Inferring causative variants in microRNA target sites

Nucleic Acids Research

Volumn 39, Issue 16, 2011, Pages

  Thomas, Laurent F ^a,b   Saito, Takaya ^a   Sætrom, Pål ^a,b  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^b Interagon AS   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

3' UNTRANSLATED REGION; ALLELE; ARTICLE; BREAST CANCER; CAUSAL ATTRIBUTION; COMPUTER PREDICTION; CONTROLLED STUDY; DATA ANALYSIS; DISEASE ASSOCIATION; GENE CONTROL; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC VARIABILITY; HAPLOTYPE MAP; HUMAN; INTERNET; MATHEMATICAL MODEL; PARKINSON DISEASE; PRIORITY JOURNAL; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; ASTHMA; BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; DISEASE; FEMALE; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MICRORNAS; PARKINSON DISEASE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 80052476453     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr414     Document Type: Article

References (36)

1. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory Functions. Cell, 136, 215-233.
2. Brennecke, J., Stark, A., Russell, R. and Cohen, S. (2005) Principles of MicroRNA-target recognition. PLoS Biol., 3, 404-418.
3. Didiano, D. and Hobert, O. (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat. Struct. Mol. Biol., 13, 849-851. (Pubitemid 44338780)
4. Gaidatzis, D., van Nimwegen, E., Hausser, J. and Zavolan, M. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics, 8, 248.
5. Saetrom, P., Heale, B.S.E., Snove, O. Jr, Aagaard, L., Alluin, J. and Rossi, J.J. (2007) Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res., 35, 2333-2342. (Pubitemid 47073716)
6. Hirschhorn, J. and Daly, M. (2005) Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet., 6, 95-108. (Pubitemid 40179532)
7. Donnelly, P. (2008) Progress and challenges in genome-wide association studies in humans. Nature, 456, 728-731.
8. Mishra, P.J. and Bertino, J.R. (2009) MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Pharmacogenomics, 10, 399-416.
9. Borel, C. and Antonarakis, S.E. (2008) Functional genetic variation of human miRNAs and phenotypic consequences. Mamm. Genome, 19, 503-509.
10. Landi, D., Gemignani, F., Naccarati, A., Pardini, B., Vodicka, P., Vodickova, L., Novotny, J., Foersti, A., Hemminki, K. and Canzian, F. (2008) Polymorphisms within micro-RNA-binding sites and risk of sporadic colorectal cancer. Carcinogenesis, 29, 579-584. (Pubitemid 351404875)
11. Sethupathy, P. and Collins, F.S. (2008) MicroRNA target site polymorphisms and human disease. Trends Genet., 24, 489-497.
12. Bao, L., Zhou, M., Wu, L., Lu, L., Goldowitz, D., Williams, R.W. and Cui, Y. (2007) PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res., 35, D51-D54. (Pubitemid 46056169)
13. Lewis, B., Burge, C. and Bartel, D. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20. (Pubitemid 40094598)
14. Georges, M., Clop, A., Marcq, F., Takeda, H., Pirottin, D., Hiard, S., Tordoir, X., Caiment, F., Meish, F., Bibe, B. et al. (2006) Polymorphic microRNA-target interactions: a novel source of phenotypic variation. Cold Spring Harb. Symp. Quant. Biol., 71, 343-350.
15. Xie, X., Lu, J., Kulbokas, E., Golub, T., Mootha, V., Lindblad-Toh, K., Lander, E. and Kellis, M. (2005) Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals. Nature, 434, 338-345. (Pubitemid 40469170)
16. Barenboim, M., Zoltick, B.J., Guo, Y. and Weinberger, D.R. (2010) MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum. Mutat., 31, 1223-1232.
17. Nicoloso, M.S., Sun, H., Spizzo, R., Kim, H., Wickramasinghe, P., Shimizu, M., Wojcik, S.E., Ferdin, J., Kunej, T., Xiao, L. et al. (2010) Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Cancer Res., 70, 2789-2798.
18. Miranda, K.C., Huynh, T., Tay, Y., Ang, Y.-S., Tam, W.-L., Thomson, A.M., Lim, B. and Rigoutsos, I. (2006) A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell, 126, 1203-1217. (Pubitemid 44380294)
19. Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M. Jr, Jungkamp, A.-C., Munschauer, M. et al. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141, 129-141.
20. Grimson, A., Farh, K.K.-H., Johnston, W.K., Garrett-Engele, P., Lim, L.P. and Bartel, D.P. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell, 27, 91-105. (Pubitemid 46991392)
21. Int HapMap Consortium. In Frazer, K.A., Ballinger, D.G., Cox, D.R., Hinds, D.A., Stuve, L.L., Gibbs, R.A., Belmont, J.W., Boudreau, A., Hardenbol, P. et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861. (Pubitemid 47598626)
22. Int Human Genome Sequencing Conso. In Lander, E., Linton, L., Birren, B., Nusbaum, C., Zody, M., Baldwin, J., Devon, K., Dewar, K., Doyle, M. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921. (Pubitemid 32165345)
23. Mouse Genome Sequencing Consor. In Waterston, R., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562. (Pubitemid 35477048)
24. Kuhn, R.M., Karolchik, D., Zweig, A.S., Wang, T., Smith, K.E., Rosenbloom, K.R., Rhead, B., Raney, B.J., Pohl, A., Pheasant, M. et al. (2009) The UCSC genome browser database: update 2009. Nucleic Acids Res., 37, D755-D761.
25. Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-D158. (Pubitemid 351149713)
26. Hunter, D.J., Kraft, P., Jacobs, K.B., Cox, D.G., Yeager, M., Hankinson, S.E., Wacholder, S., Wang, Z., Welch, R., Hutchinson, A. et al. (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nature Genet., 39, 870-874. (Pubitemid 47014500)
27. Maraganore, D., de Andrade, M., Lesnick, T., Strain, K., Farrer, M., Rocca, W., Pant, P., Frazer, K., Cox, D. and Ballinger, D. (2005) High-resolution whole-genome association study of Parkinson disease. Am. J. Hum. Genet., 77, 685-693. (Pubitemid 41513273)
28. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S. and Manolio, T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
29. Saito, T. and Saetrom, P. (2010) A two-step site and mRNA-level model for predicting microRNA targets. BMC Bioinformatics, 11, 612.
30. Barrett, J., Fry, B., Maller, J. and Daly, M. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265. (Pubitemid 40202029)
31. Kim, J. and Bartel, D.P. (2009) Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression. Nat. Biotechnol., 27, 472-477.
32. Rehmsmeier, M., Steffen, P., Hochsmann, M. and Giegerich, R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA-Publ. RNA Soc., 10, 1507-1517. (Pubitemid 39288185)
33. Saetrom, P., Biesinger, J., Li, S.M., Smith, D., Thomas, L.F., Majzoub, K., Rivas, G.E., Alluin, J., Rossi, J.J., Krontiris, T.G. et al. (2009) A risk variant in an miR-125b binding site in BMPR1B is associated with breast cancer pathogenesis. Cancer Res., 69, 7459-7465.
34. Tan, Z., Randall, G., Fan, J., Camoretti-Mercado, B., Brockman-Schneider, R., Pan, L., Solway, J., Gern, J.E., Lemanske, R.F. Jr and Nicolae, D. (2007) Allele-specific targeting of microRNAs to HLA-G and risk of asthma. Am. J. Hum. Genet., 81, 829-834. (Pubitemid 47596550)
35. Wang, G., van der Walt, J.M., Mayhew, G., Li, Y.-J., Zuechner, S., Scott, W.K., Martin, E.R. and Vance, J.M. (2008) Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein. Am. J. Hum. Genet., 82, 283-289.
36. Friedman, R.C., Farh, K.K.-H., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.