MicroRNA Screening and the Quest for Biologically Relevant Targets

Journal of Biomolecular Screening

Volumn 20, Issue 8, 2015, Pages 1003-1017

  Eulalio, Ana ^a   Mano, Miguel ^b,c  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^c UNIVERSITY OF COIMBRA   (Portugal)

Author keywords

high throughput screening; microRNA; miRNA screening; miRNA target identification

Indexed keywords

MICRORNA; MESSENGER RNA;

ARTICLE; BIBLIOGRAPHIC DATABASE; BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; CELL SCREENING; GENE EXPRESSION; GENE FUNCTION; HIGH THROUGHPUT SCREENING; HUMAN; IMMUNOPRECIPITATION; INTERACTIONS WITH RNA; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; ANIMAL; BIOLOGY; CELL LINE; GENETICS; GENOMICS; PROCEDURES; REPRODUCIBILITY; RNA INTERFERENCE;

EUKARYOTA;

ANIMALS; CELL LINE; COMPUTATIONAL BIOLOGY; GENOMICS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MICRORNAS; REPRODUCIBILITY OF RESULTS; RNA INTERFERENCE; RNA, MESSENGER;

EID: 84939793658     PISSN: 10870571     EISSN: 1552454X     Source Type: Journal    
DOI: 10.1177/1087057115578837     Document Type: Article

References (124)

1. Bartel D. P., MicroRNAs: Target Recognition and Regulatory Functions. Cell. 2009, 136 (2), 215-233.
2. Huntzinger E., Izaurralde E., Gene Silencing by MicroRNAs: Contributions of Translational Repression and mRNA Decay. Nature Rev. Genet. 2011, 12 (2), 99-110.
3. Krol J., Loedige I., Filipowicz W., The Widespread Regulation of MicroRNA Biogenesis, Function and Decay. Nature Rev. Genet. 2010, 11 (9), 597-610.
4. Friedman R. C., Farh K. K., Burge C. B.,. Most Mammalian mRNAs Are Conserved Targets of MicroRNAs. Genome Res. 2009, 19 (1), 92-105.
5. Kedde M., Agami R., Interplay between MicroRNAs and RNA-Binding Proteins Determines Developmental Processes. Cell Cycle. 2008, 7 (7), 899-903.
6. Shenoy A., Blelloch R. H., Regulation of MicroRNA Function in Somatic Stem Cell Proliferation and Differentiation. Nature Rev. Molec. Cell Biol. 2014, 15 (9), 565-576.
7. Bueno M. J., Perez de, Castro I., Malumbres M., Control of Cell Proliferation Pathways by microRNAs. Cell Cycle. 2008, 7 (20), 3143-3148.
8. Jovanovic M., Hengartner M. O., miRNAs and Apoptosis: RNAs to Die For. Oncogene. 2006, 25 (46), 6176-6187.
9. Croce C. M., Causes and Consequences of MicroRNA Dysregulation in Cancer. Nature Rev. Genet. 2009, 10 (10), 704-714.
10. Liu N. K., Xu X. M., MicroRNA in Central Nervous System Trauma and Degenerative Disorders. Physiol. Genom. 2011, 43 (10), 571-580.
11. Small E. M., Olson E. N., Pervasive Roles of MicroRNAs in Cardiovascular Biology. Nature. 2011, 469 (7330), 336-342.
12. Kim Y. K., Wee G., Park J.,. TALEN-Based Knockout Library for Human MicroRNAs. Nature Struc. Molec. Biol. 2013, 20 (12), 1458-1464.
13. Serva A., Claas C., Starkuviene V., A Potential of MicroRNAs for High-Content Screening. J. Nucl. Acids. 2011, 2011, 870903.
14. Voorhoeve P. M., le Sage C., Schrier M.,. A Genetic Screen Implicates miRNA-372 and MiRNA-373 as Oncogenes in Testicular Germ Cell Tumors. Cell. 2006, 124 (6), 1169-1181.
15. le Sage C., Nagel R., Egan D. A.,. Regulation of the p27(Kip1) Tumor Suppressor by miR-221 and miR-222 Promotes Cancer Cell Proliferation. EMBO J. 2007, 26 (15), 3699-3708.
16. Huang Q., Gumireddy K., Schrier M.,. The MicroRNAs miR-373 and miR-520c Promote Tumour Invasion and Metastasis. Nature Cell Biol. 2008, 10 (2), 202-210.
17. Wu S., Huang S., Ding J.,. Multiple MicroRNAs Modulate p21Cip1/Waf1 Expression by Directly Targeting Its 3′ Untranslated Region. Oncogene. 2010, 29 (15), 2302-2308.
18. Borgdorff V., Lleonart M. E., Bishop C. L.,. Multiple MicroRNAs Rescue from Ras-Induced Senescence by Inhibiting p21(Waf1/Cip1). Oncogene. 2010, 29 (15), 2262-2271.
19. Izumiya M., Okamoto K., Tsuchiya N.,. Functional Screening Using a MicroRNA Virus Library and Microarrays: A New High-Throughput Assay to Identify Tumor-Suppressive MicroRNAs. Carcinogenesis. 2010, 31 (8), 1354-1359.
20. Lam L. T., Lu X., Zhang H.,. A MicroRNA Screen to Identify Modulators of Sensitivity to BCL2 Inhibitor ABT-263 (Navitoclax). Molec. Cancer Ther. 2010, 9 (11), 2943-2950.
21. Nakano H., Miyazawa T., Kinoshita K.,. Functional Screening Identifies a MicroRNA, miR-491 That Induces Apoptosis by Targeting Bcl-X(L) in Colorectal Cancer Cells. Intl. J. Cancer. 2010, 127 (5), 1072-1080.
22. Zhang H., Hao Y., Yang J.,. Genome-Wide Functional Screening of miR-23b as a Pleiotropic Modulator Suppressing Cancer Metastasis. Nature Comm. 2011, 2, 554.
23. Poell J. B., van Haastert R. J., de Gunst T.,. A Functional Screen Identifies Specific MicroRNAs Capable of Inhibiting Human Melanoma Cell Viability. PloS ONE. 2012, 7 (8), e43569.
24. Du L., Borkowski R., Zhao Z.,. A High-Throughput Screen Identifies miRNA Inhibitors Regulating Lung Cancer Cell Survival and Response to Paclitaxel. RNA Biol. 2013, 10 (11), 1700-1713.
25. Christensen L. L., Holm A., Rantala J.,. Functional Screening Identifies miRNAs Influencing Apoptosis and Proliferation in Colorectal Cancer. PloS ONE. 2014, 9 (6), e96767.
26. Leivonen S. K., Sahlberg K. K., Makela R.,. High-Throughput Screens Identify MicroRNAs Essential for HER2 Positive Breast Cancer Cell Growth. Molec. Oncol. 2014, 8 (1), 93-104.
27. Zha R., Guo W., Zhang Z.,. Genome-Wide Screening Identified That miR-134 Acts as a Metastasis Suppressor by Targeting Integrin beta1 in Hepatocellular Carcinoma. PloS ONE. 2014, 9 (2), e87665.
28. Ujihira T., Ikeda K., Suzuki T.,. MicroRNA-574-3p, Identified by MicroRNA Library-Based Functional Screening, Modulates Tamoxifen Response in Breast Cancer. Scien. Rep. 2015, 5, 7641.
29. Jentzsch C., Leierseder S., Loyer X.,. A Phenotypic Screen to Identify Hypertrophy-Modulating MicroRNAs in Primary Cardiomyocytes. J. Molec. Cell. Cardiol. 2012, 52 (1), 13-20.
30. Eulalio A., Mano M., Dal Ferro M.,. Functional Screening Identifies miRNAs Inducing Cardiac Regeneration. Nature. 2012, 492 (7429), 376-381.
31. Wahlquist C., Jeong D., Rojas-Munoz A.,. Inhibition of miR-25 Improves Cardiac Contractility in the Failing Heart. Nature. 2014, 508 (7497), 531-535.
32. Santhakumar D., Forster T., Laqtom N. N.,. Combined Agonist-Antagonist Genome-Wide Functional Screening Identifies Broadly Active Antiviral MicroRNAs. Proc. Natl. Acad. Sci. USA. 2010, 107 (31), 13830-13835.
33. Maudet C., Mano M., Sunkavalli U.,. Functional High-Throughput Screening Identifies the miR-15 MicroRNA Family as Cellular Restriction Factors for Salmonella Infection. Nature Comm. 2014, 5, 4718.
34. Keklikoglou I., Koerner C., Schmidt C.,. MicroRNA-520/373 Family Functions as a Tumor Suppressor in Estrogen Receptor Negative Breast Cancer by Targeting NF-kappaB and TGF-Beta Signaling Pathways. Oncogene. 2012, 31 (37), 4150-4163.
35. Ding J., Huang S., Wang Y.,. Genome-Wide Screening Reveals That miR-195 Targets the TNF-alpha/NF-kappaB Pathway by Down-Regulating IkappaB Kinase Alpha and TAB3 in Hepatocellular Carcinoma. Hepatology. 2013, 58 (2), 654-666.
36. Pfaff N., Fiedler J., Holzmann A.,. miRNA Screening Reveals a New miRNA Family Stimulating iPS Cell Generation via Regulation of Meox2. EMBO Rep. 2011, 12 (11), 1153-1159.
37. Colas A. R., McKeithan W. L., Cunningham T. J.,. Whole-Genome MicroRNA Screening Identifies let-7 and mir-18 as Regulators of Germ Layer Formation during Early Embryogenesis. Genes Devel. 2012, 26 (23), 2567-2579.
38. Judson R. L., Greve T. S., Parchem R. J.,. MicroRNA-Based Discovery of Barriers to Dedifferentiation of Fibroblasts to Pluripotent Stem Cells. Nature Struc. Molec. Biol. 2013, 20 (10), 1227-1235.
39. Kamat V., Paluru P., Myint M.,. MicroRNA Screen of Human Embryonic Stem Cell Differentiation Reveals miR-105 as an Enhancer of Megakaryopoiesis from Adult CD34+ Cells. Stem Cells. 2014, 32 (5), 1337-1346.
40. Nagel R., Clijsters L., Agami R., The miRNA-192/194 Cluster Regulates the Period Gene Family and the Circadian Clock. FEBS J. 2009, 276 (19), 5447-5455.
41. Whittaker R., Loy P. A., Sisman E.,. Identification of MicroRNAs That Control Lipid Droplet Formation and Growth in Hepatocytes via High-Content Screening. J. Biomolec. Screen. 2010, 15 (7), 798-805.
42. Fiedler J., Stohr A., Gupta S. K.,. Functional MicroRNA Library Screening Identifies the Hypoxamir miR-24 as a Potent Regulator of Smooth Muscle Cell Proliferation and Vascularization. Antioxid. Redox. Signal. 2014, 21 (8), 1167-1176.
43. Fischer S., Buck T., Wagner A.,. A Functional High-Content miRNA Screen Identifies miR-30 Family to Boost Recombinant Protein Production in CHO Cells. Biotechnology J. 2014, 9 (10), 1279-1292.
44. Calin G. A., Dumitru C. D., Shimizu M.,. Frequent Deletions and Down-Regulation of Micro-RNA Genes miR15 and miR16 at 13q14 in Chronic Lymphocytic Leukemia. Proc. Natl. Acad. Sci. USA. 2002, 99 (24), 15524-15529.
45. Pekarsky Y., Croce C. M., Role of miR-15/16 in CLL. Cell Death Diff. 2015, 22 (1), 6-11.
46. Brass A. L., Dykxhoorn D. M., Benita Y.,. Identification of Host Proteins Required for HIV Infection through a Functional Genomic Screen. Science. 2008, 319 (5865), 921-926.
47. Konig R., Zhou Y., Elleder D.,. Global Analysis of Host-Pathogen Interactions That Regulate Early-Stage HIV-1 Replication. Cell. 2008, 135 (1), 49-60.
48. Karlas A., Machuy N., Shin Y.,. Genome-Wide RNAi Screen Identifies Human Host Factors Crucial for Influenza Virus Replication. Nature. 2010, 463 (7282), 818-822.
49. Konig R., Stertz S., Zhou Y.,. Human Host Factors Required for Influenza Virus Replication. Nature. 2010, 463 (7282), 813-817.
50. Krishnan M. N., Ng A., Sukumaran B.,. RNA Interference Screen for Human Genes Associated with West Nile Virus Infection. Nature. 2008, 455 (7210), 242-245.
51. Agaisse H., Burrack L. S., Philips J. A.,. Genome-Wide RNAi Screen for Host Factors Required for Intracellular Bacterial Infection. Science. 2005, 309 (5738), 1248-1251.
52. Kumar D., Nath L., Kamal M. A.,. Genome-Wide Analysis of the Host Intracellular Network That Regulates Survival of. Mycobacterium tuberculosis. Cell. 2010, 140 (5), 731-743.
53. Misselwitz B., Dilling S., Vonaesch P.,. RNAi Screen of Salmonella Invasion Shows Role of COPI in Membrane Targeting of Cholesterol and Cdc42. Molec. Sys. Biol. 2011, 7, 474.
54. Eulalio A., Schulte L., Vogel J., The Mammalian MicroRNA Response to Bacterial Infections. RNA Biol. 2012, 9 (6), 742-750.
55. Staedel C., Darfeuille F., MicroRNAs and Bacterial Infection. Cell. Microbiol. 2013, 15 (9), 1496-1507.
56. Maudet C., Mano M., Eulalio A., MicroRNAs in the Interaction between Host and Bacterial Pathogens. FEBS Lett. 2014, 588 (22), 4140-4147.
57. Gangaraju V. K., Lin H., MicroRNAs: Key Regulators of Stem Cells. Nature Rev. Molec. Cell Biol. 2009, 10 (2), 116-125.
58. Ritchie W., Rasko J. E., Refining MicroRNA Target Predictions: Sorting the Wheat from the Chaff. Biochem. Biophys. Res. Comm. 2014, 445 (4), 780-784.
59. Peterson S. M., Thompson J. A., Ufkin M. L.,. Common Features of MicroRNA Target Prediction Tools. Frontiers Genet. 2014, 5, 23.
60. Miranda K. C., Huynh T., Tay Y.,. A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes. Cell. 2006, 126 (6), 1203-1217.
61. Dweep H., Sticht C., Pandey P.,. miRWalk-Database: Prediction of Possible miRNA Binding Sites by 'Walking' the Genes of Three Genomes. J. Biomed. Inform. 2011, 44 (5), 839-847.
62. Kertesz M., Iovino N., Unnerstall U.,. The Role of Site Accessibility in MicroRNA Target Recognition. Nature Genet. 2007, 39 (10), 1278-1284.
63. Paraskevopoulou M. D., Georgakilas G., Kostoulas N.,. DIANA-MicroT Web Server v5.0: Service Integration into miRNA Functional Analysis Workflows. Nucl. Acids Res. 2013, 41 (Web Server issue), W169-W173.
64. Reczko M., Maragkakis M., Alexiou P.,. Functional MicroRNA Targets in Protein Coding Sequences. Bioinformatics. 2012, 28 (6), 771-776.
65. Betel D., Wilson M., Gabow A.,. The microRNA.org Resource: Targets and Expression. Nucl. Acids Res. 2008, 36 (Database issue), D149-D153.
66. Wang X., miRDB: A MicroRNA Target Prediction and Functional Annotation Database with a Wiki Interface. RNA. 2008, 14 (6), 1012-1017.
67. Wang X., El Naqa I. M., Prediction of Both Conserved and Nonconserved MicroRNA Targets in Animals. Bioinformatics. 2008, 24 (3), 325-332.
68. Krek A., Grun D., Poy M. N.,. Combinatorial MicroRNA Target Predictions. Nature Genet. 2005, 37 (5), 495-500.
69. Rehmsmeier M., Steffen P., Hochsmann M.,. Fast and Effective Prediction of MicroRNA/Target Duplexes. RNA. 2004, 10 (10), 1507-1517.
70. Garcia D. M., Baek D., Shin C.,. Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other MicroRNAs. Nature Struc. Molec. Biol. 2011, 18 (10), 1139-1146.
71. Grimson A., Farh K. K., Johnston W. K.,. MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing. Molec. Cell. 2007, 27 (1), 91-105.
72. Lewis B. P., Burge C. B., Bartel D. P., Conserved Seed Pairing, Often Flanked by Adenosines, Indicates That Thousands of Human Genes Are MicroRNA Targets. Cell. 2005, 120 (1), 15-20.
73. Rusinov V., Baev V., Minkov I. N.,. MicroInspector: A Web Tool for Detection of miRNA Binding Sites in an RNA Sequence. Nucl. Acids Res. 2005, 33 (Web Server issue), W696-W700.
74. Kim S. K., Nam J. W., Rhee J. K.,. miTarget: MicroRNA Target Gene Prediction Using a Support Vector Machine. BMC Bioinform. 2006, 7, 411.
75. Vejnar C. E., Zdobnov E. M., MiRmap: Comprehensive Prediction of MicroRNA Target Repression Strength. Nucl. Acids Res. 2012, 40 (22), 11673-11683.
76. Sethupathy P., Corda B., Hatzigeorgiou A. G., TarBase: A Comprehensive Database of Experimentally Supported Animal MicroRNA Targets. RNA. 2006, 12 (2), 192-197.
77. Vlachos I. S., Paraskevopoulou M. D., Karagkouni D.,. DIANA-TarBase v7.0: Indexing More Than Half a Million Experimentally Supported miRNA:mRNA Interactions. Nucl. Acids Res. 2015, 43 (Database issue), D153-D159.
78. Hsu S. D., Tseng Y. T., Shrestha S.,. miRTarBase Update 2014: An Information Resource for Experimentally Validated miRNA-Target Interactions. Nucl. Acids Res. 2014, 42 (Database issue), D78-D85.
79. Xiao F., Zuo Z., Cai G.,. miRecords: An Integrated Resource for MicroRNA-Target Interactions. Nucl. Acids Res. 2009, 37 (Database issue), D105-D110.
80. Lu M., Zhang Q., Deng M.,. An Analysis of Human MicroRNA and Disease Associations. PloS ONE. 2008, 3 (10), e3420.
81. Jiang Q., Wang Y., Hao Y.,. miR2Disease: A Manually Curated Database for MicroRNA Deregulation in Human Disease. Nucl. Acids Res. 2009, 37 (Database issue), D98-D104.
82. Hausser J., Zavolan M., Identification and Consequences of miRNA-Target Interactions: Beyond Repression of Gene Expression. Nature Rev. Genet. 2014, 15 (9), 599-612.
83. Karbiener M., Glantschnig C., Scheideler M., Hunting the Needle in the Haystack: A Guide to Obtain Biologically Meaningful MicroRNA Targets. Intl. J. Molec. Sci. 2014, 15 (11), 20266-20289.
84. Thomas M., Lieberman J., Lal A., Desperately Seeking MicroRNA Targets. Nature Struc. Molec. Biol. 2010, 17 (10), 1169-1174.
85. Thomson D. W., Bracken C. P., Goodall G. J., Experimental Strategies for MicroRNA Target Identification. Nucl. Acids Res. 2011, 39 (16), 6845-6853.
86. Chi S. W., Zang J. B., Mele A.,. Argonaute HITS-CLIP Decodes MicroRNA-mRNA Interaction Maps. Nature. 2009, 460 (7254), 479-486.
87. Hafner M., Landthaler M., Burger L.,. Transcriptome-Wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP. Cell. 2010, 141 (1), 129-141.
88. Helwak A., Kudla G., Dudnakova T.,. Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding. Cell. 2013, 153 (3), 654-665.
89. Betel D., Koppal A., Agius P.,. Comprehensive Modeling of MicroRNA Targets Predicts Functional Non-Conserved and Non-Canonical Sites. Genome Biol. 2010, 11 (8), R90.
90. Chi S. W., Hannon G. J., Darnell R. B., An Alternative Mode of MicroRNA Target Recognition. Nature Struc. Molec. Biol. 2012, 19 (3), 321-327.
91. Guo H., Ingolia N. T., Weissman J. S.,. Mammalian MicroRNAs Predominantly Act to Decrease Target mRNA Levels. Nature. 2010, 466 (7308), 835-840.
92. Hendrickson D. G., Hogan D. J., McCullough H. L.,. Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human MicroRNA. PLoS Biol. 2009, 7 (11), e1000238.
93. Baek D., Villen J., Shin C.,. The Impact of MicroRNAs on Protein Output. Nature. 2008, 455 (7209), 64-71.
94. Selbach M., Schwanhausser B., Thierfelder N.,. Widespread Changes in Protein Synthesis Induced by MicroRNAs. Nature. 2008, 455 (7209), 58-63.
95. Lim L. P., Lau N. C., Garrett-Engele P.,. Microarray Analysis Shows That Some MicroRNAs Downregulate Large Numbers of Target mRNAs. Nature. 2005, 433 (7027), 769-773.
96. Alexiou P., Maragkakis M., Papadopoulos G. L.,. Lost in Translation: An Assessment and Perspective for Computational MicroRNA Target Identification. Bioinformatics. 2009, 25 (23), 3049-3055.
97. Sethupathy P., Megraw M., Hatzigeorgiou A. G., A Guide through Present Computational Approaches for the Identification of Mammalian MicroRNA Targets. Nature Meth. 2006, 3 (11), 881-886.
98. Beitzinger M., Peters L., Zhu J. Y.,. Identification of Human MicroRNA Targets from Isolated Argonaute Protein Complexes. RNA Biol. 2007, 4 (2), 76-84.
99. Easow G., Teleman A. A., Cohen S. M., Isolation of MicroRNA Targets by miRNP Immunopurification. RNA. 2007, 13 (8), 1198-1204.
100. Hendrickson D. G., Hogan D. J., Herschlag D.,. Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific MicroRNAs and Corresponding Changes in Transcript Abundance. PloS ONE. 2008, 3 (5), e2126.
101. Hong X., Hammell M., Ambros V.,. Immunopurification of Ago1 miRNPs Selects for a Distinct Class of MicroRNA Targets. Proc. Natl. Acad. Sci. USA. 2009, 106 (35), 15085-15090.
102. Karginov F. V., Conaco C., Xuan Z.,. A Biochemical Approach to Identifying MicroRNA Targets. Proc. Natl. Acad. Sci. USA. 2007, 104 (49), 19291-19296.
103. Maniataki E., Mourelatos Z., Human Mitochondrial tRNAMet Is Exported to the Cytoplasm and Associates with the Argonaute 2 Protein. RNA. 2005, 11 (6), 849-852.
104. Diederichs S., Haber D. A., Dual Role for Argonautes in MicroRNA Processing and Posttranscriptional Regulation of MicroRNA Expression. Cell. 2007, 131 (6), 1097-1108.
105. Zhang X., Graves P. R., Zeng Y., Stable Argonaute2 Overexpression Differentially Regulates MicroRNA Production. Biochim. Biophys. Acta. 2009, 1789 (2), 153-159.
106. Mili S., Steitz J. A., Evidence for Reassociation of RNA-Binding Proteins after Cell Lysis: Implications for the Interpretation of Immunoprecipitation Analyses. RNA. 2004, 10 (11), 1692-1694.
107. Licatalosi D. D., Mele A., Fak J. J.,. HITS-CLIP Yields Genome-Wide Insights into Brain Alternative RNA Processing. Nature. 2008, 456 (7221), 464-469.
108. Zisoulis D. G., Lovci M. T., Wilbert M. L.,. Comprehensive Discovery of Endogenous Argonaute Binding Sites in Caenorhabditis elegans. Nature Struc. Molec. Biol. 2010, 17 (2), 173-179.
109. Sugimoto Y., Konig J., Hussain S.,. Analysis of CLIP and iCLIP Methods for Nucleotide-Resolution Studies of Protein-RNA Interactions. Genome Biol. 2012, 13 (8), R67.
110. Broughton J. P., Pasquinelli A. E., Identifying Argonaute Binding Sites in Caenorhabditis elegans Using iCLIP. Methods. 2013, 63 (2), 119-125.
111. Konig J., Zarnack K., Rot G.,. iCLIP Reveals the Function of hnRNP Particles in Splicing at Individual Nucleotide Resolution. Nature Struc. Molec. Biol. 2010, 17 (7), 909-915.
112. Konig J., Zarnack K., Rot G.,. iCLIP: Transcriptome-Wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution. JoVE. 2011, (50).
113. Orom U. A., Lund A. H., Isolation of MicroRNA Targets Using Biotinylated Synthetic MicroRNAs. Methods. 2007, 43 (2), 162-165.
114. Orom U. A., Nielsen F. C., Lund A. H., MicroRNA-10a Binds the 5′UTR of Ribosomal Protein mRNAs and Enhances Their Translation. Molec. Cell. 2008, 30 (4), 460-471.
115. Lal A., Thomas M. P., Altschuler G.,. Capture of MicroRNA-Bound mRNAs Identifies the Tumor Suppressor miR-34a as a Regulator of Growth Factor Signaling. PLoS Genet. 2011, 7 (11), e1002363.
116. Li S., Zhu J., Fu H.,. Hepato-Specific MicroRNA-122 Facilitates Accumulation of Newly Synthesized miRNA through Regulating PRKRA. Nucl. Acids Res. 2012, 40 (2), 884-891.
117. Hsu R. J., Yang H. J., Tsai H. J., Labeled MicroRNA Pull-Down Assay System: An Experimental Approach for High-Throughput Identification of MicroRNA-Target mRNAs. Nucl. Acids Res. 2009, 37 (10), e77.
118. Imig J., Brunschweiger A., Brummer A.,. miR-CLIP Capture of a miRNA Targetome Uncovers a lincRNA H19-miR-106a Interaction. Nature Chem. Biol. 2015, 11 (2), 107-114.
119. Vinther J., Hedegaard M. M., Gardner P. P.,. Identification of miRNA Targets with Stable Isotope Labeling by Amino Acids in Cell Culture. Nucl. Acids Res. 2006, 34 (16), e107.
120. Zhu S., Si M. L., Wu H.,. MicroRNA-21 Targets the Tumor Suppressor Gene Tropomyosin 1 (TPM1). J. Biol. Chem. 2007, 282 (19), 14328-14336.
121. Mavrakis K. J., Wolfe A. L., Oricchio E.,. Genome-Wide RNA-Mediated Interference Screen Identifies miR-19 Targets in Notch-Induced T-Cell Acute Lymphoblastic Leukaemia. Nature Cell Biol. 2010, 12 (4), 372-379.
122. Janssen H. L., Reesink H. W., Lawitz E. J.,. Treatment of HCV Infection by Targeting MicroRNA. New Engl. J. Med. 2013, 368 (18), 1685-1694.
123. van Rooij E., Kauppinen S., Development of MicroRNA Therapeutics Is Coming of Age. EMBO Molec. Med. 2014, 6 (7), 851-864.
124. Li Z., Rana T. M., Therapeutic Targeting of MicroRNAs: Current Status and Future Challenges. Nature Rev. Drug Discov. 2014, 13 (8), 622-638.