Identification of 21 microRNAs in maize and their differential expression under drought stress

African Journal of Biotechnology

Volumn 9, Issue 30, 2010, Pages 4741-4753

  Xu, Chen ^a   Yang, Ruo Fei ^a   Li, Wan Chen ^a   Fu, Feng Ling ^a  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

Bioinformatics; Differential expression; Drought stress; Gene cloning; Maize; MicroRNA

Indexed keywords

MICRORNA; UNCLASSIFIED DRUG; ZMA MICRORNA 1; ZMA MICRORNA 161; ZMA MICRORNA 2; ZMA MICRORNA 3; ZMA MICRORNA 397; ZMA MICRORNA 4; ZMA MICRORNA 446; ZMA MICRORNA 479; ZMA MICRORNA 5; ZMA MICRORNA 530; ZMA MICRORNA 6; ZMA MICRORNA 7; ZMA MICRORNA 776; ZMA MICRORNA 782; ZMA MICRORNA 8; ZMA MICRORNA 815A; ZMA MICRORNA 818A; ZMA MICRORNA 820; ZMA MICRORNA 828; ZMA MICRORNA 834; ZMA MICRORNA 9;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DROUGHT STRESS; DROUGHT TOLERANCE; GENE AMPLIFICATION; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE SEQUENCE; INBRED STRAIN; MAIZE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PROTEIN SECONDARY STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ARABIDOPSIS; ZEA MAYS;

EID: 77956123094     PISSN: 16845315     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V (2005). Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 18: 78-91.
2. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003). A uniform system for microRNA annotation. RNA, 9: 277-279.
3. Archak S, Nagaraju J (2007). Computational prediction of rice (Oryza sativa) miRNA targets. Genomics, Proteomics Bioinformatics, 5: 196-206.
4. Bari R, Pant BD, Stitt M, Scheible WR (2006). PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol. 141: 988-999.
5. Bartel B, Bartel DP (2003). MicroRNAs: at the root of plant development? Plant Physiol. 132: 709-717
6. Bartel D (2004). MicroRNAs: genomics, biogenesis, mechanism and function. Cell, 116: 281-297.
7. Bonnet E, Wuyts J, Rouze P, van de Peer Y (2004). Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 20: 2911-2917.
8. Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004). 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.
9. Brodersen P, Voinnet O (2006). The diversity of RNA silencing pathways in plants Trend. Genetics, 22: 268-280.
10. Chiou TJ (2007). The role of microRNAs in sensing nutrient stress. Plant Cell Environ. 30: 323-332.
11. Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL (2006). Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell, 18: 412-421.
12. Cissell KA, Deo SK (2009). Trends in microRNA detection. Anal. Bioanal. Chem. 394: 1109-1116.
13. Ding D, Zhang L, Wang H, Liu Z, Zhang Z, Zheng Y (2009). Differential expression of miRNAs in response to salt stress in maize roots. Ann. Bot. 103: 29-38.
14. Floyd SK, Bowman JL (2004). Ancient microRNA target sequences in plants. Nature, 428: 485-486.
15. Fu F-L, Feng Z-L, Gao S-B, Zhou S-F, Li W-C (2008). Evaluation and quantitative inheritance of several drought-relative traits in maize. Agric. Sci. Chin. 7: 280-290.
16. Ghosh Z, Chakrabarti J, Mallick B (2007). miRNomics-the bioinformatics of microRNA genes. Biochem. Biophys. Res. Commun. 363: 6-11.
17. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34: D140-D144.
18. Jones-Rhoades MW, Bartel DP (2004). Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell, 14: 787-799.
19. Jones-Rhoades MW, Bartel DP, Bartel B (2006). MicroRNAs and their regulatory roles in plants. Ann. Rev. Plant Biol. 57: 19-53.
20. Jung J-H, Seo PJ, Park C-M (2009). MicroRNA biogenesis and function in higher plants. Plant Biotech. Rep. 3: 111-126.
21. Kidner CA, Martienssen RA (2005). The developmental role of microRNA in plants. Curr. Opin. Plant Biol. 8: 38-44.
22. Lai EC, Tomancak P, Williams RW, Rubin GM (2003). Computational identification of Drosophila microRNA genes. Genome Biol. 4: R42.
23. Li W, Ruan K (2009). MicroRNA detection by microarray. Anal. Bioanal. Chem. 394: 1117-1124.
24. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008). Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA, 14: 1-8.
25. Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL (2005). Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell, 17: 2186-2203.
26. Mathews DH, Sabina J, Zuker M, Turner DH (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
27. Michel BE, Kaufmann MR (1973). The osmotic potential of polyethylene glycol 6000. Plant Physiol. 51: 914-916.
28. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002). MicroRNA in plants. Gene Dev. 16: 1616-1626.
29. Rhoades MW, Reinhart BJ, Lim LP, Burge CP, Bartel B, Bartel DP (2002). Prediction of plant microRNA targets. Cell, 110: 513-520.
30. Royo H, Bortolin M-L, Seitz H, Cavaille J (2006). Small non-coding RNAs and genomic imprinting. Cytogenet. Genome Res. 113: 99-108.
31. Sunkar R, Girke T, Jain PK, Zhu JK (2005). Cloning and characterization of microRNA from rice. Plant Cell, 17: 1397-1411.
32. Sunkar R, Kapoor A, Zhu JK (2006). Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance. Plant Cell, 18: 2051-2065.
33. Sunkar R, Zhu JK (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16: 2001-2019.
34. Wang J, Zhou H, Chen Y, Luo Q, Qu L (2004). Identification of 20 microRNAs from Oryza sativa. Nucleic Acids Res. 32: 1688-1695.
35. Wang XJ, Reyes JL, Chua NH, Gaasterland T (2004). Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol. 5: 1-15.
36. Zhang B, Pan X, Anderson TA (2006). Identification of 188 conserved maize microRNAs and their targets. FEBS Lett. 580: 3753-3762.
37. Zhang B, Pan X, Cobb GP, Anderson TA (2006). Plant microRNA: a small regulatory molecule with big impact. Dev. Biol. 289: 3-16.
38. Zhang B, Stellwag EJ, Pan X (2009). Large-scale genome analysis reveals unique features of microRNAs. Gene, 443: 100-109.
39. Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA (2006). Conservation and divergence of plant microRNA genes. Plant J. 46: 243-259.
40. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA (2006). Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci. 63: 246-254.
41. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005). Identification and characterization of new plant microRNAs using EST analysis. Cell Res. 15: 336-360.
42. Zhao B, Liang R, Ge L, Li W, Xiao H, Lin H, Ruan K, Jin Y (2007). Identification of drought-induced microRNAs in rice. Biochem. Biophys. Res. Commun. 354: 585-590.