Evidence that miRNAs are different from other RNAs

Cellular and Molecular Life Sciences

Volumn 63, Issue 2, 2006, Pages 246-254

  Zhang, B H ^a   Pan, X P ^a   Cox, S B ^a   Cobb, G P ^a   Anderson, T A ^a  

^a TEXAS TECH UNIVERSITY   (United States)

Author keywords

Bioinformatics; MFEI; MicroRNA; Minimal folding free energy index; mRNA; Plant; rRNA; tRNA

Indexed keywords

MICRORNA; RNA;

ANALYTIC METHOD; ARTICLE; COMPARATIVE STUDY; HYDROGEN BOND; RNA ANALYSIS; RNA SEQUENCE; STATISTICAL SIGNIFICANCE;

BASE PAIRING; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; HOMEODOMAIN PROTEINS; MICRORNAS; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; PLANT PROTEINS; RNA; RNA PRECURSORS; RNA, PLANT; SEQUENCE HOMOLOGY; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 30744468557     PISSN: 1420682X     EISSN: 15691632     Source Type: Journal    
DOI: 10.1007/s00018-005-5467-7     Document Type: Article

References (43)

1. Ambros V. (2001) MicroRNAs: tiny regulators with great potential. Cell 107: 823-826
2. Carrington J. C. and Ambros V. (2003) Role of microRNAs in plant and animal development. Science 301: 336-338
3. Bartel D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
4. Lee R. C. and Ambros V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864
5. Lagos-Quintana M., Rauhut R., Lendeckel W. and Tuschl T. (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858
6. 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
7. Ambros V. (2004) The functions of animal microRNAs. Nature 431: 350-355
8. Croce C. M. and Calin G. A. (2005) miRNAs, cancer, and stem cell division. Cell 122: 6-7
9. Eckardt N. A. (2005) MicroRNAs regulate auxin homeostasis and plant development Plant Cell 17: 1335-1338
10. Gregory R. I. and Shiekhattar R. (2005) MicroRNA biogenesis and cancer. Cancer Res. 65: 3509-3512
11. Hatfield S. D., Shcherbata H. R., Fischer K. A., Nakahara K., Carthew R. W. and Ruohola-Baker H. (2005) Stem cell division is regulated by the microRNA pathway. Nature 435: 974-978
12. Kidner C. A. and Martienssen R. A. (2005) The developmental role of microRNA in plants. Curr. Opin. Plant Biol. 8: 38-44
13. Meltzer P. S. (2005) Cancer genomics: small RNAs with big impacts. Nature 435: 745-746
14. Zhang B. H., Pan X. P., Cobb G. P. and Anderson T. A. (2006) Plant microRNA: a small regulatory molecule with big impact. Dev. Biol. 289: 3-16
15. Griffiths-Jones S. (2004) The microRNA Registry. Nucleic Acids Res. 32: D109-D111
16. Brown J. R. and Sanseau P. (2005) A computational view of microRNAs and their targets. Drug Discov. Today 10: 595-601
17. Mathews D. H., Sabina J., Zuker M. and Turner D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940
18. Zuker M. (2003) MFOLD web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415
19. Ambros V., Bartel B., Bartel D. P., Burge C. B., Carrington J. C., Chen X. et al. (2003) A uniform system for microRNA annotation. RNA 9: 277-279
20. Bonnet E., Wuyts J., Rouze P. and Van de Peer Y. (2004a) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl. Acad. Sci. USA 101: 11511-11516
21. Bonnet E., Wuyts J., Rouze P. and Van de Peer Y. (2004b) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20: 2911-2917
22. 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
23. Jones-Rhoades M. W. and Bartel D. P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14: 787-799
24. Wang X. J., Reyes J. L., Chua N. H. and Gaasterland T. (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol. 5: R65
25. Adai A., Johnson C., Mlotshwa S., Archer-Evans S., Manocha V., Vance V. et al. (2005) Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 15: 78-91
26. Zhang B. H., Pan X. P., Wang Q. L., Cobb G. P. and Anderson T. A. (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 15: 336-360
27. Llave C., Xie Z., Kasschau K. D. and Carrington J. C. (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056
28. Reinhart B. J., Weinstein E. G., Rhoades M. W., Bartel B. and Bartel D. P. (2002) MicroRNAs in plants. Genes Dev. 16: 1616-1626
29. Kasschau K. D., Xie Z., Allen E., Llave C., Chapman E. J., Krizan K. A. et al. (2003) P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev. Cell 4: 205-217
30. Palatnik J. F., Allen E., Wu X., Schommer C., Schwab R., Carrington J. C. et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263
31. Xie Z., Kasschau K. D. and Carrington J. C. (2003) Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol. 13: 784-789
32. Aukerman M. J. and Sakai H. (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741
33. Chen X. (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025
34. Mallory A. C., Bartel D. P. and Bartel B. (2005) MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17: 1360-1375
35. Vaucheret H., Vazquez F., Crete P. and Bartel D. P. (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 18: 1187-1197
36. Floyd S. K. and Bowman J. L. (2004) Ancient microRNA target sequences in plants. Nature 428: 485-486
37. Guo H. S., Xie Q., Fei J. F. and Chua N. H. (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17: 1376-1386
38. Sorin C., Bussell J. D., Camus I., Ljung K., Kowalczyk M., Geiss G. et al. (2005) Auxin and light control of adventitious rooting in Arabidopsis require ARGONAUTE1. Plant Cell 17: 1343-1359
39. Williams L., Carles C. C., Osmont K. S. and Fletcher J. C. (2005) A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes. Proc. Natl. Acad. Sci. USA 102: 9703-9978
40. Sprinzl M., Horn C., Brown M., Ioudovitch A. and Steinberg S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26: 148-153
41. Wuyts J., Perrière G. and Van de Peer Y. (2004) The European database on small subunit ribosomal RNA. Nucleic Acids Res. 32:D101-D103
42. Zuker M. and Stiegler P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9: 133-148
43. Corpet F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16: 10881-10890