Large-Scale Screens of miRNA-mRNA Interactions Unveiled That the 3′UTR of a Gene Is Targeted by Multiple miRNAs

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Zhou, Peng ^a   Xu, Weiyi ^a   Peng, Xueling ^a   Luo, Zhenhua ^a   Xing, Qinghe ^b   Chen, Xulin ^c   Hou, Chengqian ^d   Liang, Weihong ^d   Zhou, Jianwen ^a   Wu, Xiaoyan ^a   Songyang, Zhou ^a   Jiang, Songshan ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c Gene Science and Health company   (China)

^d HENAN NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

LUCIFERASE; MESSENGER RNA; MICRORNA;

3' UNTRANSLATED REGION; ALGORITHM; ARTICLE; BAYES THEOREM; BINDING SITE; CONTROLLED STUDY; GENE EXPRESSION; GENE FUNCTION; GENE INTERACTION; GENE LIBRARY; GENE TARGETING; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; IN VITRO STUDY; MAMMAL CELL; PHYLOGENY; PREDICTION; REPORTER GENE; RNA BINDING; RNA GENE; SCREENING; SUPPORT VECTOR MACHINE;

3' UNTRANSLATED REGIONS; BASE SEQUENCE; BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; BINDING SITES; CARRIER PROTEINS; CELL LINE; CONSERVED SEQUENCE; EPISTASIS, GENETIC; GENE EXPRESSION; GENE LIBRARY; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MICROFILAMENT PROTEINS; MICRORNAS; MUTATION; REPRODUCIBILITY OF RESULTS; RNA INTERFERENCE; RNA, MESSENGER; TELOMERE-BINDING PROTEINS; TELOMERIC REPEAT BINDING PROTEIN 2; TUMOR SUPPRESSOR PROTEINS;

ANIMALIA; MAMMALIA;

EID: 84879930668     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068204     Document Type: Article

References (52)

1. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
2. Kusenda B, Mraz M, Mayer J, Pospisilova S, (2006) MicroRNA biogenesis, functionality and cancer relevance. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 150: 205-215.
3. Chi SW, Zang JB, Mele A, Darnell RB, (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
4. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
5. Krol J, Loedige I, Filipowicz W, (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11: 597-610.
6. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, et al. (2008) The impact of microRNAs on protein output. Nature 455: 64-71.
7. Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
8. 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.
9. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
10. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, et al. (2005) A microRNA polycistron as a potential human oncogene. Nature 435: 828-833.
11. Vosa U, Vooder T, Kolde R, Fischer K, Valk K, et al. (2011) Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer. Genes Chromosomes Cancer 50: 812-822.
12. Voinnet O, (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
13. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
14. 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.
15. Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, et al. (2009) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10: 295.
16. John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human MicroRNA targets. PLoS Biol 2: e363.
17. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
18. Rajewsky N, (2006) microRNA target predictions in animals. Nat Genet 38Suppl: S8-13.
19. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
20. Wang X, (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14: 1012-1017.
21. Wang X, El Naqa IM, (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24: 325-332.
22. Gaidatzis D, van Nimwegen E, Hausser J, Zavolan M, (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 8: 69.
23. Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I, (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455: 1124-1128.
24. Wang Q, Li DC, Li ZF, Liu CX, Xiao YM, et al. (2011) Upregulation of miR-27a contributes to the malignant transformation of human bronchial epithelial cells induced by SV40 small T antigen. Oncogene 30: 3875-3886.
25. Wu T, Zhou H, Hong Y, Li J, Jiang X, et al. (2012) miR-30 family members negatively regulate osteoblast differentiation. J Biol Chem 287: 7503-7511.
26. Nelson PT, Kiriakidou M, Mourelatos Z, Tan GS, Jennings MH, et al. (2010) High-throughput experimental studies to identify miRNA targets directly, with special focus on the mammalian brain. Brain Research 1338: 122-130.
27. Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
28. Carmell MA, Xuan Z, Zhang MQ, Hannon GJ, (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 16: 2733-2742.
29. Shen X, Fang J, Lv X, Pei Z, Wang Y, et al. (2011) Heparin impairs angiogenesis through inhibition of microRNA-10b. J Biol Chem 286: 26616-26627.
30. Ebert MS, Neilson JR, Sharp PA, (2007) MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4: 721-726.
31. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
32. Zhang XD, (2011) Illustration of SSMD, z Score, SSMD*, z* Score, and t Statistic for Hit Selection in RNAi High-Throughput Screens. Journal of Biomolecular Screening 16: 775-785.
33. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
34. Chen CZ, Li L, Lodish HF, Bartel DP, (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83-86.
35. Varambally S, Cao Q, Mani RS, Shankar S, Wang X, et al. (2008) Genomic loss of microRNA-101 leads to overexpression of histone methyltransferase EZH2 in cancer. Science 322: 1695-1699.
36. Ma L, Teruya-Feldstein J, Weinberg RA, (2007) Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 449: 682-688.
37. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB, (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
38. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
39. Lall S, Grun D, Krek A, Chen K, Wang YL, et al. (2006) A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 16: 460-471.
40. Yousef M, Jung S, Kossenkov AV, Showe LC, Showe MK, (2007) Naive Bayes for microRNA target predictions-machine learning for microRNA targets. Bioinformatics 23: 2987-2992.
41. Keene JD, Komisarow JM, Friedersdorf MB, (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1: 302-307.
42. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, et al. (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302: 1212-1215.
43. Shirdel EA, Xie W, Mak TW, Jurisica I, (2011) NAViGaTing the micronome-using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS One 6: e17429.
44. Wu S, Huang S, Ding J, Zhao Y, Liang L, et al. (2010) Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region. Oncogene 29: 2302-2308.
45. Vo NK, Dalton RP, Liu N, Olson EN, Goodman RH, (2010) Affinity purification of microRNA-133a with the cardiac transcription factor, Hand2. Proc Natl Acad Sci U S A 107: 19231-19236.
46. Jiang Q, Feng MG, Mo YY, (2009) Systematic validation of predicted microRNAs for cyclin D1. BMC Cancer 9: 194.
47. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG, (2009) Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25: 3049-3055.
48. Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 39: D163-169.
49. Didiano D, Hobert O, (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 13: 849-851.
50. Didiano D, Hobert O, (2008) Molecular architecture of a miRNA-regulated 3′ UTR. RNA 14: 1297-1317.
51. Marin RM, Vanicek J, (2011) Efficient use of accessibility in microRNA target prediction. Nucleic Acids Res 39: 19-29.
52. Patraquim P, Warnefors M, Alonso CR, (2011) Evolution of Hox post-transcriptional regulation by alternative polyadenylation and microRNA modulation within 12 Drosophila genomes. Mol Biol Evol 28: 2453-2460.