MicroRNA target prediction and validation

Advances in Experimental Medicine and Biology

Volumn 774, Issue , 2013, Pages 39-53

  Ritchie, William ^a   Rasko, John E J ^a,b   Flamant, Stéphane ^c  

^a UNIVERSITY OF SYDNEY   (Australia)

^b ROYAL PRINCE ALFRED HOSPITAL   (Australia)

^c Centre National de la Recherche Scientifique   (France)

Author keywords

Bioinformatics; Experimental validation; Gene regulation; MicroRNA; MicroRNA expression; Target genes; Target prediction algorithms

Indexed keywords

MESSENGER RNA; MICRORNA;

ANIMAL; BIOLOGY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; REVIEW;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER;

MLCS; MLOWN;

EID: 84934442244     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-7-5590-1_3     Document Type: Article

References (86)

1. Lai EC (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative posttranscriptional regulation. Nat Genet 30:363-364
2. John B, Enright AJ, Aravin A et al (2004) Human MicroRNA targets. PLoS Biol 2:e363
3. Kruger J, Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34:W451-W454
4. Kertesz M, Iovino N, Unnerstall U et al (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39:1278-1284
5. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20
6. Grimson A, Farh KK, Johnston WK et al (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27:91-105
7. Ritchie W, Flamant S, Rasko JE (2009) MicroRNA target prediction: traps for the unwary. Nat Methods 6:397-398
8. Ritchie W, Flamant S, Rasko JE (2010) MimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Bioinformatics 26:223-227
9. Krek A, Grun D, Poy MN et al (2005) Combinatorial microRNA target predictions. Nat Genet 37:495-500
10. Xiao C, Rajewsky K (2009) MicroRNA control in the immune system: basic principles. Cell 136:26-36
11. Tsang JS, Ebert MS, van Oudenaarden A (2010) Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell 38:140-153
12. Lim LP, Lau NC, Garrett-Engele P et al (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769-773
13. Ritchie W, Rajasekhar M, Flamant S et al (2009) Conserved expression patterns predict microRNA targets. PLoS Comput Biol 5:e1000513
14. Selbach M, Schwanhausser B, Thierfelder N et al (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455:58-63
15. Brennecke J, Stark A, Russell RB et al (2005) Principles of microRNA-target recognition. PLoS Biol 3:e85
16. Lee RC, Feinbaum RL, Ambros V (1993) The C. Elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843-854
17. Reinhart BJ, Slack FJ, Basson M et al (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901-906
18. Brennecke J, Hipfner DR, Stark A et al (2003) Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113:25-36
19. Orom UA, Lund AH (2010) Experimental identification of microRNA targets. Gene 451:1-5
20. Thomas M, Lieberman J, Lal A (2010) Desperately seeking microRNA targets. Nat Struct Mol Biol 17:1169-1174
21. Thomson DW, Bracken CP, Goodall GJ (2011) Experimental strategies for microRNA target identification. Nucleic Acids Res 39:6845-6853
22. Doench JG, Petersen CP, Sharp PA (2003) SiRNAs can function as miRNAs. Genes Dev 17:438-442
23. Zeng Y, Yi R, Cullen BR (2003) MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc Natl Acad Sci U S A 100:9779-9784
24. Kiriakidou M, Nelson PT, Kouranov A et al (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18:1165-1178
25. Yekta S, Shih IH, Bartel DP (2004) MicroRNAdirected cleavage of HOXB8 mRNA. Science 304:594-596
26. Krutzfeldt J, Rajewsky N, Braich R et al (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature 438:685-689
27. Ebert MS, Neilson JR, Sharp PA (2007) MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4:721-726
28. Standart N, Jackson RJ (2007) MicroRNAs repress translation of m7Gppp-capped target mRNAs in vitro by inhibiting initiation and promoting deadenylation. Genes Dev 21:1975-1982
29. Guo H, Ingolia NT, Weissman JS et al (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835-840
30. Farh KK, Grimson A, Jan C et al (2005) The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310:1817-1821
31. Vinther J, Hedegaard MM, Gardner PP et al (2006) Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res 34:e107
32. Ong SE, Blagoev B, Kratchmarova I et al (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376-386
33. Baek D, Villen J, Shin C et al (2008) The impact of microRNAs on protein output. Nature 455:64-71
34. Zhu S, Si ML, Wu H et al (2007) MicroRNA-21 targets the tumor suppressor gene tropomyosin 1 (TPM1). J Biol Chem 282:14328-14336
35. Tian Z, Greene AS, Pietrusz JL et al (2008) MicroRNA-target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis. Genome Res 18:404-411
36. Iliopoulos D, Malizos KN, Oikonomou P et al (2008) Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and in flammatory networks. PLoS One 3:e3740
37. Jovanovic M, Reiter L, Picotti P et al (2010) A quantitative targeted proteomics approach to validate predicted microRNA targets in C. Elegans. Nat Methods 7:837-842
38. Gygi SP, Rist B, Gerber SA et al (1999) Quantitative analysis of complex protein mixtures using isotopecoded affinity tags. Nat Biotechnol 17:994-999
39. Anderson L, Hunter CL (2006) Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 5:573-588
40. Krijgsveld J, Ketting RF, Mahmoudi T et al (2003) Metabolic labeling of C. Elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol 21:927-931
41. Beitzinger M, Peters L, Zhu JY et al (2007) Identification of human microRNA targets from isolated argonaute protein complexes. RNA Biol 4:76-84
42. Easow G, Teleman AA, Cohen SM (2007) Isolation of microRNA targets by miRNP immunopurification. RNA 13:1198-1204
43. Karginov FV, Conaco C, Xuan Z et al (2007) A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A 104:19291-19296
44. Hendrickson DG, Hogan DJ, Herschlag D et al (2008) Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS One 3:e2126
45. Landthaler M, Gaidatzis D, Rothballer A et al (2008) Molecular characterization of human Argonautecontaining ribonucleoprotein complexes and their bound target mRNAs. RNA 14:2580-2596
46. Wang WX, Wilfred BR, Hu Y et al (2010) Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes. RNA 16:394-404
47. Zhang L, Ding L, Cheung TH et al (2007) Systematic identification of C. Elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol Cell 28:598-613
48. Mourelatos Z, Dostie J, Paushkin S et al (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16:720-728
49. Tan LP, Seinen E, Duns G et al (2009) A high throughput experimental approach to identify miRNA targets in human cells. Nucleic Acids Res 37:e137
50. Licatalosi DD, Mele A, Fak JJ et al (2008) HITSCLIP yields genome-wide insights into brain alternative RNA processing. Nature 456:464-469
51. Chi SW, Zang JB, Mele A et al (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460:479-486
52. Zisoulis DG, Lovci MT, Wilbert ML et al (2010) Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol 17:173-179
53. Leung AK, Young AG, Bhutkar A et al (2011) Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nat Struct Mol Biol 18:237-244
54. Hafner M, Landthaler M, Burger L et al (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129-141
55. Duursma AM, Kedde M, Schrier M et al (2008) miR-148 targets human DNMT3b protein coding region. RNA 14:872-877
56. Forman JJ, Legesse-Miller A, Coller HA (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci U S A 105:14879-14884
57. Tay Y, Zhang J, Thomson AM et al (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455:1124-1128
58. Schnall-Levin M, Zhao Y, Perrimon N et al (2010) Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3′ UTRs. Proc Natl Acad Sci U S A 107:15751-15756
59. Schnall-Levin M, Rissland OS, Johnston WK et al (2011) Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res 21:1395-1403
60. Fang Z, Rajewsky N (2011) The impact of miRNA target sites in coding sequences and in 3′ UTRs. PLoS One 6:e18067
61. Miranda KC, Huynh T, Tay Y et al (2006) A patternbased method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126:1203-1217
62. Orom UA, Lund AH (2007) Isolation of microRNA targets using biotinylated synthetic microRNAs. Methods 43:162-165
63. Orom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 5′ UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30:460-471
64. Christoffersen NR, Shalgi R, Frankel LB et al (2010) p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC. Cell Death Differ 17:236-245
65. Hsu RJ, Yang HJ, Tsai HJ (2009) Labeled microRNA pull-down assay system: an experimental approach for high-throughput identification of microRNA-target mRNAs. Nucleic Acids Res 37:e77
66. Zhao Y, Samal E, Srivastava D (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436:214-220
67. Nonne N, Ameyar-Zazoua M, Souidi M et al (2010) Tandem affinity purification of miRNA target mRNAs (TAP-Tar). Nucleic Acids Res 38:e20
68. Vatolin S, Navaratne K, Weil RJ (2006) A novel method to detect functional microRNA targets. J Mol Biol 358:983-996
69. Andachi Y (2008) A novel biochemical method to identify target genes of individual microRNAs: identification of a new Caenorhabditis elegans let-7 target. RNA 14:2440-2451
70. Llave C, Xie Z, Kasschau KD et al (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053-2056
71. Addo-Quaye C, Eshoo TW, Bartel DP et al (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18:758-762
72. German MA, Pillay M, Jeong DH et al (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26:941-946
73. Franco-Zorrilla JM, Del Toro FJ, Godoy M et al (2009) Genome-wide identification of small RNA targets based on target enrichment and microarray hybridizations. Plant J 59:840-850
74. Karginov FV, Cheloufi S, Chong MM et al (2010) Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol Cell 38:781-788
75. Li YF, Zheng Y, Addo-Quaye C et al (2010) Transcriptome-wide identification of microRNA targets in rice. Plant J 62:742-759
76. Shin C, Nam JW, Farh KK et al (2010) Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell 38:789-802
77. Bracken CP, Szubert JM, Mercer TR et al (2011) Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNAindependent endonucleolytic cleavage. Nucleic Acids Res 39:5658-5668
78. Jiao Y, Riechmann JL, Meyerowitz EM (2008) Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell 20:2571-2585
79. Xiao C, Calado DP, Galler G et al (2007) MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell 131:146-159
80. Zhao Y, Ransom JF, Li A et al (2007) Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 129:303-317
81. Johnnidis JB, Harris MH, Wheeler RT et al (2008) Regulation of progenitor cell proliferation and granulocyte function by microRNA-223. Nature 451:1125-1129
82. Ventura A, Young AG, Winslow MM et al (2008) Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 132:875-886
83. Patrick DM, Zhang CC, Tao Y et al (2010) Defective erythroid differentiation in miR-451 mutant mice mediated by 14-3-3zeta. Genes Dev 24:1614-1619
84. Park CY, Choi YS, McManus MT (2010) Analysis of microRNA knockouts in mice. Hum Mol Genet 19:R169-R175
85. Prosser HM, Koike-Yusa H, Cooper JD et al (2011) A resource of vectors and ES cells for targeted deletion of microRNAs in mice. Nat Biotechnol 29:840-845
86. Tsang JS, Ebert MS, van Oudenaarden A (2010) Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell 38:140-153