Accurate microRNA target prediction using detailed binding site accessibility and machine learning on proteomics data

Frontiers in Genetics

Volumn 2, Issue JAN, 2012, Pages

  Reczko, Martin ^a,b   Maragkakis, Manolis ^a,c,d   Alexiou, Panagiotis ^a,d,e   Papadopoulos, Giorgio L ^a   Hatzigeorgiou, Artemis G ^a  

^a BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING   (Greece)

^b Synaptic Ltd   (Greece)

^c MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

^e ARISTOTLE UNIVERSITY OF THESSALONIKI   (Greece)

Author keywords

Binding site structure; Micrornas; Target prediction

Indexed keywords

EID: 84868300633     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2011.00103     Document Type: Article

References (44)

1. Ambros, V. (2004). The functions of animal microRNAs. Nature 431, 350-355.
2. Baek, D., Villen, J., Shin, C., Camargo, F. D., Gygi, S. P., and Bartel, D. P. (2008). The impact of microRNAs on protein output. Nature 455, 64-71.
3. Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233.
4. Brennecke, J., Stark, A., Russell, R. B., and Cohen, S. M. (2005). Principles of microRNA-target recognition. PLoS Biol. 3, e85. doi:10.1371/journal.pbio.0030085
5. Chi, S. W., Zang, J. B., Mele, A., and Darnell, R. B. (2009). Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460, 479-486.
6. Ding, Y., Chan, C. Y., and Lawrence, C. E. (2004). Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32, W135-W141.
7. Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D. S. (2003). MicroRNA targets in Drosophila. Genome Biol. 5, R1.
8. Filipowicz, W., Bhattacharyya, S. N., and Sonenberg, N. (2008). Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 9, 102-114.
9. Flicek, P., Aken, B. L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, S. C., Eyre, T., Fitzgerald, S., Fernandez-Banet, J., Graf, S., Haider, S., Hammond, M., Holland, R., Howe, K. L., Howe, K., Johnson, N., Jenkinson, A., Kahari, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A. J., Vogel, J., White, S., Wood, M., Birney, E., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, T. J., Kasprzyk, A., Proctor, G., Smith, J., Ureta-Vidal, A., and Searle, S. (2008). Ensembl 2008. Nucleic Acids Res. 36, D707-D714.
10. Friedman, R. C., Farh, K. K., Burge, C. B., and Bartel, D. P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105.
11. Gaidatzis, D., Van Nimwegen, E., Hausser, J., and Zavolan, M. (2007). Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics 8, 69. doi:10.1186/1471-2105-8-69
12. 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.
13. Grimson, A., Farh, K. K., 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.
14. Hammell, M., Long, D., Zhang, L., Lee, A., Carmack, C. S., Han, M., Ding, Y., and Ambros, V. (2008). mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat. Methods 5, 813-819.
15. John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004). Human MicroRNA targets. PLoS Biol. 2, e363. doi:10.1371/journal.pbio.0020363
16. Karolchik, D., Hinrichs, A. S., and Kent, W. J. (2007). The UCSC genome browser. Curr. Protoc. Bioinformatics Chapter 1, Unit 1.4.
17. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., and Segal, E. (2007). The role of site accessibility in microRNA target recognition. Nat. Genet. 39, 1278-1284.
18. Kiriakidou, M., Nelson, P. T., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z., and Hatzigeorgiou, A. (2004). A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18, 1165-1178.
19. Kolda, T. G., Lewis, R. M., and Torczon, V. (2003). Optimization by direct search: new perspectives on some classical and modern methods. SIAM Rev. 45, 385-482.
20. Krek, A., Grun, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., Macmenamin, P., Da Piedade, I., Gunsalus, K. C., Stoffel, M., and Rajewsky, N. (2005). Combinatorial microRNA target predictions. Nat. Genet. 37, 495-500.
21. Krutzfeldt, J., Rajewsky, N., Braich, R., Rajeev, K. G., Tuschl, T., Manoharan, M., and Stoffel, M. (2005). Silencing of microRNAs in vivo with 'antagomirs'. Nature 438, 685-689.
22. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science 294, 853-858.
23. Lall, S., Grun, D., Krek, A., Chen, K., Wang, Y. L., Dewey, C. N., Sood, P., Colombo, T., Bray, N., Macmenamin, P., Kao, H. L., Gunsalus, K. C., Pachter, L., Piano, F., and Rajewsky, N. (2006). A genome-wide map of conserved microRNA targets in C. elegans. Curr. Biol. 16, 460-471.
24. Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862.
25. Lee, R. C., and Ambros, V. (2001). An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862-864.
26. Lee, R. C., Feinbaum, R. L., and Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
27. Lewis, B. P., Burge, C. B., and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20.
28. Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P., and Burge, C. B. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798.
29. Liang, Y. (2008). An expression meta-analysis of predicted microRNA targets identifies a diagnostic signature for lung cancer. BMC Med. Genomics 1, 61. doi:10.1186/1755-8794-1-61
30. Lim, L. P., Lau, N. C., Garrett-Engele, P., Grimson, A., Schelter, J. M., Castle, J., Bartel, D. P., Linsley, P. S., and Johnson, J. M. (2005). Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773.
31. Long, D., Lee, R., Williams, P., Chan, C. Y., Ambros, V., and Ding, Y. (2007). Potent effect of target structure on microRNA function. Nat. Struct. Mol. Biol. 14, 287-294.
32. Maragkakis, M., Alexiou, P., Papadopoulos, G. L., Reczko, M., Dalamagas, T., Giannopoulos, G., Goumas, G., Koukis, E., Kourtis, K., Simossis, V. A., Sethupathy, P., Vergoulis, T., Koziris, N., Sellis, T., Tsanakas, P., and Hatzigeorgiou, A. G. (2009a). Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10, 295. doi:10.1186/1471-2105-10-295
33. Maragkakis, M., Reczko, M., Simossis, V. A., Alexiou, P., Papadopoulos, G. L., Dalamagas, T., Giannopoulos, G., Goumas, G., Koukis, E., Kourtis, K., Vergoulis, T., Koziris, N., Sellis, T., Tsanakas, P., and Hatzigeorgiou, A. G. (2009b). DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res. 37, W273-W276.
34. 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.
35. Papadopoulos, G. L., Alexiou, P., Maragkakis, M., Reczko, M., and Hatzigeorgiou, A. G. (2009a). DIANA-mirPath: integrating human and mouse microRNAs in pathways. Bioinformatics 25, 1991-1993.
36. Papadopoulos, G. L., Reczko, M., Simossis, V. A., Sethupathy, P., and Hatzigeorgiou, A. G. (2009b). The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res. 37, D155-D158.
37. Quek, C., Pasquier, M., and Kumar, N. (2008). A novel recurrent neural network-based prediction system for option trading and hedging. Appl. Intell. 29, 138-151.
38. Reczko, M., and Hatzigeorgiou, A. (2004). Prediction of the subcellular localization of eukaryotic proteins using sequence signals and composition. Proteomics 4, 1591-1596.
39. Rehmsmeier, M., Steffen, P., Hochsmann, M., and Giegerich, R. (2004). Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507-1517.
40. Robinson, A. J., Cook, G., Ellis, D., Fosler-Lussier, E., Renals, S., and Williams, D. A. G. (2002). Connectionist speech recognition of broadcast news. Speech Commun. 37, 27-45.
41. Selbach, M., Schwanhausser, B., Thierfelder, N., Fang, Z., Khanin, R., and Rajewsky, N. (2008). Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58-63.
42. Sethupathy, P., Corda, B., and Hatzigeorgiou, A. G. (2006). TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12, 192-197.
43. Stark, A., Brennecke, J., Russell, R. B., and Cohen, S. M. (2003). Identification of Drosophila MicroRNA targets. PLoS Biol. 1, E60. doi:10.1371/journal.pbio.0000060
44. Tian, Z., Greene, A. S., Pietrusz, J. L., Matus, I. R., and Liang, M. (2008). MicroRNA-target pairs in the rat kidney identified by microRNA microarray, proteomic, and bioinformatic analysis. Genome Res. 18, 404-411.