Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity

Nucleic Acids Research

Volumn 40, Issue 10, 2012, Pages 4681-4690

  Cao, Song ^a,b   Chen, Shi Jie ^a,b  

^a UNIVERSITY OF MISSOURI   (United States)

^b University of Missouri   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ARTICLE; BASE PAIRING; BINDING AFFINITY; CONTROLLED STUDY; GENE FUNCTION; GENE REPRESSION; GENE TARGETING; GENETIC ALGORITHM; HUMAN; MATHEMATICAL MODEL; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; PREDICTION; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA STRUCTURE;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; HIV-1; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; RNA, VIRAL;

EID: 84861537681     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks052     Document Type: Article

References (53)

1. Neilson, J.R. and Sharp, P.A. (2008) Small RNA regulators of gene expression. Cell, 134, 899-902.
2. Bartel, D.P. (2009) MicroRNAs: Target Recognition and Regulatory Functions. Cell, 136, 215-233.
3. Zhao, Y., Zhao, Y., He, S., Liu, C., Ru, S., Zhao, H., Yang, Z., Yang, P., Yuan, X., Sun, S. et al. (2008) MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends Gene., 24, 323-327.
4. 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.
5. Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. and Enright, A.J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140-D144.
6. Ruby, J.G., Stark, A., Johnston, W.K., Kellis, M., Bartel, D.P. and Lai, E.C. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res., 17, 1850-1864.
7. Fontana, L., Sorrentino, A., Condorelli, G. and Peschle, C. (2008) Role of microRNAs in haemopoiesis, heart hypertrophy and cancer. Biochem. Soc. Trans., 36, 1206-1210.
8. Kota, J., Chivukula, R.R., O'Donnell, K.A., Wentzel, E.A., Montgomery, C.L., Hwang, H.-W., Chang, T.-C., Vivekanandan, P., Torbenson, M., Clark, K.R. et al. (2009) Therapeutic microRNA delivery suppresses tumorigenesis in a murine liver cancer model. Cell, 137, 1005-1017.
9. Cevec, M., Thibaudeau, C. and Plavec, J. (2008) Solution structure of a let-7 miRNA: Lin-41 mRNA complex from C. elegans. Nucleic Acids Res., 36, 2330-2337.
10. Sashital, D.G. and Doudna, J.A. (2010) Structural insights into RNA interference. Curr. Opin. Struct. Biol., 20, 90-97.
11. Sethupathy, P., Megraw, M. and Hatzigeorgiou, A.G. (2006) A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods, 3, 881-886.
12. Ritchie, W., Flamant, S. and Rasko, J.E.J. (2009) Predicting microRNA targets and functions: traps for the unwary. Nat. Methods, 6, 397-398.
13. 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.
14. 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.
15. Rajewsky, N. (2006) MicroRNA target predictions in animals. Nat. Genet., 39, S8-S13.
16. Rehmsmeier, M., Steffen, P., Hchsmann, M. and Giegerich, R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA, 10, 1507-1517.
17. 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.
18. Stark, A., Brennecke, J., Russell, R.B. and Cohen, S.M. (2003) Identification of Drosophila microRNA targets. PLoS. Biol., 1, 397-409.
19. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C. and Marks, D.S. (2003) MicroRNA targets in Drosophila. Genome Biol., 5, R1.
20. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. and Marks, D.S. (2004) Human microRNA targets. PLoS Biol., 2, 1862-1879.
21. Kiriakidou, M., Nelson, P.T., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z. and Hatzigeorgiou, A. (2004) A combined computational- experimental approach predicts human miRNA targets. Genes Dev., 18, 1165-1178.
22. Krek, A., Grün, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., Da Piedade, I., Gunsalus, K.C., Stoffel, M. et al. (2005) Combinatorial microRNA target predictions. Nat. Genet., 37, 495-500.
23. Grun, D., Wang, Y.-L., Langenberger, D., Gunsalus, K.C. and Rajewsky, N. (2005) MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol., 1, 51-66.
24. Saetrom, O., Snove, O. Jr and Saetrom, P. (2005) Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA, 11, 995-1003.
25. 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.
26. 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 ribonucleoproteinenriched transcripts. Nat. Methods, 5, 813-819.
27. Marin, R. and Vanicek, J. (2011) Efficient use of accessibility in microRNA target prediction. Nucleic Acids. Res., 39, 19-29.
28. Hofacker, I.L. (2007) How microRNAs choose their targets. Nat. Genet., 39, 1191-1192.
29. Obernosterer, G., Tafer, H. and Martinez, J. (2008) Target site effects in the RNA interference and microRNA pathways. Biochem Soc. Trans., 36, 1216-1219.
30. Cao, S. and Chen, S.-J. (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res., 34, 2634-2652.
31. Cao, S. and Chen, S.-J. (2009) Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA, 15, 696-706.
32. Andronescu, M.S., Pop, C. and Condon, A. (2010) Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA, 16, 26-42.
33. Andronescu, M., Condon, A., Hoos, H.H., Mathews, D.H. and Murphy, K.P. (2010) Computational approaches for RNA energy parameter estimation. RNA, 16, 2304-2318.
34. Sperschneider, J., Datta, A. and Wise, M.J. (2011) Heuristic RNA pseudoknot prediction including intramolecular kissing hairpins. RNA, 17, 27-38.
35. Abraham, M., Dror, O., Nussinov, R. and Wolfson, H.J. (2008) Analysis and classification of RNA tertiary structures. RNA, 14, 2274-2289.
36. Seetin, M.G. and Mathews, D.H. (2011) Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J. Comput. Chem., 32, 2232-2244.
37. Cao, S. and Chen, S.-J. (2011) Physics-based de novo prediction of RNA 3D structures. J. Phys. Chem. B, 115, 4216-4226.
38. Cao, S. and Chen, S.-J. (2006) Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes. J. Mol. Biol., 357, 292-312.
39. Ameres, S.L., Martinez, J. and Schroeder, R. (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell, 130, 101-112.
40. Westerhout, E.M. and Berkhout, B. (2007) A systematic analysis of the effect of target RNA structure on RNA interference. Nucleic Acids Res., 35, 4322-4330.
41. Tafer, H., Ameres, S.L., Obernosterer, G., Gebeshuber, C.A., Schroeder, R., Martinez, J. and Hofacker, I.L. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat. Biotechnol., 26, 578-583.
42. Cao, S. and Chen, S.-J. (2012) A domain-based model for predicting large and complex pseudoknotted structures. RNA Biol., 9, 201-212.
43. Cao, S. and Chen, S.-J. (2005) Predicting RNA folding thermodynamics with a reduced chain representation model. RNA, 11, 1884-1897.
44. Brennecke, J., Stark, A., Russell, R.B. and Cohen, S.M. (2005) Principles of microRNA-target recognition. PLoS Biol., 3, 0404-0418.
45. Li, Y., Wang, F., Lee, J.-A. and Gao, F.-B. (2006) MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila. Genes Dev., 20, 2793-2805.
46. Teleman, A.A., Maitra, S. and Cohen, S.M. (2006) Drosophila lacking microRNA miR-278 are defective in energy homeostasis. Genes Dev., 20, 417-422.
47. Pekarsky, Y., Santanam, U., Cimmino, A., Palamarchuk, A., Efanov, A., Maximov, V., Volinia, S., Alder, H., Liu, C.-G., Rassenti, L. et al. (2006) Tcl1 expression in chronic lymphocytic leukemia is regulated by miR-29 and miR-181. Cancer Res., 66, 11590-11593.
48. Xia, T., SantaLucia, J. Jr, Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C. and Turner, D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
49. Yekta, S., Shih, I.-H. and Bartel, D.P. (2004) microRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594-596.
50. Harris, T.A., Yamakuchi, M., Ferlito, M., Mendell, J.T. and Lowenstein, C.J. (2008) MicroRNA-126 regulates endothelial expression of vascular cell adhesion molecule 1. Proc. Natl Acad. Sci. USA, 105, 1516-1521.
51. Wang, H.-W., Noland, C., Siridechadilok, B., Taylor, D.W., Ma, E., Felderer, K., Doudna, J.A. and Nogales, E. (2009) Structural insights into RNA processing by the human RISC-loading complex. Nat. Struct. Mol. Biol., 16, 1148-1153.
52. Busch, A., Richter, A.S. and Backofen, R. (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics, 24, 2849-2856.
53. Serra, M.J. and Turner, D.H. (1995) Predicting thermodynamic properties of RNA. Methods Enzymol., 259, 242-261.