Computational evidence for hundreds of non-conserved plant microRNAs

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Lindow, Morten ^a   Krogh, Anders ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; PLANT RNA;

ARTICLE; BIOINFORMATICS; CONSERVATION GENETICS; GENE EXPRESSION REGULATION; GENOME; NONHUMAN; PLANT GENETICS; RNA ANALYSIS; RNA GENE; RNA SEQUENCE;

ANIMALIA; ARABIDOPSIS; METAZOA;

EID: 25444490438     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-119     Document Type: Article

References (51)

1. He L, Hannon GJ: MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 2004, 5: 522-531.
2. Tomari Y, Zamore PD: Perspective: machines for RNAi. Genes Dev 2005, 19: 517-529.
3. Floyd SK, Bowman JL: Gene regulation: ancient microRNA target sequences in plants. Nature 2004, 428: 485-486.
4. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP: Vertebrate microRNA genes. Science 2003, 299: 1540.
5. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW et al.: The microRNAs of Caenorhabditis elegans. Genes Dev 2003, 17: 991-1008.
6. Jones-Rhoades MW, Bartel DP: Computational Identification of Plant MicroRNAs and Their Targets, Including a Stress-Induced miRNA. Mol Cell 2004, 14: 787-799.
7. Bonnet E, Wuyts J, Rouze P, Van de PY: Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A 2004, 101: 11511-11516.
8. Wang XJ, Reyes JL, Chua NH, Gaasterland T: Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 2004, 5: R65.
9. Baulcombe D: RNA silencing in plants. Nature 2004, 431: 356-363.
10. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O et al.: Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 2005, 37: 766-770.
11. Nelson DR, Schuler MA, Paquette SM, Werck-Reichhart D, Bak S: Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot. Plant Physiol 2004, 135: 756-772.
12. Griffiths-Jones S: The microRNA Registry. Nucleic Acids Res 2004, 32 Database issue: D109-D111.
13. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X et al.: A uniform system for microRNA annotation. RNA 2003, 9: 277-279.
14. Doench JG, Petersen CP, Sharp PA: siRNAs can function as miRNAs. Genes Dev 2003, 17: 438-442.
15. Doench JG, Sharp PA: Specificity of microRNA target selection in translational repression. Genes Dev 2004, 18: 504-511.
16. Doench JG, Sharp PA: Specificity of microRNA target selection in translational repression. Genes Dev 2004, 18: 504-511.
17. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS: MicroRNA targets in Drosophila. Genome Biol 2003, 5: R1.
18. Stark A, Brennecke J, Russell RB, Cohen SM: Identification of Drosophila MicroRNA Targets. PLoS Biol 2003, 1: E60.
19. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB: Prediction of mammalian microRNA targets. Cell 2003, 115: 787-798.
20. Adai A, Johnson C, Mlotshwa S, rcher-Evans S, Manocha V, Vance V et al.: Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 2005, 15: 78-91.
21. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB: Prediction of mammalian microRNA targets. Cell 2003, 115: 787-798.
22. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP: Prediction of plant microRNA targets. Cell 2002, 110: 513-520.
23. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP: Prediction of plant microRNA targets. Cell 2002, 110: 513-520.
24. Llave C, Xie Z, Kasschau KD, Carrington JC: Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297: 2053-2056.
25. Aukerman MJ, Sakai H: Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 2003, 15: 2730-2741.
26. http://www.binf.ku.dk/users/morten/mimatcher/arabidopsis/ mirnapredictions.html
27. Meyers BC, Lee DK, Vu TH, Tej SS, Edberg SB, Matvienko M et al.: Arabidopsis MPSS. An online resource for quantitative expression analysis. Plant Physiol 2004, 135: 801-813.
28. Mattick JS, Makunin IV: Small regulatory RNAs in mammals. Hum Mol Genet 2005, 14 Spec No 1: R121-R132.
29. Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC: Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 2004, 36: 1282-1290.
30. Bonnet E, Wuyts J, Rouze P, Van de PY: Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A 2004, 101: 11511-11516.
31. Bonnet E, Wuyts J, Rouze P, Van de PY: Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A 2004, 101: 11511-11516.
32. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K et al.: Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 2005, 434: 338-345.
33. Adai A, Johnson C, Mlotshwa S, rcher-Evans S, Manocha V, Vance V et al.: Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res 2005, 15: 78-91.
34. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A: Identification of Mammalian microRNA Host Genes and Transcription Units. Genome Res 2004.
35. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S et al.: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005, 308: 1149-1154.
36. Stolc V, Samanta MP, Tongprasit W, Sethi H, Liang S, Nelson DC et al.: Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A 2005, 102: 4453-4458.
37. Lai EC, Wiel C, Rubin GM: Complementary miRNA pairs suggest a regulatory role for miRNA:miRNA duplexes. RNA 2004, 10: 171-175.
38. Mathieu O, Bender J: RNA-directed DNA methylation. J Cell Sci 2004, 117: 4881-4888.
39. Griffiths-Jones S: The microRNA Registry. Nucleic Acids Res 2004, 32 Database issue: D109-D111.
40. Kurtz S. The Vmatch large scale sequence analysis software. 4-12-2003. Ref Type: Computer Program
41. Hofacker IL: Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31: 3429-3431.
42. www.repeatmasker.org
43. Hofacker IL: Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31: 3429-3431.
44. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D et al.: Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2004, 2: E104.
45. http://cgrb.orst.edu/smallRNA/db/
46. Kurtz S. The Vmatch large scale sequence analysis software. 4-12-2003. Ref Type: Computer Program
47. http://www.arabidopsis.org
48. Kurtz S. The Vmatch large scale sequence analysis software. 4-12-2003. Ref Type: Computer Program
49. Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P et al.: Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol 2004, 135: 745-755.
50. http://www.r-project.org
51. Storey JD: A direct approach to false discovery rates. Journal of the Royal Statistical Society, Series B 2002, 64: 479-498.