Predicting the fate of microRNA target genes based on sequence features

Journal of Theoretical Biology

Volumn 261, Issue 1, 2009, Pages 17-22

  Pei, Yunfei ^a   Wang, Xi ^a   Zhang, Xuegong ^a  

^a TSINGHUA NATIONAL LABORATORY FOR INFORMATION SCIENCE AND TECHNOLOGY   (China)

Author keywords

Degradation; MicroRNA; Repression; Target mRNA

Indexed keywords

MESSENGER RNA; MICRORNA;

GENE EXPRESSION; LEARNING; NUMERICAL MODEL; PREDICTION; RNA;

3' UNTRANSLATED REGION; ARTICLE; BINDING SITE; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENE TARGETING; MACHINE LEARNING; MATHEMATICAL MODEL; PREDICTION; PRIORITY JOURNAL; REGULATORY MECHANISM; RNA BINDING; RNA DEGRADATION; SUPPORT VECTOR MACHINE; TRANSCRIPTION REGULATION;

3' UNTRANSLATED REGIONS; GENE EXPRESSION REGULATION; GENE TARGETING; HELA CELLS; HUMANS; MICRORNAS; MODELS, GENETIC; RNA, MESSENGER;

EID: 70349505739     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.07.022     Document Type: Article

References (31)

1. Aleman L.M., Doench J., and Sharp P.A. Comparison of siRNA-induced off-target RNA and protein effects. RNA 13 3 (2007) 385-395
2. Ambros V. The functions of animal microRNAs. Nature 431 7006 (2004) 350-355
3. Baek D., Villen J., Shin C., Camargo F.D., Gygi S.P., and Bartel D.P. The impact of microRNAs on protein output. Nature 455 7209 (2008) 64-71
4. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 2 (2004) 281-297
5. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 136 2 (2009) 215-233
6. Brodersen P., and Voinnet O. Revisiting the principles of microRNA target recognition and mode of action. Nat. Rev. Mol. Cell Biol. 10 2 (2009) 141-148
7. Dai M., Wang P., Boyd A.D., Kostov G., Athey B., Jones E.G., Bunney W.E., Myers R.M., Speed T.P., Akil H., Watson S.J., and Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 33 20 (2005) e175
8. Doench J.G., and Sharp P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 18 5 (2004) 504-511
9. Eulalio A., Huntzinger E., and Izaurralde E. Getting to the root of miRNA-mediated gene silencing. Cell 132 1 (2008) 9-14
10. Farh K.K., Grimson A., Jan C., Lewis B.P., Johnston W.K., Lim L.P., Burge C.B., and Bartel D.P. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310 5755 (2005) 1817-1821
11. Filipowicz W., Bhattacharyya S.N., and Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat. Rev. Genet. 9 2 (2008) 102-114
12. Flynt A.S., and Lai E.C. Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat. Rev. Genet. 9 11 (2008) 831-842
13. Forman J.J., Legesse-Miller A., and Coller H.A. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc. Natl. Acad. Sci. USA 105 39 (2008) 14879-14884
14. Grimson A., Farh K.K., Johnston W.K., Garrett-Engele P., Lim L.P., and Bartel D.P. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27 1 (2007) 91-105
15. Guyon, I., Gunn, S., Nikravesh, M., Zadeh, L.A., 2006. Feature Extraction: Foundations and Applications. In: Studies in Fuzziness and Soft Computing. Physica, Springer (Chapter 4).
16. Jinek M., and Doudna J.A. A three-dimensional view of the molecular machinery of RNA interference. Nature 457 7228 (2009) 405-412
17. Kertesz M., Iovino N., Unnerstall U., Gaul U., and Segal E. The role of site accessibility in microRNA target recognition. Nat. Genet. 39 10 (2007) 1278-1284
18. Leung A.K., and Sharp P.A. Function and localization of microRNAs in mammalian cells. Cold Spring Harb. Symp. Quant. Biol. 71 (2006) 29-38
19. Lewis B.P., Burge C.B., and Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 1 (2005) 15-20
20. Lewis B.P., Shih I.H., Jones-Rhoades M.W., Bartel D.P., and Burge C.B. Prediction of mammalian microRNA targets. Cell 115 7 (2003) 787-798
21. Liu X., Fortin K., and Mourelatos Z. MicroRNAs: biogenesis and molecular functions. Brain Pathol. 18 1 (2008) 113-121
22. Nielsen C.B., Shomron N., Sandberg R., Hornstein E., Kitzman J., and Burge C.B. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13 11 (2007) 1894-1910
23. Nilsen T.W. Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet. 23 5 (2007) 243-249
24. Pillai R.S., Bhattacharyya S.N., and Filipowicz W. Repression of protein synthesis by miRNAs: how many mechanisms?. Trends Cell Biol. 17 3 (2007) 118-126
25. Schwanhausser B., Gossen M., Dittmar G., and Selbach M. Global analysis of cellular protein translation by pulsed SILAC. Proteomics 9 1 (2009) 205-209
26. Selbach M., Schwanhausser B., Thierfelder N., Fang Z., Khanin R., and Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature 455 7209 (2008) 58-63
27. Tokumaru S., Suzuki M., Yamada H., Nagino M., and Takahashi T. Let-7 regulates Dicer expression and constitutes a negative feedback loop. Carcinogenesis 29 11 (2008) 2073-2077
28. Vapnik V.N. The Nature of Statistical Learning Theory (1995), Springer, New York
29. Vapnik V.N. An overview of statistical learning theory. IEEE Trans. Neural Networks 10 (1999) 988-999
30. Vella M.C., Reinert K., and Slack F.J. Architecture of a validated microRNA::target interaction. Chem. Biol. 11 12 (2004) 1619-1623
31. Ye W., Lv Q., Wong C.K., Hu S., Fu C., Hua Z., Cai G., Li G., Yang B.B., and Zhang Y. The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation. PLoS ONE 3 3 (2008) e1719