z, Lai TC, Jan YH, Lin FM, Wang WC, Xiao H, Wang YT, Sun W, Cui X, Li YS, Fang T, Zhao H, Padmanabhan C, Sun R, Wang DL, Jin H, Chau GY, Huang HD, Hsiao M, and Shyy JY. Hypoxia-responsive miRNAs target argonaute 1 to promote angiogenesis. J Clin Invest 123: 1057-1067, 2013
34. Chen Z, Li Y, Zhang H, Huang P, and Luthra R. Hypoxiaregulated microRNA-210 modulates mitochondrial function and decreases ISCU and COX10 expression. Oncogene 29: 4362-4368, 2010
35. Chi SW, Hannon GJ, and Darnell RB. An alternative mode of microRNA target recognition. Nat Struct Mol Biol 19: 321-327, 2012
36. Chi SW, Zang JB, Mele A, and Darnell RB. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486, 2009
37. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I, Muller RU, Straka E, Su L, Burki EA, Crowell RE, Patel R, Kulkarni T, Homer R, Zelterman D, Kidd KK, Zhu Y, Christiani DC, Belinsky SA, Slack FJ, and Weidhaas JB. A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk. Cancer Res 68: 8535-8540, 2008
38. Chio CC, Lin JW, Cheng HA, Chiu WT, Wang YH, Wang JJ, HsingCH, andChenRM. MicroRNA-210 targets antiapoptotic Bcl-2 expression and mediates hypoxia-induced apoptosis of neuroblastoma cells. Arch Toxicol 87: 459-468, 2013
39. Cho S, Jang I, Jun Y, Yoon S, Ko M, Kwon Y, Choi I, Chang H, Ryu D, Lee B, Kim VN, Kim W, and Lee S. MiRGator v3.0: A microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucleic Acids Res 41: D252-D257, 2013
40. Choi WY, Giraldez AJ, and Schier AF. Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430. Science 318: 271-274, 2007
41. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, and Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819-823, 2013
42. Crosby ME, Kulshreshtha R, Ivan M, and Glazer PM. MicroRNA regulation of DNA repair gene expression in hypoxic stress. Cancer Res 69: 1221-1229, 2009
43. Ding Y, Chan CY, and Lawrence CE. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32: W135-W141, 2004
44. Doench JG and Sharp PA. Specificity of microRNA target selection in translational repression. Genes Dev 18: 504-511, 2004
45. Dorsett Y, McBride KM, Jankovic M, Gazumyan A, Thai TH, Robbiani DF, Di Virgilio M, San-Martin BR, Heidkamp G, Schwickert TA, Eisenreich T, Rajewsky K, and Nussenzweig MC. MicroRNA-155 suppresses activationinduced cytidine deaminase-mediated Myc-Igh translocation. Immunity 28: 630-638, 2008
46. Dweep H, Sticht C, Pandey P, and Gretz N. miRWalk- database: Prediction of possible miRNA binding sites by 'walking' the genes of three genomes. J Biomed Inform 44: 839-847, 2011
47. Easow G, Teleman AA, and Cohen SM. Isolation of microRNA targets by miRNP immunopurification. RNA 13: 1198-1204, 2007
48. Ebert MS, Neilson JR, and Sharp PA. MicroRNA sponges: Competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4: 721-726, 2007
49. Ebert MS and Sharp PA. Roles for microRNAs in conferring robustness to biological processes. Cell 149: 515-524, 2012
50. Ebner OA and Selbach M. Whole cell proteome regulation by microRNAs captured in a pulsed SILAC mass spectrometry approach. Methods Mol Biol 725: 315-331, 2011
51. Eichner LJ, Perry MC, Dufour CR, Bertos N, Park M, St-Pierre J, and Giguere V. miR-378(.) mediates metabolic shift in breast cancer cells via the PGC-1beta/ERRgamma transcriptional pathway. Cell Metab 12: 352-361, 2010
52. Enright AJ, John B, Gaul U, Tuschl T, Sander C, and Marks DS. MicroRNA targets in Drosophila. Genome Biol 5: R1, 2003
53. Eulalio A, Tritschler F, and Izaurralde E. The GW182 protein family in animal cells: New insights into domains required for miRNA-mediated gene silencing. RNA 15: 1433-1442, 2009
54. Fang Z and Rajewsky N. The impact of miRNA target sites in coding sequences and in 3¢UTRs. PLoS One 6: E18067, 2011
55. Fasanaro P, D"Alessandra Y, Di Stefano V, Melchionna R, Romani S, Pompilio G, Capogrossi MC, and Martelli F. MicroRNA-210 modulates endothelial cell response to hypoxia and inhibits the receptor tyrosine kinase ligand Ephrin-A3. J Biol Chem 283: 15878-15883, 2008
56. Fasanaro P, Greco S, Lorenzi M, Pescatori M, Brioschi M, Kulshreshtha R, Banfi C, Stubbs A, Calin GA, Ivan M, Capogrossi MC, and Martelli F. An integrated approach for experimental target identification of hypoxia-induced miR-210. J Biol Chem 284: 35134-35143, 2009
57. Fasanaro P, Romani S, Voellenkle C, Maimone B, Capogrossi MC, and Martelli F. ROD1 is a seedless target gene of hypoxia-induced miR-210. PLoS One 7: E44651, 2012
58. Favaro E, Ramachandran A, McCormick R, Gee H, Blancher C, Crosby M, Devlin C, Blick C, Buffa F, Li JL, Vojnovic B, Pires das Neves R, Glazer P, Iborra F, Ivan M, Ragoussis J, and Harris AL. MicroRNA-210 regulates mitochondrial free radical response to hypoxia and krebs cycle in cancer cells by targeting iron sulfur cluster protein ISCU. PLoS One 5: E10345, 2010
59. Fazi F, Rosa A, Fatica A, Gelmetti V, De Marchis ML, Nervi C, and Bozzoni I. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell 123: 819-831, 2005
60. Filipowicz W, Bhattacharyya SN, and Sonenberg N. Mechanisms of post-Transcriptional regulation by microRNAs: Are the answers in sight?. Nat Rev Genet 9: 102-114, 2008
61. Gaidatzis D, van Nimwegen E, Hausser J, and Zavolan M. Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinform 8: 69, 2007
62. Galban S, Fan J, Martindale JL, Cheadle C, Hoffman B, Woods MP, Temeles G, Brieger J, Decker J, and Gorospe M. von Hippel-Lindau protein-mediated repression of tumor necrosis factor alpha translation revealed through use of cDNA arrays. Mol Cell Biol 23: 2316-2328, 2003
63. Garcia DM, Baek D, Shin C, Bell GW, Grimson A, and Bartel DP. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18: 1139-1146, 2011
64. Gennarino VA, Sardiello M, Mutarelli M, Dharmalingam G, Maselli V, Lago G, and Banfi S. HOCTAR database: A unique resource for microRNA target prediction. Gene 480: 51-58, 2011
65. Ghosh G, Subramanian IV, Adhikari N, Zhang X, Joshi HP, Basi D, Chandrashekhar YS, Hall JL, Roy S, Zeng Y, and Ramakrishnan S. Hypoxia-induced microRNA-424 expression in human endothelial cells regulates HIF-Alpha isoforms and promotes angiogenesis. J Clin Invest 120: 4141-4154, 2010
66. Giannakakis A, Sandaltzopoulos R, Greshock J, Liang S, Huang J, Hasegawa K, Li C, O"Brien-Jenkins A, Katsaros D, Weber BL, Simon C, Coukos G, and Zhang L. miR-210 links hypoxia with cell cycle regulation and is deleted in human epithelial ovarian cancer. Cancer Biol Ther 7: 255-264, 2008
67. Glorian V, Maillot G, Poles S, Iacovoni JS, Favre G, and Vagner S. 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 Differ 18: 1692-1701, 2011
68. Gorospe M, Tominaga K, Wu X, Fahling M, and Ivan M. Post-Transcriptional control of the hypoxic response by RNA-binding proteins and microRNAs. Front Mol Neurosci 4: 7, 2011
69. Griffiths-Jones S. miRBase: The microRNA sequence database. Methods Mol Biol 342: 129-138, 2006
70. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, and Enright AJ. miRBase: MicroRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34: D140-D144, 2006
71. Griffiths-Jones S, Saini HK, van Dongen S, and Enright AJ. miRBase: Tools for microRNA genomics. Nucleic Acids Res 36: D154-D158, 2008
72. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, and Bartel DP. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Mol Cell 27: 91-105, 2007
73. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, and Mello CC. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106: 23-34, 2001
74. Grosso S, Doyen J, Parks SK, Bertero T, Paye A, Cardinaud B, Gounon P, Lacas-Gervais S, Noel A, Pouyssegur J, Barbry P, Mazure NM, and Mari B. MiR-210 promotes a hypoxic phenotype and increases radioresistance in human lung cancer cell lines. Cell Death Dis 4: E544, 2013
75. Guo H, Ingolia NT, Weissman JS, and Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840, 2010
76. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jr., Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, and Tuschl T. Transcriptome-wide identification of RNAbinding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141, 2010
77. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, and Tuschl T. PAR-CliP-A method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp pii: 2034, 2010
78. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, and Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature 495: 384-388, 2013
79. He J, Wu J, Xu N, Xie W, Li M, Li J, Jiang Y, Yang BB, and Zhang Y. MiR-210 disturbs mitotic progression through regulating a group of mitosis-related genes. Nucleic Acids Res 41: 498-508, 2013
80. Hebert C, Norris K, Scheper MA, Nikitakis N, and Sauk JJ. High mobility group A2 is a target for miRNA-98 in head and neck squamous cell carcinoma. Mol Cancer 6: 5, 2007
81. Helwak A, Kudla G, Dudnakova T, and Tollervey D. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153: 654-665, 2013
82. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, and Brown PO. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol 7: E1000238, 2009
83. Henze AT and Acker T. Feedback regulators of hypoxiainducible factors and their role in cancer biology. Cell Cycle 9: 2749-2763, 2010
84. Hobert O. miRNAs play a tune. Cell 131: 22-24, 2007
85. Holcik M and Sonenberg N. Translational control in stress and apoptosis. Nat Rev Mol Cell Biol 6: 318-327, 2005
86. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, and Huang HD. miRTarBase: A database curates experimentally validated microRNA-Target interactions. Nucleic Acids Res 39: D163-D169, 2011
87. Huang X, Ding L, Bennewith KL, Tong RT, Welford SM, Ang KK, Story M, Le QT, and Giaccia AJ. Hypoxia-inducible mir-210 regulates normoxic gene expression involved in tumor initiation. Mol Cell 35: 856-867, 2009
88. Hutvagner G and Zamore PD. A microRNA in a multipleturnover RNAi enzyme complex. Science 297: 2056-2060, 2002
89. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, and Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosomeprotected mRNA fragments. Nat Protoc 7: 1534-1550, 2012
90. Ingolia NT, Ghaemmaghami S, Newman JR, and Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223, 2009
91. Ishibashi O, Ohkuchi A, Ali MM, Kurashina R, Luo SS, Ishikawa T, Takizawa T, Hirashima C, Takahashi K, Migita M, Ishikawa G, Yoneyama K, Asakura H, Izumi A, Matsubara S, and Takeshita T. Hydroxysteroid (17-beta) dehydrogenase 1 is dysregulated by miR-210 and miR-518c that are aberrantly expressed in preeclamptic placentas: A novel marker for predicting preeclampsia. Hypertension 59: 265-273, 2012
92. Ivan M, Kondo K, Yang H, Kim W, Valiando J, Ohh M, Salic A, Asara JM, Lane WS, and Kaelin WG, Jr. HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: Implications for O2 sensing. Science 292: 464-468, 2001
93. Jaakkola P, Mole DR, Tian YM, Wilson MI, Gielbert J, Gaskell SJ, von Kriegsheim A, Hebestreit HF, Mukherji M, Schofield CJ, Maxwell PH, Pugh CW, and Ratcliffe PJ. Targeting of HIF-Alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292: 468-472, 2001
94. Jafarifar F, Yao P, Eswarappa SM, and Fox PL. Repression of VEGFA by CA-rich element-binding microRNAs is modulated by hnRNP L. EMBO J 30: 1324-1334, 2011
95. John B, Enright AJ, Aravin A, Tuschl T, Sander C, and Marks DS. Human MicroRNA targets. PLoS Biol 2: E363, 2004
96. Kaelin WG, Jr. and Ratcliffe PJ. Oxygen sensing by metazoans: The central role of the HIF hydroxylase pathway. Mol Cell 30: 393-402, 2008
97. Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, and Hannon GJ. A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A 104: 19291-19296, 2007
98. Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA, Krauthammer M, Halaban R, Provero P, Adams DJ, Tuveson DA, and Pandolfi PP. In vivo identification of tumorsuppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147: 382-395, 2011
99. Keane FK and Ratner ES. The KRAS-variant genetic test as a marker of increased risk of ovarian cancer. Rev Obstet Gynecol 3: 118-121, 2010
100. Kelly TJ, Souza AL, Clish CB, and Puigserver P. A hypoxiainduced positive feedback loop promotes hypoxia-inducible factor 1alpha stability through miR-210 suppression of glycerol-3-phosphate dehydrogenase 1-like. Mol Cell Biol 31: 2696-2706, 2011
101. Kertesz M, Iovino N, Unnerstall U, Gaul U, and Segal E. The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284, 2007
102. Khan AA, Betel D, Miller ML, Sander C, Leslie CS, and Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 27: 549-555, 2009
103. Khorshid M, Hausser J, Zavolan M, and van Nimwegen E. A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat Methods 10: 253-255, 2013
104. Kim HW, Haider HK, Jiang S, and Ashraf M. Ischemic preconditioning augments survival of stem cells via MIR-210 expression by targeting caspase-8 associated protein 2. J Biol Chem 284: 33161-33168, 2009
105. Kim HW, Mallick F, Durrani S, Ashraf M, Jiang S, and Haider KH. Concomitant activation of miR-107/PDCD10 and Hypoxamir-210/Casp8ap2 and their role in cytoprotection During ischemic preconditioning of stem cells. Antioxid Redox Signal 17: 1053-1065, 2012
106. Kim JH, Park SG, Song SY, Kim JK, and Sung JH. Reactive oxygen species-responsive miR-210 regulates proliferation and migration of adipose-derived stem cells via PTPN2. Cell Death Dis 4: E588, 2013
107. Kloosterman WP, Wienholds E, Ketting RF, and Plasterk RH. Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res 32: 6284-6291, 2004
108. Koritzinsky M, Magagnin MG, van Den Beucken T, Seigneuric R, Savelkouls K, Dostie J, Pyronnet S, Kaufman RJ, Weppler SA, Voncken JW, Lambin P, Koumenis C, Sonenberg N, and Wouters BG. Gene expression During acute and prolonged hypoxia is regulated by distinct mechanisms of translational control. EMBO J 25: 1114-1125, 2006
109. Koritzinsky M and Wouters BG. Hypoxia and regulation of messenger RNA translation. Methods Enzymol 435: 247-273, 2007
110. Kozomara A and Griffiths-Jones S. miRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157, 2011
111. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, and Rajewsky N. Combinatorial microRNA target predictions. Nat Genet 37: 495-500, 2005
112. Krutzfeldt J, Kuwajima S, Braich R, Rajeev KG, Pena J, Tuschl T, Manoharan M, and Stoffel M. Specificity, duplex degradation and subcellular localization of antagomirs. Nucleic Acids Res 35: 2885-2892, 2007
113. Kuhn DE, Martin MM, Feldman DS, Terry AV, Jr., Nuovo GJ, and Elton TS. Experimental validation of miRNA targets. Methods 44: 47-54, 2008
114. Kulshreshtha R, Ferracin M, Wojcik SE, Garzon R, Alder H, Agosto-Perez FJ, Davuluri R, Liu CG, Croce CM, Negrini M, Calin GA, and Ivan M. A microRNA signature of hypoxia. Mol Cell Biol 27: 1859-1867, 2007
115. Laczny C, Leidinger P, Haas J, Ludwig N, Backes C, Gerasch A, Kaufmann M, Vogel B, Katus HA, Meder B, Stahler C, Meese E, Lenhof HP, and Keller A. miRTrail-A comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in Diseases. BMC Bioinform 13: 36, 2012
116. Laloo B, Maurel M, Jalvy-Delvaille S, Sagliocco F, and Grosset CF. Analysis of post-Transcriptional regulation using the FunREG method. Biochem Soc Trans 38: 1608-1614, 2010
117. Le Brigand K, Robbe-Sermesant K, Mari B, and Barbry P. MiRonTop: Mining microRNAs targets across large scale gene expression studies. Bioinformatics 26: 3131-3132, 2010
118. Lee DW, Futami M, Carroll M, Feng Y, Wang Z, Fernandez M, Whichard Z, Chen Y, Kornblau S, Shpall EJ, Bueso-Ramos CE, and Corey SJ. Loss of SHIP-1 protein expression in high-risk myelodysplastic syndromes is associated with miR-210 and miR-155. Oncogene 31: 4085-4094, 2012
119. Lee RC, Feinbaum RL, and Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854, 1993
120. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, and Kim VN. The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419, 2003
121. Lei Z, Li B, Yang Z, Fang H, Zhang GM, Feng ZH, and Huang B. Regulation of HIF-1alpha and VEGF by miR-20b tunes tumor cells to adapt to the alteration of oxygen concentration. PLoS One 4: E7629, 2009
122. Lewis BP, Burge CB, and Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20, 2005
123. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, and Burge CB. Prediction of mammalian microRNA targets. Cell 115: 787-798, 2003
124. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, and Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773, 2005
125. Lino Cardenas CL, Henaoui IS, Courcot E, Roderburg C, Cauffiez C, Aubert S, Copin MC, Wallaert B, Glowacki F, Dewaeles E, Milosevic J, Maurizio J, Tedrow J, Marcet B, Lo-Guidice JM, Kaminski N, Barbry P, Luedde T, Perrais M, Mari B, and Pottier N. miR-199a-5p is upregulated during fibrogenic response to tissue injury and mediates TGFbeta-induced lung fibroblast activation by targeting caveolin-1. PLoS Genet 9: E1003291, 2013
126. Liu C, Mallick B, Long D, Rennie WA, Wolenc A, Carmack CS, and Ding Y. CLIP-based prediction of mammalian microRNA binding sites. Nucleic Acids Res 41: E138, 2013
127. Liu L, Cash TP, Jones RG, Keith B, Thompson CB, and Simon MC. Hypoxia-induced energy stress regulates mRNA translation and cell growth. Mol Cell 21: 521-531, 2006
128. Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, and Rudensky AY. Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol Cell 48: 760-770, 2012
129. Long D, Chan CY, and Ding Y. Analysis of microRNAtarget interactions by a target structure based hybridization model. Pac Symp Biocomput 64-74, 2008
130. Long D, Lee R, Williams P, Chan CY, Ambros V, and Ding Y. Potent effect of target structure on microRNA function. Nat Struct Mol Biol 14: 287-294, 2007
131. Lytle JR, Yario TA, and Steitz JA. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5¢ UTR as in the 3¢ UTR. Proc Natl Acad Sci U S A 104: 9667-9672, 2007
132. Majmundar AJ, Wong WJ, and Simon MC. Hypoxiainducible factors and the response to hypoxic stress. Mol Cell 40: 294-309, 2010
133. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, and Church GM. RNA-guided human genome engineering via Cas9. Science 339: 823-826, 2013
134. Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, and Hatzigeorgiou AG. Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinform 10: 295, 2009
135. Marcet B, Chevalier B, Luxardi G, Coraux C, Zaragosi LE, Cibois M, Robbe-Sermesant K, Jolly T, Cardinaud B, Moreilhon C, Giovannini-Chami L, Nawrocki-Raby B, Birembaut P, Waldmann R, Kodjabachian L, and Barbry P. Control of vertebrate multiciliogenesis by miR-449 through direct repression of the Delta/Notch pathway. Nat Cell Biol 13: 693-699, 2011
136. Marin RM and Vanicek J. Efficient use of accessibility in microRNA target prediction. Nucleic Acids Res 39: 19-29, 2011
137. Marin RM and Vanicek J. Optimal use of conservation and accessibility filters in microRNA target prediction. PLoS One 7: E32208, 2012
138. Martin L and Chang HY. Uncovering the role of genomic "dark matter" in human Disease. J Clin Invest 122: 1589-1595, 2012
139. Martinez NJ and Walhout AJ. The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays 31: 435-445, 2009
140. Mazure NM, Brahimi-Horn MC, Berta MA, Benizri E, Bilton RL, Dayan F, Ginouves A, Berra E, and Pouyssegur J. HIF-1: Master and commander of the hypoxic world. A pharmacological approach to its regulation by siRNAs. Biochem Pharmacol 68: 971-980, 2004
141. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, and Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495: 333-338, 2013
142. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, Thomson AM, Lim B, and Rigoutsos I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217, 2006
143. Mizuno Y, Tokuzawa Y, Ninomiya Y, Yagi K, Yatsuka-Kanesaki Y, Suda T, Fukuda T, Katagiri T, Kondoh Y, Amemiya T, Tashiro H, and Okazaki Y. miR-210 promotes osteoblastic differentiation through inhibition of AcvR1b. FEBS Lett 583: 2263-2268, 2009
144. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, and Dreyfuss G. miRNPs: A novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16: 720-728, 2002
145. Mullokandov G, Baccarini A, Ruzo A, Jayaprakash AD, Tung N, Israelow B, Evans MJ, Sachidanandam R, and Brown BD. High-Throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries. Nat Methods 9: 840-846, 2012
146. Naguibneva I, Ameyar-Zazoua M, Nonne N, Polesskaya A, Ait-Si-Ali S, Groisman R, Souidi M, Pritchard LL, and Harel-Bellan A. An LNA-based loss-of-function assay for micro-RNAs. Biomed Pharmacother 60: 633-638, 2006
147. Neal CS, Michael MZ, Rawlings LH, Van Der Hoek MB, and Gleadle JM. The VHL-dependent regulation of micro-RNAs in renal cancer. BMC Med 8: 64, 2010
148. Noman MZ, Buart S, Romero P, Ketari S, Janji B, Mari B, Mami-Chouaib F, and Chouaib S. Hypoxia-inducible miR-210 regulates the susceptibility of tumor cells to lysis by cytotoxic T cells. Cancer Res 72: 4629-4641, 2012
149. Orom UA, Kauppinen S, and Lund AH. LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene 372: 137-141, 2006
150. Orom UA and Lund AH. Experimental identification of microRNA targets. Gene 451: 1-5, 2010
151. Osella M, Bosia C, Cora D, and Caselle M. The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol 7: E1001101, 2011
152. Paranjape T, Heneghan H, Lindner R, Keane FK, Hoffman A, Hollestelle A, Dorairaj J, Geyda K, Pelletier C, Nallur S, Martens JW, Hooning MJ, Kerin M, Zelterman D, Zhu Y, Tuck D, Harris L, Miller N, Slack F, and Weidhaas J. A 3"-untranslated region KRAS variant and triple-negative breast cancer: A case-control and genetic analysis. Lancet Oncol 12: 377-386, 2011
153. Perez-Pinera P, Ousterout DG, and Gersbach CA. Advances in targeted genome editing. Curr Opin Chem Biol 16: 268-277, 2012
154. Pharoah PD, Palmieri RT, Ramus SJ, Gayther SA, Andrulis IL, Anton-Culver H, Antonenkova N, Antoniou AC, Goldgar D, Beattie MS, Beckmann MW, Birrer MJ, Bogdanova N, Bolton KL, Brewster W, Brooks-Wilson A, Brown R, Butzow R, Caldes T, Caligo MA, Campbell I, Chang-Claude J, Chen YA, Cook LS, Couch FJ, Cramer DW, Cunningham JM, Despierre E, Doherty JA, Dork T, Durst M, Eccles DM, Ekici AB, Easton D, Fasching PA, de Fazio A, Fenstermacher DA, Flanagan JM, Fridley BL, Friedman E, Gao B, Sinilnikova O, Gentry-Maharaj A, Godwin AK, Goode EL, Goodman MT, Gross J, Hansen TV, Harnett P, Rookus M, Heikkinen T, Hein R, Hogdall C, Hogdall E, Iversen ES, Jakubowska A, Johnatty SE, Karlan BY, Kauff ND, Kaye SB, Chenevix-Trench G, Kelemen LE, Kiemeney LA, Kjaer SK, Lambrechts D, Lapolla JP, Lazaro C, Le ND, Leminen A, Leunen K, Levine DA, Lu Y, Lundvall L, Macgregor S, Marees T, Massuger LF, McLaughlin JR, Menon U, Montagna M, Moysich KB, Narod SA, Nathanson KL, Nedergaard L, Ness RB, Nevanlinna H, Nickels S, Osorio A, P ul J, Pearce CL, Phelan CM, Pike MC, Radice P, Rossing MA, Schildkraut JM, Sellers TA, Singer CF, Song H, Stram DO, Sutphen R, Lindblom A, Terry KL, Tsai YY, van Altena AM, Vergote I, Vierkant RA, Vitonis AF, Walsh C, Wang-Gohrke S, Wappenschmidt B, Wu AH, Ziogas A, Berchuck A, and Risch HA. The role of KRAS rs61764370 in invasive epithelial ovarian cancer: Implications for clinical testing. Clin Cancer Res 17: 3742-3750, 2011
155. Pocock R. Invited review: Decoding the microRNA response to hypoxia. Pflugers Arch 461: 307-315, 2011
156. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, and Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465: 1033-1038, 2010
157. Pottier N, Maurin T, Chevalier B, Puissegur MP, Lebrigand K, Robbe-Sermesant K, Bertero T, Lino Cardenas CL, Courcot E, Rios G, Fourre S, Lo-Guidice JM, Marcet B, Cardinaud B, Barbry P, and Mari B. Identification of keratinocyte growth factor as a target of microRNA-155 in lung fibroblasts: Implication in epithelial-mesenchymal interactions. PLoS One 4: E6718, 2009
158. Puissegur MP, Eichner R, Quelen C, Coyaud E, Mari B, Lebrigand K, Broccardo C, Nguyen-Khac F, Bousquet M, and Brousset P. B-cell regulator of immunoglobulin heavy chain transcription (Bright)/ARID3a is a direct target of the oncomir microRNA-125b in progenitor B-cells. Leukemia 26: 2224-2232, 2012
159. Puissegur MP, Mazure NM, Bertero T, Pradelli L, Grosso S, Robbe-Sermesant K, Maurin T, Lebrigand K, Cardinaud B, Hofman V, Fourre S, Magnone V, Ricci JE, Pouyssegur J, Gounon P, Hofman P, Barbry P, and Mari B. miR-210 is overexpressed in late stages of lung cancer and mediates mitochondrial alterations associated with modulation of HIF-1 activity. Cell Death Differ 18: 465-478, 2011
160. Pulkkinen K, Malm T, Turunen M, Koistinaho J, and Yla-Herttuala S. Hypoxia induces microRNA miR-210 in vitro and in vivo ephrin-A3 and neuronal pentraxin 1 are potentially regulated by miR-210. FEBS Lett 582: 2397-2401, 2008
161. Rajewsky N and Socci ND. Computational identification of microRNA targets. Dev Biol 267: 529-535, 2004
162. Rane S, He M, Sayed D, Vashistha H,Malhotra A, Sadoshima J, Vatner DE, Vatner SF, and AbdellatifM. Downregulation of miR-199a derepresses hypoxia-inducible factor-1alpha and Sirtuin 1 and recapitulates hypoxia preconditioning in cardiac myocytes. Circ Res 104: 879-886, 2009
163. Ratner E, Lu L, Boeke M, Barnett R, Nallur S, Chin LJ, Pelletier C, Blitzblau R, Tassi R, Paranjape T, Hui P, Godwin AK, Yu H, Risch H, Rutherford T, Schwartz P, Santin A, Matloff E, Zelterman D, Slack FJ, and Weidhaas JB. A KRAS-variant in ovarian cancer acts as a genetic marker of cancer risk. Cancer Res 70: 6509-6515, 2010
164. Rehmsmeier M, Steffen P, Hochsmann M, and Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517, 2004
165. Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P, Soond DR, van Dongen S, Grocock RJ, Das PP, Miska EA, Vetrie D, Okkenhaug K, Enright AJ, Dougan G, Turner M, and Bradley A. Requirement of bic/microRNA-155 for normal immune function. Science 316: 608-611, 2007
166. Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, and Romualdi C. MAGIA, aweb-based tool formiRNA and genes integrated analysis. Nucleic Acids Res 38: W352-W359, 2010
167. Sarkar J, Gou D, Turaka P, Viktorova E, Ramchandran R, and Raj JU. MicroRNA-21 plays a role in hypoxia-mediated pulmonary artery smooth muscle cell proliferation and migration. Am J Physiol Lung Cell Mol Physiol 299: L861-L871, 2010
168. Schramedei K, Morbt N, Pfeifer G, Lauter J, Rosolowski M, Tomm JM, von Bergen M, Horn F, and Brocke-Heidrich K. MicroRNA-21 targets tumor suppressor genes ANP32A and SMARCA4. Oncogene 30: 2975-2985, 2011
169. Seitz H. Redefining microRNA targets. Curr Biol 19: 870-873, 2009
170. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, and Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63, 2008
171. Sethupathy P, Megraw M, and Hatzigeorgiou AG. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 3: 881-886, 2006
172. Shin C, Nam JW, Farh KK, Chiang HR, Shkumatava A, and Bartel DP. Expanding the microRNA targeting code: Functional sites with centered pairing. Mol Cell 38: 789-802, 2010
173. Shirdel EA, Xie W, Mak TW, and Jurisica I. NAViGaTing the micronome-using multiple microRNA prediction Databases to identify signalling pathway-Associated micro-RNAs. PLoS One 6: E17429, 2011
174. Song XW, Li Q, Lin L, Wang XC, Li DF, Wang GK, Ren AJ, Wang YR, Qin YW, Yuan WJ, and Jing Q. MicroRNAs are dynamically regulated in hypertrophic hearts, and miR-199a is essential for the maintenance of cell size in cardiomyocytes. J Cell Physiol 225: 437-443, 2010
175. Spriggs KA, Stoneley M, Bushell M, and Willis AE. Reprogramming of translation following cell stress allows IRESmediated translation to predominate. Biol Cell 100: 27-38, 2008
176. Sturm M, Hackenberg M, Langenberger D, and Frishman D. TargetSpy: A supervised machine learning approach for microRNA target prediction. BMC Bioinform 11: 292, 2010
177. Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, and Califano A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147: 370-381, 2011
178. Taguchi A, Yanagisawa K, Tanaka M, Cao K, Matsuyama Y, Goto H, and Takahashi T. Identification of hypoxiainducible factor-1 alpha as a novel target for miR-17-92 microRNA cluster. Cancer Res 68: 5540-5545, 2008
179. Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, Karreth F, Poliseno L, Provero P, Di Cunto F, Lieberman J, Rigoutsos I, and Pandolfi PP. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147: 344-357, 2011
180. Teng G, Hakimpour P, Landgraf P, Rice A, Tuschl T, Casellas R, and Papavasiliou FN. MicroRNA-155 is a negative regulator of activation-induced cytidine deaminase. Immunity 28: 621-629, 2008
181. Thai TH, Calado DP, Casola S, Ansel KM, Xiao C, Xue Y, Murphy A, Frendewey D, Valenzuela D, Kutok JL, Schmidt-Supprian M, Rajewsky N, Yancopoulos G, Rao A, and Rajewsky K. Regulation of the germinal center response by microRNA-155. Science 316: 604-608, 2007
182. Thomas JD and Johannes GJ. Identification of mRNAs that continue to associate with polysomes during hypoxia. RNA 13: 1116-1131, 2007
183. Thomson DW, Bracken CP, and Goodall GJ. Experimental strategies for microRNA target identification. Nucleic Acids Res 39: 6845-6853, 2011
184. Uniacke J, Holterman CE, Lachance G, Franovic A, Jacob MD, Fabian MR, Payette J, Holcik M, Pause A, and Lee S. An oxygen-regulated switch in the protein synthesis machinery. Nature 486: 126-129, 2012
185. Van Den Bergh G and Arckens L. Fluorescent two-dimensional difference gel electrophoresis unveils the potential of gel-based proteomics. Curr Opin Biotechnol 15: 38-43, 2004
186. van Dongen S, Abreu-Goodger C, and Enright AJ. Detecting microRNA binding and siRNA off-Target effects from expression Data. Nat Methods 5: 1023-1025, 2008
187. Vejnar CE and Zdobnov EM. MiRmap: Comprehensive prediction of microRNA target repression strength. Nucleic Acids Res 40: 11673-11683, 2012
188. Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, and Hatzigeorgiou AG. TarBase 6.0: Capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 40: D222-D229, 2012
189. Vigorito E, Perks KL, Abreu-Goodger C, Bunting S, Xiang Z, Kohlhaas S, Das PP, Miska EA, Rodriguez A, Bradley A, Smith KG, Rada C, Enright AJ, Toellner KM, Maclennan IC, and Turner M. microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity 27: 847-859, 2007
190. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, Prueitt RL, Yanaihara N, Lanza G, Scarpa A, Vecchione A, Negrini M, Harris CC, and Croce CM. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103: 2257-2261, 2006
191. Wang X. miRDB: A microRNA target prediction and functional annotation Database with a wiki interface. RNA 14: 1012-1017, 2008
192. Wang X and El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24: 325-332, 2008
193. Wightman B, Ha I, and Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862, 1993
194. Wouters BG, van Den Beucken T, Magagnin MG, Koritzinsky M, Fels D, and Koumenis C. Control of the hypoxic response through regulation of mRNA translation. Semin Cell Dev Biol 16: 487-501, 2005
195. Xiao F, Zuo Z, Cai G, Kang S, Gao X, and Li T. miRecords: An integrated resource for microRNA-Target interactions. Nucleic Acids Res 37: D105-D110, 2009
196. Xiong Q, Zhong Q, Zhang J, Yang M, Li C, Zheng P, Bi LJ, and Ge F. Identification of novel miR-21 target proteins in multiple myeloma cells by quantitative proteomics. J Proteome Res 11: 2078-2090, 2012
197. Yan GR, Xu SH, Tan ZL, Liu L, and He QY. Global identification of miR-373-regulated genes in breast cancer by quantitative proteomics. Proteomics 11: 912-920, 2011
198. Yang D, Sun Y, Hu L, Zheng H, Ji P, Pecot CV, Zhao Y, Reynolds S, Cheng H, Rupaimoole R, Cogdell D, Nykter M, Broaddus R, Rodriguez-Aguayo C, Lopez-Berestein G, Liu J, Shmulevich I, Sood AK, Chen K, and Zhang W. Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer. Cancer Cell 23: 186-199, 2013
199. Yang JH, Li JH, Shao P, Zhou H, Chen YQ, and Qu LH. starBase: A database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39: D202-D209, 2011
200. Yang W, Sun T, Cao J, Liu F, Tian Y, and Zhu W. Downregulation of miR-210 expression inhibits proliferation, induces apoptosis and enhances radiosensitivity in hypoxic human hepatoma cells in vitro. ExpCellRes 318: 944-954, 2012
201. Ying Q, Liang L, Guo W, Zha R, Tian Q, Huang S, Yao J, Ding J, Bao M, Ge C, Yao M, Li J, and He X. Hypoxiainducible microRNA-210 augments the metastatic potential of tumor cells by targeting vacuole membrane protein 1 in hepatocellular carcinoma. Hepatology 54: 2064-2075, 2011
202. Yoo AS and Greenwald I. LIN-12/Notch activation leads to microRNA-mediated down-regulation of Vav in C. elegans. Science 310: 1330-1333, 2005
203. Yoshioka Y, Kosaka N, Ochiya T, and Kato T. Micromanaging iron homeostasis: Hypoxia-inducible micro-RNA-210 suppresses iron homeostasis-related proteins. J Biol Chem 287: 34110-34119, 2012
204. Young RM, Wang SJ, Gordan JD, Ji X, Liebhaber SA, and Simon MC. Hypoxia-mediated selective mRNA translation by an internal ribosome entry site-independent mechanism. J Biol Chem 283: 16309-16319, 2008
205. Zhang Z, Sun H, Dai H, Walsh RM, Imakura M, Schelter J, Burchard J, DaiX,Chang AN,DiazRL, Marszalek JR, Bartz SR, Carleton M, Cleary MA, Linsley PS, and Grandori C. MicroRNA miR-210 modulates cellular response to hypoxia through the MYC antagonist MNT. Cell Cycle 8: 2756-2768, 2009
206. Zhou L, Chen J, Li Z, Li X, Hu X, Huang Y, Zhao X, Liang C, Wang Y, Sun L, Shi M, Xu X, Shen F, Chen M, Han Z, Peng Z, Zhai Q, Zhang Z, Yang R, Ye J, Guan Z, Yang H, Gui Y, Wang J, Cai Z, and Zhang X. Integrated profiling of micro-RNAs and mRNAs: MicroRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. PLoS One 5: E15224, 2010
207. Zhou P, Xu W, Peng X, Luo Z, Xing Q, Chen X, Hou C, Liang W, Zhou J, Wu X, Songyang Z, and Jiang S. Largescale screens of miRNA-mRNA interactions unveiled that the 3¢UTR of a gene is targeted by multiple miRNAs. PLoS One 8: E68204, 2013
208. Zhu S, Si ML, Wu H, and Mo YY. MicroRNA-21 targets the tumor suppressor gene tropomyosin 1 (TPM1). J Biol Chem 282: 14328-14336, 2007