Potent effect of target structure on microRNA function

Nature Structural and Molecular Biology

Volumn 14, Issue 4, 2007, Pages 287-294

  Long, Dang ^a   Lee, Rosalind ^b   Williams, Peter ^b   Chan, Chi Yu ^a   Ambros, Victor ^b   Ding, Ye ^a  

^a WADSWORTH CENTER   (United States)

^b DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENE STRUCTURE; GENE TARGETING; GENETIC ANALYSIS; HYBRIDIZATION; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA TRANSLATION;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; DROSOPHILA MELANOGASTER; MICRORNAS; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDES; REGRESSION ANALYSIS; RNA, HELMINTH; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS; TRANSCRIPTION FACTORS;

ANIMALIA; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER;

EID: 34247258888     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1226     Document Type: Article

References (42)

1. Ambros, V. The functions of animal microRNAs. Nature 431, 350-355 (2004).
2. Bentwich, I. et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37, 766-770 (2005).
3. Boehm, M. & Slack, F. A developmental timing microRNA and its target regulate life span in C. elegans. Science 310, 1954-1957 (2005).
4. Calin, G.A. & Croce, C.M. MicroRNA-cancer connection: the beginning of a new tale. Cancer Res. 66, 7390-7394 (2006).
5. Cuellar, T.L. & McManus, M.T. MicroRNAs and endocrine biology. J. Endocrinol. 187, 327-332 (2005).
6. Brennecke, J., Stark, A., Russell, R.B. & Cohen, S.M. Principles of microRNA-target recognition. PLoS Biol. 3, e85 (2005).
7. Sethupathy, P., Corda, B. & Hatzigeorgiou, A.G. TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12, 192-197 (2006).
8. Jones-Rhoades, M.W. & Bartel, D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14, 787-799 (2004).
9. Lai, E.C. Predicting and validating microRNA targets. Genome Biol. 5, 115 (2004).
10. Lewis, B.P., Burge, C.B. & Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
11. Doench, J.G. & Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504-511 (2004).
12. Kiriakidou, M. et al. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18, 1165-1178 (2004).
13. Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P. & Burge, C.B. Prediction of mammalian microRNA targets. Cell 115, 787-798 (2003).
14. Rajewsky, N. microRNA target predictions in animals. Nat. Genet. 38 Suppl, S8-S13 (2006).
15. Vella, M.C., Choi, E.Y., Lin, S.Y., Reinert, K. & Slack, F.J. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev. 18, 132-137 (2004).
16. Vella, M.C., Reinert, K. & Slack, F.J. Architecture of a validated microRNA:target interaction. Chem. Biol. 11, 1619-1623 (2004).
17. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003).
18. Robins, H., Li, Y. & Padgett, R.W. Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. USA 102, 4006-4009 (2005).
19. Rehmsmeier, M., Steffen, P., Hochsmann, M. & Giegerich, R. Fast and effective prediction of microRNA-target duplexes. RNA 10, 1507-1517 (2004).
20. Ding, Y., Chan, C.Y. & Lawrence, C.E. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32, W135-W141 (2004).
21. Ding, Y. & Lawrence, C.E. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res. 29, 1034-1046 (2001).
22. Ding, Y. & Lawrence, C.E. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 31, 7280-7301 (2003).
23. Hargittai, M.R., Gorelick, R.J., Rouzina, I. & Musier-Forsyth, K. Mechanistic insights into the kinetics of HIV-1 nucleocapsid protein-facilitated tRNA annealing to the primer binding site. J. Mol. Biol. 337, 951-968 (2004).
24. Xia, T. et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37, 14719-14735 (1998).
25. Clote, P., Ferre, F., Kranakis, E. & Krizanc, D. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11, 578-591 (2005).
26. Seggerson, K., Tang, L. & Moss, E.G. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev. Biol. 243, 215-225 (2002).
27. Didiano, D. & Hobert, O. Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat. Struct. Mol. Biol. 13, 849-851 (2006).
28. Johnston, R.J. & Hobert, O. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845-849 (2003).
29. Ding, Y., Chan, C.Y. & Lawrence, C.E. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11, 1157-1166 (2005).
30. Ding, Y., Chan, C.Y. & Lawrence, C.E. Clustering of RNA secondary structures with application to messenger RNAs. J. Mol. Biol. 359, 554-571 (2006).
31. Overhoff, M. et al. Local RNA target structure influences siRNA efficacy: a systematic global analysis. J. Mol. Biol. 348, 871-881 (2005).
32. Schubert, S., Grunweller, A., Erdmann, V.A. & Kurreck, J. Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. J. Mol. Biol. 348, 883-893 (2005).
33. Zhao, Y., Samal, E. & Srivastava, D. Serum response factor regulates a musclespecific microRNA that targets Hand2 during cardiogenesis. Nature 436, 214-220 (2005).
34. Farh, K.K. et al. The widespread impact of mammalian MicroRNAs on mRNA repression and evolution. Science 310, 1817-1821 (2005).
35. Enright, A.J. et al. MicroRNA targets in Drosophila. Genome Biol. 5, R1 (2003).
36. Krek, A. et al. Combinatorial microRNA target predictions. Nat. Genet. 37, 495-500 (2005).
37. Miranda, K.C. et al. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203-1217 (2006).
38. Cullen, B.R. Viruses and microRNAs. Nat. Genet. 38 Suppl, S25-S30 (2006).
39. Paillart, J.C., Skripkin, E., Ehresmann, B., Ehresmann, C. & Marquet, R. A loop-loop "kissing" complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proc. Natl. Acad. Sci. USA 93, 5572-5577 (1996).
40. Reynaldo, L.P., Vologodskii, A.V., Neri, B.P. & Lyamichev, V.I. The kinetics of oligonucleotide replacements. J. Mol. Biol. 297, 511-520 (2000).
41. Milner, N., Mir, K.U. & Southern, E.M. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat. Biotechnol. 15, 537-541 (1997).
42. Kolb, F.A. et al. Bulged residues promote the progression of a loop-loop interaction to a stable and inhibitory antisense-target RNA complex. Nucleic Acids Res. 29, 3145-3153 (2001).