Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum)

Gene

Volumn 414, Issue 1-2, 2008, Pages 60-66

  Yin, Zujun ^a   Li, Chunhe ^a   Han, Xiulan ^a   Shen, Fafu ^a  

^a SHANDONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Conserved microRNAs; Homology; MFEI; Target genes; Tomato

Indexed keywords

MICRORNA;

ARTICLE; EXPRESSED SEQUENCE TAG; GENE CONTROL; GENE FUNCTION; MOLECULAR EVOLUTION; NONHUMAN; PLANT GENETICS; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; TOMATO;

COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DNA PRIMERS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; LYCOPERSICON ESCULENTUM; MICRORNAS; RNA, PLANT;

EMBRYOPHYTA; LYCOPERSICON ESCULENTUM;

EID: 41949100147     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.02.007     Document Type: Article

References (58)

1. Adai A., et al. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 15 (2005) 78-91
2. Achard P., Herr A., Baulcombe D.C., and Harberd N.P. Modulation of floral development by a gibberellin-regulated microRNA. Development 131 (2004) 3357-3365
3. Aukerman M.J., and Sakai H. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15 (2003) 2730-2741
4. Axtell M.J., and Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 17 (2005) 1658-1673
5. Axtell M.J., Snyder J.A., and Bartel D.P. Common functions for diverse small RNAs of land plants. Plant Cell 19 (2007) 1750-1769
6. Cardon G., et al. Molecular characterisation of the Arabidopsis SBP-box genes. Gene 237 (1999) 91-104
7. Carrington J.C., and Ambros V. Role of microRNAs in plant and animal development. Science 301 (2003) 336-338
8. Chen X. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303 (2004) 2022-2025
9. Chen X. MicroRNA biogenesis and function in plants. FEBS Lett. 579 (2005) 5923-5931
10. Cimmino A., et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Natl. Acad. Sci. U. S. A 102 (2005) 13944-13949
11. Dharmasiri S., and Estelle M. The role of regulated protein degradation in auxin response. Plant Mol. Biol 49 (2002) 401-409
12. Fahlgren N., et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS. ONE. 2 (2007) e219
13. Gandikota M., Birkenbihl R.P., Hohmann S., Cardon G.H., Saedler H., and Huijser P. The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 49 (2007) 683-693
14. Gleave A.P., et al. Identification and characterisation of primary microRNAs from apple (Malus domestica cv. Royal Gala) expressed sequence tags. Tree Genetics & Genomes 4 (2008) 343-358
15. Guilfoyle T.J., Ulmasov T., and Hagen G. The ARF family of transcription factors and their role in plant hormone-responsive transcription. Cell. Mol. Life Sci 54 (1998) 619-627
16. Guo H.S., Xie Q., Fei J.F., and Chua N.H. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. Plant Cell 17 (2005) 1376-1386
17. Ioshikhes I., Roy S., and Sen C.K. Algorithms for mapping of mRNA targets for microRNA. DNA Cell Biol. 26 (2007) 265-272
18. Itaya A., et al. Small RNAs in tomato fruit and leaf development. Biochim. Biophys. Acta. 1779 (2008) 99-107
19. Jones-Rhoades M.W., and Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14 (2004) 787-799
20. Kurihara Y., and Watanabe Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl. Acad. Sci. U. S. A 101 (2004) 12753-12758
21. Lai E.C., Tomancak P., Williams R.W., and Rubin G.M. Computational identification of Drosophila microRNA genes. Genome Biol. 4 (2003) R42
22. Lall S., et al. A genome-wide map of conserved microRNA targets in C. elegans. Curr. Biol. 16 (2006) 460-471
23. Laufs P., Peaucelle A., Morin H., and Traas J. MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131 (2004) 4311-4322
24. Lauter N., Kampani A., Carlson S., Goebel M., and Moose S.P. microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proc. Natl. Acad. Sci. U. S. A 102 (2005) 9412-9417
25. Leonardi C., Ambrosino P., Esposito F., and Fogliano V. Antioxidative activity and carotenoid and tomatine contents in different typologies of fresh consumption tomatoes. J. Agric. Food Chem. 48 (2000) 4723-4727
26. Li Y., Li W., and Jin Y.X. Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa. Acta Biochim. Biophys. Sin. (Shanghai) 37 (2005) 75-87
27. Liang C.Y., et al. Construction of a BAC library of Physcomitrella patens and isolation of a LEA gene. Plant Sci. 167 (2004) 491-498
28. Lin S.L., Chang D., and Ying S.Y. Asymmetry of intronic pre-miRNA structures in functional RISC assembly. Gene 356 (2005) 32-38
29. Liscum E., and Reed J.W. Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol. Biol 49 (2002) 387-400
30. Mallory A.C., Bartel D.P., and Bartel B. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17 (2005) 1360-1375
31. Mallory A.C., Dugas D.V., Bartel D.P., and Bartel B. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr. Biol. 14 (2004) 1035-1046
32. Megraw M., Baev V., Rusinov V., Jensen S.T., Kalantidis K., and Hatzigeorgiou A.G. MicroRNA promoter element discovery in Arabidopsis. RNA. 12 (2006) 1612-1619
33. Nilsson L., Carlsbecker A., Sundas-Larsson A., and Vahala T. APETALA2 like genes from Picea abies show functional similarities to their Arabidopsis homologues. Planta 225 (2007) 589-602
34. Nole-Wilson S., and Krizek B.A. DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. Nucleic Acids Res. 28 (2000) 4076-4082
35. Pan X., Zhang B., San F.M., and Cobb G.P. Characterizing viral microRNAs and its application on identifying new microRNAs in viruses. J. Cell Physiol. 211 (2007) 10-18
36. Park M.Y., Wu G., Gonzalez-Sulser A., Vaucheret H., and Poethig R.S. Nuclear processing and export of microRNAs in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A 102 (2005) 3691-3696
37. Pilcher R.L., et al. Identification of novel small RNAs in tomato (Solanum lycopersicum). Planta 226 (2007) 709-717
38. Qiu C.X., et al. Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 395 (2007) 49-61
39. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., and Bartel D.P. Prediction of plant microRNA targets. Cell 110 (2002) 513-520
40. Riechmann J.L., and Meyerowitz E.M. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379 (1998) 633-646
41. Riese M., Hohmann S., Saedler H., Munster T., and Huijser P. Comparative analysis of the SBP-box gene families in P. patens and seed plants. Gene 401 (2007) 28-37
42. Ru P., Xu L., Ma H., and Huang H. Plant fertility defects induced by the enhanced expression of microRNA167. Cell Res. 16 (2006) 457-465
43. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., and Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8 (2005) 517-527
44. Sunkar R., and Zhu J.K. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16 (2004) 2001-2019
45. Theissen G., and Saedler H. The golden decade of molecular floral development (1990-1999): A cheerful obituary. Dev Genet. 25 (1999) 181-193
46. Tiwari S.B., Hagen G., and Guilfoyle T.J. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell 16 (2004) 533-543
47. Vaucheret H., Vazquez F., Crete P., and Bartel D.P. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev. 18 (2004) 1187-1197
48. Wang J.W., Wang L.J., Mao Y.B., Cai W.J., Xue H.W., and Chen X.Y. Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17 (2005) 2204-2216
49. Willmann M.R., and Poethig R.S. Conservation and evolution of miRNA regulatory programs in plant development. Curr. Opin. Plant Biol. 10 (2007) 503-511
50. Wu G., and Poethig R.S. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133 (2006) 3539-3547
51. Wu M.F., Tian Q., and Reed J.W. Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133 (2006) 4211-4218
52. Zhang B.H., Pan X.P., Wang Q.L., Cobb G.P., and Anderson T.A. Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 15 (2005) 336-360
53. Zhang B.H., Pan X.P., Cannon C.H., Cobb G.P., and Anderson T.A. Conservation and divergence of plant microRNA genes. Plant J. 46 (2006) 243-259
54. Zhang B.H., Pan X.P., Cobb G.P., and Anderson T.A. Plant microRNA: a small regulatory molecule with big impact. Dev. Biol. 289 (2006) 3-16
55. Zhang B.H., Pan X.P., Cox S.B., Cobb G.P., and Anderson T.A. Evidence that miRNAs are different from other RNAs. Cell Mol. Life Sci. 63 (2006) 246-254
56. Zhang B.H., Pan X.P., Wang Q.L., Cobb G.P., and Anderson T.A. Computational identification of microRNAs and their targets. Comput. Biol. Chem. 30 (2006) 395-407
57. Zhang B.H., et al. Identification of cotton microRNAs and their targets. Gene 397 (2007) 26-37
58. Zhang Y. miRU: an automated plant miRNA target prediction server. Nucleic Acids Res. 33 (2005) W701-W704