Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences

Bioinformatics

Volumn 20, Issue 17, 2004, Pages 2911-2917

  Bonnet, Eric ^a   Wuyts, Jan ^a   Rouzé, Pierre ^b   Van de Peer, Yves ^a  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RIBOSOME RNA; RNA PRECURSOR; TRANSFER RNA; UNTRANSLATED RNA;

ANIMAL CELL; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EUKARYOTE; GENETIC DATABASE; INTERNET; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; RANDOMIZATION; RNA SEQUENCE; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; TAXONOMY;

EUKARYOTA;

EID: 10244243802     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth374     Document Type: Article

References (45)

1. Ambros,V., Bartel,B., Bartel,D.P., Burge,C.B., Carrington,J.C., Chen,X., Dreyfuss,G., Eddy,S.R., Griffiths-Jones,S., Marshall,M. et al. (2003) A uniform system for microRNA annotation. RNA, 9, 277-279.
2. Bartel,B. and Bartel,D.P. (2003) MicroRNAs: at the root of plant development? Plant Physiol., 132, 709-717.
3. Bartel,D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
4. Bonnet,E., Wuyts,J., Rouzé,P. and Van de Peer,Y. (2004) Detection of 71 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl Acad. Sci., USA, (in press).
5. Calin,G.A., Dumitru,C.D., Shimizu,M., Bichi,R., Zupo,S., Noch,E., Aldler,H., Rattan,S., Keating,M., Rai,K. et al. (2002) Frequent deletions and down-regulation of microRNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl Acad. Sci., USA 99, 15524-15529.
6. Carrington,J.C. and Ambros,V. (2003) Role of microRNAs in plant and animal development. Science, 301, 336-338.
7. Chen,J.H., Le,S.Y., Shapiro,B., Currey,K.M. and Maizel,J.V. (1990) A computational procedure for assessing the significance of RNA secondary structure. Comput. Appl. Biosci., 6, 7-18.
8. Durbin,R., Eddy,S.R., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge.
9. Eddington,E.S. (1995) Randomization Tests. Marcel Dekker, New York.
10. Eddy,S.R. (2001) Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet., 2, 919-929.
11. Edwards,D. (1985) Exact simulation based inference: a survey, with additions. J. Stat. Comput. Sim., 22, 307-326.
12. Efron,B. (1979) Computers and the theory of statistics: thinking the unthinkable. Soc. Indus. Appl. Math., 21, 460-480.
13. Griffiths-Jones,S. (2004) The microRNA Registry. Nucleic Acids Res., 32, D109-D111.
14. Griffiths-Jones,S., Bateman,A., Marshall,M., Khanna,A. and Eddy,S.R. (2003) Rfam: an RNA family database. Nucleic Acids Res., 31, 439-441.
15. Hofacker,I.L., Fontana,W., Stadler,P.F., Bonhoeffer,L.S., Tacker,M. and Schuster,P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem., 125, 167-188.
16. Hutvagner,G. and Zamore,P.D. (2002) RNAi: nature abhors a double-strand. Curr. Opin. Genet. Dev., 12, 225-232.
17. Jockel,K.H. (1986) Finite sample properties and asymptotic efficiency of Monte Carlo tests. J. Stat. Comput. Sim., 14, 336-347.
18. Katz,L. and Burge,C.B. (2003) Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res., 13, 2042-2051.
19. Lagos-Quintana,M., Rauhut,R., Lendeckel,W. and Tuschl,T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
20. Lai,E.C., Tomancak,P., Williams,R.W. and Rubin,G.M. (2003) Computational identification of Drosophila microRNA genes. Genome Biol., 4, R42.
21. 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.
22. Le,S.V., Chen,J.H., Currey,K.M. and Maizel,J.V.,Jr (1988) A program for predicting significant RNA secondary structures. Comput. Appl. Biosci., 4, 153-159.
23. Le,S.Y., Chen,J.H. and Maizel,J.V. (1989) Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses. Nucleic Acids Res. 17, 6143-6152.
24. Lee,R.C. and Ambros,V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862-864.
25. 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.
26. Lee,Y., Ahn,C., Han,J., Choi,H., Kim,J., Yim,J., Lee,J., Provost,P., Radmark,O., Kim,S. and Kim,V.N. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 425, 415-419.
27. Lee,Y., Jeon,K., Lee,J.T., Kim,S. and Kim,V.N. (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J., 21, 4663-4670.
28. Lim,L.P., Glasner,M.E., Yekta,S., Burge,C.B. and Bartel,D.P. (2003a) Vertebrate microRNA genes. Science, 299, 1540.
29. Lim,L.P., Lau,N.C., Weinstein,E.G., Abdelhakim,A., Yekta,S., Rhoades,M.W., Burge,C.B. and Bartel,D.P. (2003b) The microRNAs of Caenorhabditis elegans. Genes Dev., 17, 991-1008.
30. Llave,C., Kasschau,K.D., Rector,M.A. and Carrington,J.C. (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell, 14, 1605-1619.
31. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
32. Manly,B.F.J. (1997) Randomization, Bootstrap and Monte Carlo Methods in Biology. Chapman Hall, London.
33. Pervouchine,D.D., Graber,J.H. and Kasif,S. (2003) On the normalization of RNA equilibrium free energy to the length of the sequence. Nucleic Acids Res., 31, e49.
34. Reinhart,B.J., Slack,F.J., Basson,M., Pasquinelli,A.E., Bettinger,J.C., Rougvie,A.E., Horvitz,H.R. and Ruvkun,G. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901-906.
35. Reinhart,B.J., Weinstein,E.G., Rhoades,M.W., Bartel,B. and Bartel,D.P. (2002) MicroRNAs in plants. Genes Dev., 16, 1616-1626.
36. Rivas,E. and Eddy,S.R. (2000) Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics, 16, 583-605.
37. Schauer,S.E., Jacobsen,S.E., Meinke,D.W. and Ray,A. (2002) DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci., 7, 487-491.
38. Schmittgen,T.D., Jiang,J., Liu,Q. and Yang,L. (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res., 32, e43.
39. Schuster,P., Fontana,W., Stadler,P.F. and Hofacker,I.L. (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B Biol. Sci., 255, 279-284.
40. Seffens,W. and Digby,D. (1999) mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res., 27, 1578-1584.
41. Workman,C. and Krogh,A. (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res., 27, 4816-4822.
42. Wuyts,J., Perrière,G. and Van de Peer,Y. (2004) The European database on small subunit ribosomal RNA. Nucleic Acids Res. 32, D101-D103.
43. Wuyts,J., Van de Peer,Y. and De Wachter,R. (2001) Distribution of substitution rates and location of insertion sites in the tertiarv structure of ribosomal RNA. Nucleic Acids Res., 29, 5017-5028.
44. Xing,Y. and Draper,D.E. (1995) Stabilization of a ribosomal RNA tertiary structure by ribosomal protein L11. J. Mol. Biol., 249, 319-331.
45. Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.