Tiny giants of gene regulation: Experimental strategies for microRNA functional studies

Wiley Interdisciplinary Reviews: Developmental Biology

Volumn 5, Issue 3, 2016, Pages 311-362

  Steinkraus, Bruno R ^a   Toegel, Markus ^a   Fulga, Tudor A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA 1 ANTITRYPSIN; ANTISENSE OLIGONUCLEOTIDE; INTERLEUKIN 8; LOCKED NUCLEIC ACID; LONG UNTRANSLATED RNA; MICRORNA; PROTEIN TYROSINE KINASE; PROTEOME; RIBONUCLEASE; RNA BINDING PROTEIN; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR NUCLEASE; TRANSCRIPTOME;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BIOINFORMATICS; CAENORHABDITIS ELEGANS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DOUBLE STRANDED DNA BREAK; DROSOPHILA; GENE CONTROL; GENE ONTOLOGY; GENE REGULATORY NETWORK; HIGH THROUGHPUT SEQUENCING; MACHINE LEARNING; MUTAGENESIS; POLYADENYLATION; POLYSOME; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; STOICHIOMETRY; SUPPORT VECTOR MACHINE; ANIMAL; BIOLOGY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; METABOLISM; PROCEDURES;

ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS;

EID: 84960193171     PISSN: 17597684     EISSN: 17597692     Source Type: Journal    
DOI: 10.1002/wdev.223     Document Type: Article

References (344)

1. Bartel DP . MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
2. Hausser J, Zavolan M . Identification and consequences of miRNA-target interactions - beyond repression of gene expression. Nat Rev Genet 2014, 15:599-612.
3. Lee RC, Feinbaum RL, Ambros V . The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
4. Wightman B, Ha I, Ruvkun G . Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans . Cell 1993, 75:855-862.
5. Friedman RC, Farh KK-H, Burge CB, Bartel DP . Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19:92-105.
6. Wu Y-C, Chen C-H, Mercer A, Sokol NS . Let-7-complex microRNAs regulate the temporal identity of Drosophila mushroom body neurons via chinmo. Dev Cell 2012, 23:202-209.
7. 2 sensory systems. Science 2008, 319:1256-1260.
8. Shcherbata HR, Ward EJ, Fischer KA, Yu J-Y, Reynolds SH, Chen C-H, Xu P, Hay BA, Ruohola-Baker H . Stage-specific differences in the requirements for germline stem cell maintenance in the Drosophila ovary. Cell Stem Cell 2007, 1:698-709.
9. Soifer HS, Rossi JJ, Saetrom P . MicroRNAs in disease and potential therapeutic applications. Mol Ther 2007, 15:2070-2079.
10. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, et al. A microRNA polycistron as a potential human oncogene. Nature 2005, 435:828-833.
11. Johnson SM, Großhans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D, Slack FJ . RAS is regulated by the let-7 microRNA family. Cell 2005, 120:635-647.
12. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, et al. MicroRNA expression profiles classify human cancers. Nature 2005, 435:834-838.
13. Janssen HLA, Reesink HW, Lawitz EJ, Zeuzem S, Rodriguez-Torres M, Patel K, van der Meer AJ, Patick AK, Chen A, Zhou Y, et al. Treatment of HCV infection by targeting microRNA. N Engl J Med 2013, 368:1685-1694.
14. Li QJ, Chau J, Ebert PJ, Sylvester G, Min H, Liu G, Braich R, Manoharan M, Soutschek J, Skare P, et al. miR-181a is an intrinsic modulator of T cell sensitivity and selection. Cell 2007, 129:147-161.
15. Bartel DP . MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
16. Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Blüthgen N, Marks DS, van Oudenaarden A . Gene expression. MicroRNA control of protein expression noise. Science 2015, 348:128-132.
17. Chandradoss SD, Schirle NT, Szczepaniak M, MacRae IJ, Joo C . A dynamic search process underlies microRNA targeting. Cell 2015, 162:96-107.
18. Salomon WE, Jolly SM, Moore MJ, Zamore PD, Serebrov V . Single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides. Cell 2015, 162:84-95.
19. Jo MH, Shin S, Jung S-R, Kim E, Song J-J, Hohng S . Human argonaute 2 has diverse reaction pathways on target RNAs. Mol Cell 2015, 59:117-124.
20. Helwak A, Kudla G, Dudnakova T, Tollervey D . Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 2013, 153:654-665.
21. Loeb GB, Aa K, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY . Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. Mol Cell 2012, 48:760-770.
22. Grosswendt S, Filipchyk A, Manzano M, Klironomos F, Schilling M, Herzog M, Gottwein E, Rajewsky N . Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol Cell 2014, 54:1042-1054.
23. Chi SW, Hannon GJ, Darnell RB . An alternative mode of microRNA target recognition. Nat Struct Mol Biol 2012, 19:321-327.
24. Shin C, Nam J-W, Farh KK-H, Chiang HR, Shkumatava A, Bartel DP . Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell 2010, 38:789-802.
25. Yekta S, I-h S, Bartel DP . MicroRNA-directed cleavage of HOXB8 mRNA. Science 2004, 304:594-596.
26. Grimson A, Farh KKH, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP . MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 2007, 27:91-105.
27. Khorshid M, Hausser J, Zavolan M, van Nimwegen E . A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nat Methods 2013, 10:253-255.
28. Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, Corcoran DL, Cullen BR, Ohler U . MicroRNA target site identification by integrating sequence and binding information. Nat Methods 2013, 10:630-633.
29. Agarwal V, Bell GW, Nam JW, Bartel DP . Predicting effective microRNA target sites in mammalian mRNAs. Elife 2015, 12:4.
30. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E . The role of site accessibility in microRNA target recognition. Nat Genet 2007, 39:1278-1284.
31. Mitchell SF, Parker R . Principles and properties of eukaryotic mRNPs. Mol Cell 2014, 54:547-558.
32. Ho JJ, Marsden PA . Competition and collaboration between RNA-binding proteins and microRNAs. WIREs RNA 2014, 5:69-86.
33. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012, 149:1393-1406.
34. Kedde M, van Kouwenhove M, Zwart W . A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol 2010, 12:1014-1020.
35. Miles WO, Tschöp K, Herr A, Ji J-Y, Dyson NJ . Pumilio facilitates miRNA regulation of the E2F3 oncogene. Genes Dev 2012, 26:356-368.
36. Kedde M, Strasser MJ, Boldajipour B, Oude Vrielink JAF, Slanchev K, le Sage C, Nagel R, Voorhoeve PM, van Duijse J, Ørom UA, et al. RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell 2007, 131:1273-1286.
37. Bhattacharyya SN, Habermacher R, Martine U, Closs EI, Filipowicz W . Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 2006, 125:1111-1124.
38. Kim HH, Kuwano Y, Srikantan S, Lee E-K, Martindale JL, Gorospe M . HuR recruits let-7/RISC to repress c-Myc expression. Genes Dev 2009, 23:1743-1748.
39. Bhattacharyya SN, Habermacher R, Martine U, Closs EI, Filipowicz W . Stress-induced reversal of microRNA repression and mRNA P-body localization in human cells. Cold Spring Harb Symp Quant Biol 2006, 71:513-521.
40. Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, Hafner M, Ascano M, Tuschl T, Ohler U, Keene JD . Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell 2011, 43:327-339.
41. Lebedeva S, Jens M, Theil K, Schwanhäusser B, Selbach M, Landthaler M, Rajewsky N . Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol Cell 2011, 43:340-352.
42. Lu YC, Chang SH, Hafner M, Li X, Tuschl T, Elemento O, Hla T . ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages. Cell Rep 2014, 9:2330-2343.
43. Kundu P, Fabian MR, Sonenberg N, Bhattacharyya SN, Filipowicz W . HuR protein attenuates miRNA-mediated repression by promoting miRISC dissociation from the target RNA. Nucleic Acids Res 2012, 40:5088-5100.
44. Jing Q, Huang S, Guth S, Zarubin T, Motoyama A, Chen J, Di Padova F, Lin S-C, Gram H, Han J . Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 2005, 120:623-634.
45. Sun G, Li H, Rossi JJ . Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3′UTR. Nucleic Acids Res 2010, 38:239-252.
46. Walters RW, Bradrick SS, Gromeier M . Poly(A)-binding protein modulates mRNA susceptibility to cap-dependent miRNA-mediated repression. RNA (New York, NY) 2010, 16:239-250.
47. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, et al. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell 2009, 35:868-880.
48. Hammell CM, Lubin I, Boag PR, Blackwell TK, Ambros V . nhl-2 modulates microRNA activity in Caenorhabditis elegans . Cell 2009, 136:926-938.
49. Schwamborn JC, Berezikov E, Knoblich JA . The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors. Cell 2009, 136:913-925.
50. Meister G . Argonaute proteins: functional insights and emerging roles. Nat Rev Genet 2013, 14:447-459.
51. Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, et al. A novel miRNA processing pathway independent of Dicer requires argonaute2 catalytic activity. Science 2010, 328:1694-1698.
52. Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ . A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 2010, 465:584-589.
53. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF . Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006, 312:75-79.
54. Wu L, Fan J, Belasco JG . MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci USA 2006, 103:4034-4039.
55. Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E . mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev 2006, 20:1885-1898.
56. Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP . The impact of microRNAs on protein output. Nature 2008, 455:64-71.
57. Eulalio A, Huntzinger E, Nishihara T, Rehwinkel J, Fauser M, Izaurralde E . Deadenylation is a widespread effect of miRNA regulation. RNA (New York, NY) 2009, 15:21-32.
58. Hendrickson DG, Hogan DJ, McCullough HL, Myers JW, Herschlag D, Ferrell JE, Brown PO . Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol 2009, 7:e1000238.
59. Guo H, Ingolia NT, Weissman JS, Bartel DP . Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466:835-840.
60. Bazzini AA, Lee MT, Giraldez AJ . Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 2012, 336:233-237.
61. Djuranovic S, Nahvi A, Green R . miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 2012, 336:237-240.
62. Meijer HA, Kong YW, Lu WT, Wilczynska A, Spriggs RV, Robinson SW, Godfrey JD, Willis AE, Bushell M . Translational repression and eIF4A2 activity are critical for microRNA-mediated gene regulation. Science 2013, 340:82-85.
63. Olsen PH, Ambros V . The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol 1999, 216:671-680.
64. Humphreys DT, Westman BJ, Martin DIK, Preiss T . MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc Natl Acad Sci USA 2005, 102:16961-16966.
65. Maroney PA, Yu Y, Fisher J, Nilsen TW . Evidence that microRNAs are associated with translating messenger RNAs in human cells. Nat Struct Mol Biol 2006, 13:1102-1107.
66. Krol J, Loedige I, Filipowicz W . The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010, 11:597-610.
67. Kim VN, Han J, Siomi MC . Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 2009, 10:126-139.
68. Ha M, Kim VN . Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 2014, 15:509-524.
69. Bentwich I . Prediction and validation of microRNAs and their targets. FEBS Lett 2005, 579:5904-5910.
70. Sethupathy P, Megraw M, Hatzigeorgiou AG . A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 2006, 3:881-886.
71. Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA . Computational identification of microRNAs and their targets. Comput Biol Chem 2006, 30:395-407.
72. Mazière P, Enright AJ . Prediction of microRNA targets. Drug Discov Today 2007, 12:452-458.
73. Mendes ND, Freitas aT, Sagot M-F . Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 2009, 37:2419-2433.
74. Yue D, Liu H, Huang Y . Survey of computational algorithms for MicroRNA target prediction. Curr Genomics 2009, 10:478-492.
75. Li L, Xu J, Yang D, Tan X, Wang H . Computational approaches for microRNA studies: a review. Mamm Genome 2010, 21:1-12.
76. Min H, Yoon S . Got target? Computational methods for microRNA target prediction and their extension. Exp Mol Med 2010, 42:233-244.
77. Saito T, Saetrom P . MicroRNAs-targeting and target prediction. N Biotechnol 2010, 27:243-249.
78. Hammell M . Computational methods to identify miRNA targets. Semin Cell Dev Biol 2010, 21:738-744.
79. Kleftogiannis D, Korfiati A, Theofilatos K, Likothanassis S, Tsakalidis A, Mavroudi S . Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. J Biomed Inform 2013, 46:563-573.
80. Tarang S, Weston MD . Macros in microRNA target identification: a comparative analysis of in silico, in vitro, and in vivo approaches to microRNA target identification. RNA Biol 2014, 11:324-333.
81. Li Y, Zhang Z . Computational biology in microRNA. WIREs RNA 2015, 6:435-452.
82. Rajewsky N . microRNA target predictions in animals. Nat Genet 2006, 38(Suppl):S8-S13.
83. Chi SW, Zang JB, Mele A, Darnell RB . Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 2009, 460:479-486.
84. Schnall-Levin M, Rissland OS, Johnston WK, Perrimon N, Bartel DP, Berger B . Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res 2011, 21:1395-1403.
85. Lai EC . MicroRNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 2002, 30:363-364.
86. Lewis BP, I-h S, Jones-Rhoades MW, Bartel DP, Burge CB . Prediction of mammalian microRNA targets. Cell 2003, 115:787-798.
87. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS . MicroRNA targets in Drosophila. Genome Biol 2003, 5:R1.
88. Stark A, Brennecke J, Russell RB, Cohen SM . Identification of Drosophila microRNA targets. PLoS Biol 2003, 1:e60.
89. Hofacker IL . Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31:3429-3431.
90. Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP . Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 2011, 18:1139-1146.
91. Betel D, Koppal A, Agius P, Sander C, Leslie C . Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 2010, 11:R90.
92. Krek A, Grün D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al. Combinatorial microRNA target predictions. Nat Genet 2005, 37:495-500.
93. Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C . doRiNA: a database of RNA interactions in post-transcriptional regulation. Nucleic Acids Res 2012, 40:D180-D186.
94. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A . A combined computational-experimental approach predicts human microRNA targets. Genes Dev 2004, 18:1165-1178.
95. Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, et al. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 2009, 37:W273-W276.
96. Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG . Functional microRNA targets in protein coding sequences. Bioinformatics (Oxford, Engl) 2012, 28:771-776.
97. Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG . DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res 2013, 41:W169-W173.
98. Hsu PD, Lander ES, Zhang F . Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014, 157:1262-1278.
99. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T . miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009, 37:D105-D110.
100. Kim S-K, Nam J-W, Rhee J-K, Lee W-J, Zhang B-T . miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinform 2006, 7:411.
101. Sturm M, Hackenberg M, Langenberger D, Frishman D . TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinform 2010, 11:292.
102. Bandyopadhyay S, Mitra R . TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples. Bioinformatics (Oxford, Engl) 2009, 25:2625-2631.
103. Mitra R, Bandyopadhyay S . MultiMiTar: a novel multi objective optimization based miRNA-target prediction method. PLoS One 2011, 6:e24583.
104. Dweep H, Sticht C, Pandey P, Gretz N . miRWalk-database: prediction of possible miRNA binding sites by "walking" the genes of three genomes. J Biomed Inform 2011, 44:839-847.
105. Dweep H, Gretz N . miRWalk2.0: a comprehensive atlas of microRNA-target interactions. Nat Methods 2015, 12:697.
106. Naifang S, Minping Q, Deng M . Integrative approaches for microRNA target prediction: combining sequence information and the paired mRNA and miRNA expression profiles. Curr Bioinform 2013, 8:37-45.
107. Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S . MicroRNA target prediction by expression analysis of host genes. Genome Res 2009, 19:481-490.
108. Cho S, Jang I, Jun Y, Yoon S, Ko M, Kwon Y, Choi I, Chang H, Ryu D, Lee B, et al. miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. Nucleic Acids Res 2012, 41:D252-D257.
109. Mukherji S, Ebert MS, Zheng GXY, Tsang JS, Pa S, van Oudenaarden A . MicroRNAs can generate thresholds in target gene expression. Nat Genet 2011, 43:854-859.
110. Mullokandov G, Baccarini A, Ruzo A, Jayaprakash AD, Tung N, Israelow B, Evans MJ, Sachidanandam R, Brown BD . High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries. Nat Methods 2012, 9:840-846.
111. Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW . System-wide identification of RNA-binding proteins by interactome capture. Nat Protoc 2013, 8:491-500.
112. Incarnato D, Neri F, Diamanti D, Oliviero S . MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets. Nucleic Acids Res 2013, 41:8421-8433.
113. Chang T-H, Huang H-Y, Hsu JB-K, Weng S-L, Horng J-T, Huang H-D . An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinform 2013, 14(Suppl 2):S4.
114. Ritchie W, Flamant S, Rasko JEJ . Predicting microRNA targets and functions: traps for the unwary. Nat Methods 2009, 6:397-398.
115. Majoros WH, Ohler U . Spatial preferences of microRNA targets in 3′ untranslated regions. BMC Genomics 2007, 8:152.
116. Tian B, Hu J, Zhang H, Lutz CS . A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 2005, 33:201-212.
117. Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP . Extensive alternative polyadenylation during zebrafish development. Genome Res 2012, 22:2054-2066.
118. Mayr C, Bartel DP . Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 2009, 138:673-684.
119. Nam J-W, Rissland OS, Koppstein D, Abreu-Goodger C, Jan CH, Agarwal V, Yildirim MA, Rodriguez A, Bartel DP . Global analyses of the effect of different cellular contexts on microRNA targeting. Mol Cell 2014, 53:1031-1043.
120. Lee T, Wang N, Houel S, Couts K, Old W, Ahn N . Dosage and temporal thresholds in microRNA proteomics. Mol Cell Proteomics 2015, 14:289-302.
121. Akbari Moqadam F, Pieters R, den Boer ML . The hunting of targets: challenge in miRNA research. Leukemia 2013, 27:16-23.
122. Bertero T, Robbe-Sermesant K, Brigand KL, Ponzio G, Pottier N, Rezzonico R, Mazure NM, Barbry P, Mari B . MicroRNA target identification: lessons from HypoxamiRs. Antioxid Redox Signal 2014, 21:1249-1268.
123. Huang Y, Zou Q, Song H, Song F, Wang L, Zhang G, Shen X . A study of miRNAs targets prediction and experimental validation. Protein Cell 2010, 1:979-986.
124. Jin H, Tuo W, Lian H, Liu Q, Zhu X-Q, Gao H . Strategies to identify microRNA targets: new advances. N Biotechnol 2010, 27:734-738.
125. Kuhn DE, Martin MM, Feldman DS, Terry AV, Nuovo GJ, Elton TS . Experimental validation of miRNA targets. Methods (San Diego, Calif) 2008, 44:47-54.
126. Nelson PT, Kiriakidou M, Mourelatos Z, Tan GS, Jennings MH, Xie K, Wang W-X . High-throughput experimental studies to identify miRNA targets directly, with special focus on the mammalian brain. Brain Res 2010, 1338:122-130.
127. Ørom UA, Lund AH . Experimental identification of microRNA targets. Gene 2010, 451:1-5.
128. Thomson DW, Bracken CP, Goodall GJ . Experimental strategies for microRNA target identification. Nucleic Acids Res 2011, 39:6845-6853.
129. Vasudevan S . Functional validation of microRNA-target RNA interactions. Methods (San Diego, Calif) 2012, 58:126-134.
130. Ziegelbauer JM . Viral microRNA genomics and target validation. Curr Opin Virol 2014, 7C:33-39.
131. Mittal N, Zavolan M . Seq and CLIP through the miRNA world. Genome Biol 2014, 15:202.
132. Karbiener M, Glantschnig C, Scheideler M . Hunting the needle in the haystack: a guide to obtain biologically meaningful microRNA targets. Int J Mol Sci 2014, 15:20266-20289.
133. Lima SA, Pasquinelli AE . Identification of miRNAs and their targets in C. elegans . Adv Exp Med Biol 2014, 825:431-450.
134. Pasquinelli AE . MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 2012, 13:271-282.
135. Smith SM, Murray DW . An overview of microRNA methods: expression profiling and target identification. Methods Mol Biol 2012, 823:119-138.
136. van Rooij E . The art of microRNA research. Circ Res 2011, 108:219-234.
137. Thomas M, Lieberman J, Lal A . Desperately seeking microRNA targets. Nat Struct Mol Biol 2010, 17:1169-1174.
138. Dalmay T . Identification of genes targeted by microRNAs. Biochem Soc Trans 2008, 36:1194-1196.
139. Stefani G, Slack F . MicroRNAs in search of a target. Cold Spring Harb Symp Quant Biol 2006, 71:129-134.
140. Krützfeldt J, Poy MN, Stoffel M . Strategies to determine the biological function of microRNAs. Nat Genet 2006, 38(Suppl):S14-S19.
141. Wilbert ML, Yeo GW . Genome-wide approaches in the study of microRNA biology. WIREs Syst Biol Med 2011, 3:491-512.
142. Ea M, Alvarez-Saavedra E, Abbott AL, Lau NC, Hellman AB, McGonagle SM, Bartel DP, Ambros VR, Horvitz HR . Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 2007, 3:2395-2403.
143. Park CY, Jeker LT, Carver-Moore K, Oh A, Liu HJ, Cameron R, Richards H, Li Z, Adler D, Yoshinaga Y, et al. A resource for the conditional ablation of microRNAs in the mouse. Cell Rep 2012, 1:385-391.
144. Iliopoulos D, Malizos KN, Oikonomou P, Tsezou A . Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks. PLoS One 2008, 3:e3740.
145. Cui Y, Xie S, Luan J, Zhou X, Han J . Identification of the receptor tyrosine kinases (RTKs)-oriented functional targets of miR-206 by an antibody-based protein array. FEBS Lett 2015, 589:2131-2135.
146. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM . Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433:769-773.
147. Benderska N, Dittrich A-L, Knaup S, Rau TT, Neufert C, Wach S, Fahlbusch FB, Rauh M, Wirtz RM, Agaimy A, et al. miRNA-26b overexpression in ulcerative colitis-associated carcinogenesis. Inflamm Bowel Dis 2015, 21:2039-2051.
148. Fujita Y, Kojima T, Kawakami K, Mizutani K, Kato T, Deguchi T, Ito M . miR-130a activates apoptotic signaling through activation of caspase-8 in taxane-resistant prostate cancer cells. Prostate 2015, 75:1568-1578.
149. Xu G, Fewell C, Taylor C, Deng N, Hedges D, Wang X, Zhang K, Lacey M, Zhang H, Yin Q, et al. Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq. RNA (New York, NY) 2010, 16:1610-1622.
150. Gaidatzis D, Burger L, Florescu M, Stadler MB . Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol 2015, 33:722-729.
151. Zhu S, Si ML, Wu H, Mo YY . MicroRNA-21 targets the tumor suppressor gene tropomyosin 1 (TPM1). J Biol Chem 2007, 282:14328-14336.
152. Schramedei K, Mörbt N, Pfeifer G, Läuter J, Rosolowski M, Tomm JM, von Bergen M, Horn F, Brocke-Heidrich K . MicroRNA-21 targets tumor suppressor genes ANP32A and SMARCA4. Oncogene 2011, 30:2975-2985.
153. Fasanaro P, Greco S, Lorenzi M, Pescatori M, Brioschi M, Kulshreshtha R, Banfi C, Stubbs A, Ga C, Ivan M, et al. An integrated approach for experimental target identification of hypoxia-induced miR-210. J Biol Chem 2009, 284:35134-35143.
154. Tian Z, Greene AS, Pietrusz JL, Matus IR, Liang M . MicroRNA-target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis. Genome Res 2008, 18:404-411.
155. Chahrour O, Cobice D, Malone J . Stable isotope labelling methods in mass spectrometry-based quantitative proteomics. J Pharm Biomed Anal 2015, 113:2-20.
156. Yang Y, Chaerkady R, Beer MA, Mendell JT, Pandey A . Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics 2009, 9:1374-1384.
157. Ou M, Zhang X, Dai Y, Gao J, Zhu M, Yang X, Li Y, Yang T, Ding M . Identification of potential microRNA-target pairs associated with osteopetrosis by deep sequencing, iTRAQ proteomics and bioinformatics. Eur J Hum Genet 2014, 22:625-632.
158. Khan AP, Poisson LM, Bhat VB, Fermin D, Zhao R, Kalyana-Sundaram S, Michailidis G, Nesvizhskii AI, Omenn GS, Chinnaiyan AM, et al. Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer. Mol Cell Proteomics 2010, 9:298-312.
159. Chen QR, Yu LR, Tsang P, Wei JS, Song YK, Cheuk A, Chung JY, Hewitt SM, Veenstra TD, Khan J . Systematic proteome analysis identifies transcription factor YY1 as a direct target of miR-34a. J Proteome Res 2011, 10:479-487.
160. Lange V, Picotti P, Domon B, Aebersold R . Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008, 4:222.
161. Jovanovic M, Reiter L, Picotti P, Lange V, Bogan E, Hurschler B, Blenkiron C, Lehrbach NJ, Ding XC, Weiss M, et al. A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans . Nat Methods 2010, 7:837-842.
162. Jovanovic M, Reiter L, Clark A, Weiss M, Picotti P, Rehrauer H, Frei A, Neukomm LJ, Kaufman E, Wollscheid B, et al. RIP-chip-SRM-a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans . Genome Res 2012, 22:1360-1371.
163. Ong S-E, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M . Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
164. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N . Widespread changes in protein synthesis induced by microRNAs. Nature 2008, 455:58-63.
165. Vinther J, Hedegaard MM, Gardner PP, Andersen JS, Arctander P . Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res 2006, 34:2-7.
166. Yang Y, Chaerkady R, Kandasamy K, Huang T-C, Selvan LDN, Dwivedi SB, Oa K, Mendell JT, Pandey A . Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst 2010, 6:1873-1882.
167. Kaller M, Liffers S-T, Oeljeklaus S, Kuhlmann K, Röh S, Hoffmann R, Warscheid B, Hermeking H . Genome-wide characterization of miR-34a induced changes in protein and mRNA expression by a combined pulsed SILAC and microarray analysis. Mol Cell Proteomics 2011, 10:M111.010462.
168. Lößner C, Meier J, Warnken U, Ma R, Lichter P, Pscherer A, Schnölzer M . Quantitative proteomics identify novel miR-155 target proteins. PLoS One 2011, 6:1-11.
169. Liu Q, Halvey PJ, Shyr Y, Slebos RJC, Liebler DC, Zhang B . Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation. Mol Cell Proteomics 2013, 12:1900-1911.
170. Yan GR, Xu SH, Tan ZL, Liu L, He QY . Global identification of miR-373-regulated genes in breast cancer by quantitative proteomics. Proteomics 2011, 11:912-920.
171. Xiong Q, Zhong Q, Zhang J, Yang M, Li C, Zheng P, Bi LJ, Ge F . Identification of novel miR-21 target proteins in multiple myeloma cells by quantitative proteomics. J Proteome Res 2012, 11:2078-2090.
172. Meleady P, Gallagher M, Clarke C, Henry M, Sanchez N, Barron N, Clynes M . Impact of miR-7 over-expression on the proteome of Chinese hamster ovary cells. J Biotechnol 2012, 160:251-262.
173. Gamez-Pozo A, Berges-Soria J, Arevalillo JM, Nanni P, Lopez-Vacas R, Navarro H, Grossmann J, Castaneda CA, Main P, Diaz-Almiron M, et al. Combined label-free quantitative proteomics and microRNA expression analysis of breast cancer unravel molecular differences with clinical implications. Cancer Res 2015, 75:2243-2253.
174. Ingolia NT . Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 2014, 15:205-213.
175. Eichhorn Stephen W, Guo H, McGeary Sean E, Rodriguez-Mias Ricard A, Shin C, Baek D, S-h H, Ghoshal K, Villén J, Bartel David P . mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell 2014, 56:104-115.
176. Easow G, Teleman A, Cohen SM . Isolation of microRNA targets by miRNP immunopurification. RNA (New York, NY) 2007, 13:1198-1204.
177. Dölken L, Malterer G, Erhard F, Kothe S, Friedel CC, Suffert G, Marcinowski L, Motsch N, Barth S, Beitzinger M, et al. Systematic analysis of viral and cellular microRNA targets in cells latently infected with human γ-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe 2010, 7:324-334.
178. Hendrickson DG, Hogan DJ, Herschlag D, Ferrell JE, Brown PO . Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One 2008, 3:e2126.
179. Beitzinger M, Peters L, Zhu JY, Kremmer E, Meister G . Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol 2007, 4:76-84.
180. Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ . A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci USA 2007, 104:19291-19296.
181. Hong X, Hammell M, Ambros V, Cohen SM . Immunopurification of Ago1 miRNPs selects for a distinct class of microRNA targets. Proc Natl Acad Sci USA 2009, 106:15085-15090.
182. Wang W-X, Wilfred BR, Hu Y, Stromberg AJ, Nelson PT . Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes. RNA (New York, NY) 2010, 16:394-404.
183. Meier J, Hovestadt V, Zapatka M, Pscherer A, Lichter P, Seiffert M . Genome-wide identification of translationally inhibited and degraded miR-155 targets using RNA-interacting protein-IP. RNA Biol 2013, 10:1018-1029.
184. Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, Sewell AK, Liu X, Yates JR, Han M . Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 2007, 28:598-613.
185. Zhang L, Hammell M, Kudlow B, Ambros V, Han M . Systematic analysis of dynamic miRNA-target interactions during C. elegans development. Development 2009, 136:3043-3055.
186. Ba K, Zhang L, Han M . Systematic analysis of tissue-restricted miRISCs reveals a broad role for microRNAs in suppressing basal activity of the C. elegans pathogen response. Mol Cell 2012, 46:530-541.
187. Xa C, Shen R, Auer PL, Goodman RH . Capturing microRNA targets using an RNA-induced silencing complex (RISC)-trap approach. Proc Natl Acad Sci USA 2012, 109:20473-20478.
188. Darnell RB . HITS-CLIP: panoramic views of protein-RNA regulation in living cells. WIREs RNA 2010, 1:266-286.
189. Mili S, Steitz JA . Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA (New York, NY) 2004, 10:1692-1694.
190. Riley KJ, Yario T, Steitz J . Association of Argonaute proteins and microRNAs can occur after cell lysis. RNA (New York, NY) 2012, 18:1581-1585.
191. Jaskiewicz L, Bilen B, Hausser J, Zavolan M . Argonaute CLIP-a method to identify in vivo targets of miRNAs. Methods (San Diego, Calif) 2012, 58:106-112.
192. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Ta C, Schweitzer AC, Blume JE, Wang X, et al. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 2008, 456:464-469.
193. Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB . Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc 2014, 9:263-293.
194. Zhang C, Darnell RB . Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol 2011, 29:607-614.
195. Leung AKL, Young AG, Bhutkar A, Zheng GX, Bosson AD, Nielsen CB, Pa S . Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol 2011, 18:237-244.
196. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW . Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans . Nat Struct Mol Biol 2010, 17:173-179.
197. Haecker I, Gay L, Yang Y, Hu J, Morse AM, McIntyre LM, Renne R . Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas. PLoS Pathog 2012, 8:e1002884.
198. Riley KJ, Rabinowitz GS, Ta Y, Luna JM, Darnell RB, Ja S . EBV and human microRNAs co-target oncogenic and apoptotic viral and human genes during latency. EMBO J 2012, 31:2207-2221.
199. Hausser J, Syed AP, Bilen B, Zavolan M . Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res 2013, 23:604-615.
200. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp A-C, Munschauer M, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
201. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp A-C, Munschauer M, et al. PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp 2010, pii:2034.
202. Hafner M, Lianoglou S, Tuschl T, Betel D . Genome-wide identification of miRNA targets by PAR-CLIP. Methods (San Diego, Calif) 2012, 58:94-105.
203. Ascano M, Hafner M, Cekan P, Gerstberger S, Tuschl T . Identification of RNA-protein interaction networks using PAR-CLIP. WIREs RNA 2012, 3:159-177.
204. Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, et al. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe 2011, 10:515-526.
205. Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Kang D, Hafner M, Nusbaum JD, Feederle R, Delecluse H-J, Luftig M, et al. The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog 2012, 8:e1002484.
206. Farazi T, Ten Hoeve JJ, Brown M, Mihailovic A, Horlings HM, van de Vijver MJ, Tuschl T, Wessels LF . Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets. Genome Biol 2014, 15:R9.
207. Burger K, Mühl B, Kellner M, Rohrmoser M, Gruber-eber A, Windhager L, Friedel CC, Dölken L, Eick D . 4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response. RNA Biol 2013, 10:1623-1630.
208. Kemény-Beke A, Berényi E, Facskó A, Damjanovich J, Horváth A, Bodnár A, Berta A, Aradi J . Antiproliferative effect of 4-thiouridylate on OCM-1 uveal melanoma cells. Eur J Ophthalmol 2008, 16:680-685.
209. Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M . A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods 2011, 8:559-564.
210. König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J . iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 2010, 17:909-915.
211. König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J . iCLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp 2011, pii:2638.
212. Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J, Ule J . iCLIP: protein-RNA interactions at nucleotide resolution. Methods (San Diego, Calif) 2014, 65:274-287.
213. Broughton JP, Pasquinelli AE . Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP. Methods (San Diego, Calif) 2013, 63:119-125.
214. Bosson AD, Zamudio JR, Pa S . Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell 2014, 56:347-359.
215. Kudla G, Granneman S, Hahn D, Beggs JD, Tollervey D . Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast. Proc Natl Acad Sci USA 2011, 108:10010-10015.
216. Erhard F, Dölken L, Jaskiewicz L, Zimmer R . PARma: identification of microRNA target sites in AGO-PAR-CLIP data. Genome Biol 2013, 14:R79.
217. Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U . PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol 2011, 12:R79.
218. Chou C-H, Lin F-M, Chou M-T, Hsu S-D, Chang T-H, Weng S-L, Shrestha S, Hsiao C-C, Hung J-H, Huang H-D . A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics 2013, 14(Suppl 1):S2.
219. Chen B, Yun J, Kim MS, Mendell JT, Xie Y . PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. Genome Biol 2014, 15:R18.
220. Wang T, Xie Y, Xiao G . dCLIP: a computational approach for comparative CLIP-seq analyses. Genome Biol 2014, 15:R11.
221. Khorshid M, Rodak C, Zavolan M . CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res 2011, 39:D245-D252.
222. Yang J-H, Li J-H, Shao P, Zhou H, Chen Y-Q, Qu L-H . starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 2011, 39:D202-D209.
223. Li J-H, Liu S, Zhou H, Qu L-H, Yang J-H . starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 2014, 42:D92-D97.
224. Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG . TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 2012, 40:D222-D229.
225. Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos IL, Maniou S, Karathanou K, Kalfakakou D, et al. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res 2015, 43:D153-D159.
226. Clark PM, Loher P, Quann K, Brody J, Londin ER, Rigoutsos I . Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci Rep 2014, 4:5947.
227. Vo NK, Dalton RP, Liu N, Olson EN, Goodman RH . Affinity purification of microRNA-133a with the cardiac transcription factor, Hand2. Proc Natl Acad Sci USA 2010, 107:19231-19236.
228. Yoon JH, Srikantan S, Gorospe M . MS2-TRAP (MS2-tagged RNA affinity purification): tagging RNA to identify associated miRNAs. Methods 2012, 58:81-87.
229. Braun J, Misiak D, Busch B, Krohn K, Hüttelmaier S . Rapid identification of regulatory microRNAs by miTRAP (miRNA trapping by RNA in vitro affinity purification). Nucleic Acids Res 2014, 42:e66.
230. Shi M, Han W, Spivack SD . A quantitative method to identify microRNAs targeting a messenger RNA using a 3′UTR RNA affinity technique. Anal Biochem 2013, 443:1-12.
231. Hassan T, Smith SGJ, Gaughan K, Oglesby IK, O'Neill S, McElvaney NG, Greene CM . Isolation and identification of cell-specific microRNAs targeting a messenger RNA using a biotinylated anti-sense oligonucleotide capture affinity technique. Nucleic Acids Res 2013, 41:e71.
232. Wei K, Yan F, Xiao H, Yang X, Xie G, Xiao Y, Wang T, Xun Y, Huang Z, Han M, et al. Affinity purification of binding miRNAs for messenger RNA fused with a common tag. Int J Mol Sci 2014, 15:14753-14765.
233. Lal A, Thomas MP, Altschuler G, Navarro F, O'Day E, Li XL, Concepcion C, Han YC, Thiery J, Rajani DK, et al. Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PLoS Genet 2011, 7:19-21.
234. Orom UA, Lund AH . Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods (San Diego, Calif) 2007, 43:162-165.
235. Li S, Zhu J, Fu H, Wan J, Hu Z, Liu S, Li J, Tie Y, Xing R, Zhu J, et al. Hepato-specific microRNA-122 facilitates accumulation of newly synthesized miRNA through regulating PRKRA. Nucleic Acids Res 2012, 40:884-891.
236. 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. Nucleic Acids Res 2009, 37:e77.
237. Nonne N, Ameyar-Zazoua M, Souidi M, Harel-Bellan A . Tandem affinity purification of miRNA target mRNAs (TAP-Tar). Nucleic Acids Res 2010, 38:e20.
238. Baigude H, Ahsanullah Li Z, Zhou Y, Rana TM . miR-TRAP: a benchtop chemical biology strategy to identify microRNA targets. Angew Chem Int Ed Engl 2012, 51:5880-5883.
239. Imig J, Brunschweiger A, Brümmer A, Guennewig B, Mittal N, Kishore S, Tsikrika P, Gerber AP, Zavolan M, Hall J . miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol 2014, 11:107-114.
240. Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J . Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol 2012, 13:R67.
241. Vatolin S, Navaratne K, Weil RJ . A novel method to detect functional microRNA targets. J Mol Biol 2006, 358:983-996.
242. Andachi Y . A novel biochemical method to identify target genes of individual microRNAs: identification of a new Caenorhabditis elegans let-7 target. RNA (New York, NY) 2008, 14:2440-2451.
243. Aldred SF, Collins P, Trinklein N . Identifying targets of human microRNAs with the lightswitch luciferase assay system using 3′UTR-reporter constructs and a microRNA mimic in adherent cells. J Vis Exp 2011, pii:3343.
244. Boutz DR, Collins PJ, Suresh U, Lu M, Ramirez CM, Fernandez-Hernando C, Huang Y, Abreu Rde S, Le SY, Shapiro BA, et al. Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122. J Biol Chem 2011, 286:18066-18078.
245. Zhou P, Xu W, Peng X, Luo Z, Xing Q, Chen X, Hou C, Liang W, Zhou J, Wu X, et al. Large-scale screens of miRNA-mRNA interactions unveiled that the 3′UTR of a gene is targeted by multiple miRNAs. PLoS One 2013, 8:e68204.
246. Yuva-Aydemir Y, Xu XL, Aydemir O, Gascon E, Sayin S, Zhou W, Hong Y, Gao FB . Downregulation of the host gene jigr1 by miR-92 is essential for neuroblast self-renewal in Drosophila. PLoS Genet 2015, 11:e1005264.
247. Chalfie M, Horvitz HR, Sulston JE . Mutations that lead to reiterations in the cell lineages of C. elegans . Cell 1981, 24:59-69.
248. Horvitz HR, Sulston JE . Isolation and genetic characterization of cell-lineage mutants of the nematode Caenorhabditis elegans . Genetics 1980, 96:435-454.
249. Ruvkun G, Giusto J . The Caenorhabditis elegans heterochronic gene lin-14 encodes a nuclear protein that forms a temporal developmental switch. Nature 1989, 338:313-319.
250. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G . The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans . Nature 2000, 403:901-906.
251. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408:86-89.
252. Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM . bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 2003, 113:25-36.
253. Bejarano F, Smibert P, Lai EC . miR-9a prevents apoptosis during wing development by repressing Drosophila LIM-only. Dev Biol 2010, 338:63-73.
254. Da Ros VG, Gutierrez-Perez I, Ferres-Marco D, Dominguez M . Dampening the signals transduced through hedgehog via microRNA miR-7 facilitates notch-induced tumourigenesis. PLoS Biol 2013, 11:e1001554.
255. Weng R, Cohen SM . Drosophila miR-124 regulates neuroblast proliferation through its target anachronism. Development 2012, 139:1427-1434.
256. Liu N, Landreh M, Cao K, Abe M, Hendriks G-J, Kennerdell JR, Zhu Y, Wang L-S, Bonini NM . The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila. Nature 2013, 482:519-523.
257. de Lencastre A, Pincus Z, Zhou K, Kato M, Lee SS, Slack FJ . MicroRNAs both promote and antagonize longevity in C. elegans . Curr Biol 2010, 20:2159-2168.
258. Li Y, Wang F, Lee J-A, Gao F-B . MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev 2006, 20:2793-2805.
259. van Rooij E, Sutherland LB, Qi X, Richardson JA, Hill J, Olson EN . Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 2007, 316:575-579.
260. Alvarez-Saavedra E, Horvitz HR . Many families of C. elegans microRNAs are not essential for development or viability. Curr Biol 2010, 20:367-373.
261. Brenner JL, Jasiewicz KL, Fahley AF, Kemp BJ, Abbott AL . Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans . Curr Biol 2010, 20:1321-1325.
262. Chen Y-W, Song S, Weng R, Verma P, Kugler J-M, Buescher M, Rouam S, Cohen SM . Systematic study of drosophila microRNA functions using a collection of targeted knockout mutations. Dev Cell 2014, 31:784-800.
263. Ge W, Chen YW, Weng R, Lim SF, Buescher M, Zhang R, Cohen SM . Overlapping functions of microRNAs in control of apoptosis during Drosophila embryogenesis. Cell Death Differ 2012, 19:839-846.
264. Prosser HM, Koike-Yusa H, Cooper JD, Law FC, Bradley A . A resource of vectors and ES cells for targeted deletion of microRNAs in mice. Nat Biotechnol 2011, 29:840-845.
265. Kim H, Kim JS . A guide to genome engineering with programmable nucleases. Nat Rev Genet 2014, 15:321-334.
266. Xiao A, Wang Z, Hu Y, Wu Y, Luo Z, Yang Z, Zu Y, Li W, Huang P, Tong X, et al. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res 2013, 41:e141.
267. Uhde-Stone C, Sarkar N, Antes T, Otoc N, Kim Y, Jiang YJ, Lu B . A TALEN-based strategy for efficient bi-allelic miRNA ablation in human cells. RNA (New York, NY) 2014, 20:948-955.
268. Ho T-T, Zhou N, Huang J, Koirala P, Xu M, Fung R, Wu F, Mo Y-Y . Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res 2015, 43:e17.
269. Jiang Q, Meng X, Meng L, Chang N, Xiong J, Cao H, Liang Z . Small indels induced by CRISPR/Cas9 in the 5′ region of microRNA lead to its depletion and Drosha processing retardance. RNA Biol 2014, 11:1243-1249.
270. Kim Y-K, Wee G, Park J, Kim J, Baek D, Kim J-S, Kim VN . TALEN-based knockout library for human microRNAs. Nat Struct Mol Biol 2013, 20:1458-1464.
271. Krützfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M, Stoffel M . Silencing of microRNAs in vivo with 'antagomirs'. Nature 2005, 438:685-689.
272. Ebert MS, Neilson JR, Sharp PA . MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 2007, 4:721-726.
273. Loya CM, Lu CS, Van Vactor D, Fulga TA . Transgenic microRNA inhibition with spatiotemporal specificity in intact organisms. Nat Methods 2009, 6:897-903.
274. Haraguchi T, Ozaki Y, Iba H . Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells. Nucleic Acids Res 2009, 37:e43.
275. Xie J, Ameres SL, Friedline R, Hung J-H, Zhang Y, Xie Q, Zhong L, Su Q, He R, Li M, et al. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nat Methods 2012, 9:403-409.
276. Boutla A, Delidakis C, Tabler M . Developmental defects by antisense-mediated inactivation of micro-RNAs 2 and 13 in Drosophila and the identification of putative target genes. Nucleic Acids Res 2003, 31:4973-4980.
277. Meister G, Landthaler M, Dorsett Y, Tuschl T . Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA (New York, NY) 2004, 10:544-550.
278. Hutvágner G, Simard MJ, Mello CC, Zamore PD . Sequence-specific inhibition of small RNA function. PLoS Biol 2004, 2:E98.
279. Esau C, Davis S, Murray SF, Yu XX, Pandey SK, Pear M, Watts L, Booten SL, Graham M, McKay R, et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab 2006, 3:87-98.
280. Krutzfeldt J, Kuwajima S, Braich R, Rajeev KG, Pena J, Tuschl T, Manoharan M, Stoffel M . Specificity, duplex degradation and subcellular localization of antagomirs. Nucleic Acids Res 2007, 35:2885-2892.
281. Chan JA, Krichevsky AM, Kosik KS . MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 2005, 65:6029-6033.
282. Ørom UA, Kauppinen S, Lund AH . LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene 2006, 372:137-141.
283. Elmén J, Lindow M, Silahtaroglu A, Bak M, Christensen M, Lind-Thomsen A, Hedtjärn M, Hansen JB, Hansen HF, Straarup EM, et al. Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver. Nucleic Acids Res 2008, 36:1153-1162.
284. Elmén J, Lindow M, Schütz S, Lawrence M, Petri A, Obad S, Lindholm M, Hedtjärn M, Hansen HF, Berger U, et al. LNA-mediated microRNA silencing in non-human primates. Nature 2008, 452:896-899.
285. Lanford RE, Hildebrandt-Eriksen ES, Petri A, Persson R, Lindow M, Munk ME, Kauppinen S, Ørum H . Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 2010, 327:198-201.
286. Gebert LFR, Rebhan MAE, Crivelli SEM, Denzler R, Stoffel M, Hall J . Miravirsen (SPC3649) can inhibit the biogenesis of miR-122. Nucleic Acids Res 2014, 42:609-621.
287. Obad S, dos Santos CO, Petri A, Heidenblad M, Broom O, Ruse C, Fu C, Lindow M, Stenvang J, Straarup EM, et al. Silencing of microRNA families by seed-targeting tiny LNAs. Nat Genet 2011, 43:371-378.
288. Ebert MS, Sharp PA . MicroRNA sponges: progress and possibilities. RNA (New York, NY) 2010, 16:2043-2050.
289. Bak RO, Mikkelsen JG . miRNA sponges: soaking up miRNAs for regulation of gene expression. WIREs RNA 2014, 5:317-333.
290. Carè A, Catalucci D, Felicetti F, Bonci D, Addario A, Gallo P, Bang M-L, Segnalini P, Gu Y, Dalton ND, et al. MicroRNA-133 controls cardiac hypertrophy. Nat Med 2007, 13:613-618.
291. Fulga TA, McNeill EM, Binari R, Yelick J, Blanche A, Booker M, Steinkraus BR, Schnall-Levin M, Zhao Y, DeLuca T, et al. A transgenic resource for conditional competitive inhibition of conserved Drosophila microRNAs. Nat Commun 2015, 6:7279.
292. Gentner B, Schira G, Giustacchini A, Amendola M, Brown BD, Ponzoni M, Naldini L . Stable knockdown of microRNA in vivo by lentiviral vectors. Nat Methods 2009, 6:63-66.
293. Li W, Cressy M, Qin H, Fulga T, Van Vactor D, Dubnau J . MicroRNA-276a functions in ellipsoid body and mushroom body neurons for naive and conditioned olfactory avoidance in Drosophila. J Neurosci 2013, 33:5821-5833.
294. Santa-Maria I, Alaniz ME, Renwick N, Cela C, Fulga TA, Van Vactor D, Tuschl T, Clark LN, Shelanski ML, McCabe BD, et al. Dysregulation of microRNA-219 promotes neurodegeneration through post-transcriptional regulation of tau. J Clin Invest 2015, 125:681-686.
295. Mugat B, Akkouche A, Serrano V, Armenise C, Li B, Brun C, Fulga TA, Van Vactor D, Pelisson A, Chambeyron S . MicroRNA-dependent transcriptional silencing of transposable elements in Drosophila follicle cells. PLoS Genet 2015, 11:e1005194.
296. Busto GU, Guven-Ozkan T, Fulga TA, Van Vactor D, Davis RL . microRNAs that promote or inhibit memory formation in Drosophila melanogaster. Genetics 2015, 200:569-580.
297. Lu CS, Zhai B, Mauss A, Landgraf M, Gygi S, Van Vactor D . MicroRNA-8 promotes robust motor axon targeting by coordinate regulation of cell adhesion molecules during synapse development. Philos Trans R Soc Lond B Biol Sci 2014, 369:20130517.
298. Loya CM, McNeill EM, Bao H, Zhang B, Van Vactor D . miR-8 controls synapse structure by repression of the actin regulator enabled. Development 2014, 141:1864-1874.
299. Gao L, Wu L, Hou X, Zhang Q, Zhang F, Ye X, Yang Y, Lin X . Drosophila miR-932 modulates hedgehog signaling by targeting its co-receptor Brother of ihog. Dev Biol 2013, 377:166-176.
300. Markstein M, Pitsouli C, Villalta C, Celniker SE, Perrimon N . Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat Genet 2008, 40:476-483.
301. Becam I, Rafel N, Hong X, Cohen SM, Milán M . Notch-mediated repression of bantam miRNA contributes to boundary formation in the Drosophila wing. Development 2011, 138:3781-3789.
302. Yoon WH, Meinhardt H, Montell DJ . miRNA-mediated feedback inhibition of JAK/STAT morphogen signalling establishes a cell fate threshold. Nature 2011, 13:1062-1069.
303. Zhu Q, Sun W, Okano K, Chen Y, Zhang N, Maeda T, Palczewski K . Sponge transgenic mouse model reveals important roles for the microRNA-183 (miR-183)/96/182 cluster in postmitotic photoreceptors of the retina. J Biol Chem 2011, 286:31749-31760.
304. Chen Z, Liang S, Zhao Y, Han Z . miR-92b regulates Mef2 levels through a negative-feedback circuit during Drosophila muscle development. Development 2012, 139:3543-3552.
305. Herranz H, Hong X, Cohen SM . Mutual repression by bantam miRNA and Capicua links the EGFR/MAPK and Hippo pathways in growth control. Curr Biol 2012, 22:651-657.
306. Otaegi G, Pollock A, Sun T . An optimized sponge for microRNA miR-9 affects spinal motor neuron development in vivo. Front Neurosci 2011, 5:146.
307. Kluiver J, Gibcus JH, Hettinga C, Adema A, Richter MK . Rapid generation of microRNA sponges for microRNA inhibition. PloS One 2012, 7:e29275.
308. Kluiver J, Slezak-Prochazka I, Smigielska-Czepiel K, Halsema N, Kroesen B-J, van den Berg A . Generation of miRNA sponge constructs. Methods 2012, 58:113-117.
309. Haraguchi T, Nakano H, Tagawa T, Ohki T, Ueno Y, Yoshida T, Iba H . A potent 2'-O-methylated RNA-based microRNA inhibitor with unique secondary structures. Nucleic Acids Res 2012, 40:e58.
310. Bak RO, Hollensen AK, Primo MN, Sorensen CD, Mikkelsen JG . Potent microRNA suppression by RNA Pol II-transcribed 'Tough Decoy' inhibitors. RNA (New York, NY) 2013, 19:280-293.
311. Hollensen AK, Bak RO, Haslund D, Mikkelsen JG . Suppression of microRNAs by dual-targeting and clustered tough decoy inhibitors. RNA Biol 2013, 10:406-414.
312. Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A, Farzan-Kashani R, Zuker M, Pasquinelli AE, Ruvkun G, et al. MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet 2004, 36:1079-1083.
313. Jin M, Zhang T, Liu C, Badeaux MA, Liu B, Liu R, Jeter C, Chen X, Vlassov AV, Tang DG . miRNA-128 suppresses prostate cancer by inhibiting BMI-1 to inhibit tumor-initiating cells. Cancer Res 2014, 74:4183-4195.
314. Brennecke J, Stark A, Russell RB, Cohen SM . Principles of microRNA-target recognition. PLoS Biol 2005, 3:e85.
315. Yoo B, Kavishwar A, Ghosh SK, Barteneva N, Yigit MV, Moore A, Medarova Z . Detection of miRNA expression in intact cells using activatable sensor oligonucleotides. Chem Biol 2014, 21:199-204.
316. Schratt GM, Tuebing F, Nigh EA, Kane CG, Sabatini ME, Kiebler M, Greenberg ME . A brain-specific microRNA regulates dendritic spine development. Nature 2006, 439:283-289.
317. Luo W, Sehgal A . Regulation of circadian behavioral output via a microRNA-JAK/STAT circuit. Cell 2012, 148:765-779.
318. Ameres SL, Martinez J, Schroeder R . Molecular basis for target RNA recognition and cleavage by human RISC. Cell 2007, 130:101-112.
319. Choi W-Y, Giraldez AJ, Schier AF . Target protectors reveal dampening and balancing of nodal agonist and antagonist by miR-430. Science 2007, 318:271-274.
320. Staton AA, Giraldez AJ . Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo. Nat Protoc 2011, 6:2035-2049.
321. Staton AA, Knaut H, Giraldez AJ . miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration. Nat Genet 2011, 43:204-211.
322. Gehrke S, Imai Y, Sokol N, Lu B . Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression. Nature 2010, 466:637-641.
323. Cacchiarelli D, Incitti T, Martone J, Cesana M, Cazzella V, Santini T, Sthandier O, Bozzoni I . miR-31 modulates dystrophin expression: new implications for Duchenne muscular dystrophy therapy. EMBO Rep 2011, 12:136-141.
324. Knauss JL, Bian S, Sun T . Plasmid-based target protectors allow specific blockade of miRNA silencing activity in mammalian developmental systems. Front Cell Neurosci 2013, 7:163.
325. Schmid B, Hruscha A, Hogl S, Banzhaf-Strathmann J, Strecker K, van der Zee J, Teucke M, Eimer S, Hegermann J, Kittelmann M, et al. Loss of ALS-associated TDP-43 in zebrafish causes muscle degeneration, vascular dysfunction, and reduced motor neuron axon outgrowth. Proc Natl Acad Sci USA 2013, 110:4986-4991.
326. Chen S, Xue Y, Wu X, Cong L, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA . Global microRNA depletion suppresses tumor angiogenesis. Genes Dev 2014, 28:1054-1067.
327. Bassett AR, Azzam G, Wheatley L, Tibbit C, Rajakumar T, McGowan S, Stanger N, Ewels PA, Taylor S, Ponting CP, et al. Understanding functional miRNA-target interactions in vivo by site-specific genome engineering. Nat Commun 2014, 5:4640.
328. Ecsedi M, Rausch M, Großhans H . The let-7 microRNA directs vulval development through a single target. Dev Cell 2015, 32:335-344.
329. Shalem O, Sanjana NE, Zhang F . High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet 2015, 16:299-311.
330. Osella M, Bosia C, Corá D, Caselle M . The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol 2011, 7:e1001101.
331. Denzler R, Agarwal V, Stefano J, Bartel DP, Stoffel M . Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell 2014, 54:766-776.
332. Tay Y, Rinn J, Pandolfi PP . The multilayered complexity of ceRNA crosstalk and competition. Nature 2014, 505:344-352.
333. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J . Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 2007, 39:1033-1037.
334. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP . A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 2010, 465:1033-1038.
335. Tay Y, Kats L, Salmena L, Weiss D, Tan SM, Ala U, Karreth F, Poliseno L, Provero P, Di Cunto F, et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 2011, 147:344-357.
336. Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA, et al. In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 2011, 147:382-395.
337. Sumazin P, Yang X, Chiu H-S, Chung W-J, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, et al. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 2011, 147:370-381.
338. Poliseno L, Pandolfi PP . PTEN ceRNA networks in human cancer. Methods 2015, 77-78:41-50.
339. Karreth FA, Reschke M, Ruocco A, Ng C, Chapuy B, Léopold V, Sjoberg M, Keane TM, Verma A, Ala U, et al. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 2015, 161:319-332.
340. Tan JY, Vance KW, Varela MA, Sirey T, Watson LM, Curtis HJ, Marinello M, Alves S, Steinkraus BR, Cooper S, et al. Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7. Nat Struct Mol Biol 2014, 21:955-961.
341. Luna JM, Scheel TKH, Danino T, Shaw KS, Mele A, Fak JJ, Nishiuchi E, Takacs CN, Catanese MT, de Jong YP, et al. Hepatitis C virus RNA functionally sequesters miR-122. Cell 2015, 160:1099-1110.
342. Jeck WR, Sharpless NE . Detecting and characterizing circular RNAs. Nat Biotechnol 2014, 32:453-461.
343. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J . Natural RNA circles function as efficient microRNA sponges. Nature 2013, 495:384-388.
344. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013, 495:333-338.