Identification and validation of potential conserved micrornas and their targets in peach (prunus persica)

Molecules and Cells

Volumn 34, Issue 3, 2012, Pages 239-249

  Gao, Zhihong ^a   Luo, Xiaoyan ^a   Shi, Ting ^a   Cai, Bin ^a   Zhang, Zhen ^a   Cheng, Zongming ^b   Zhuang, Weibing ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Computational prediction; MicroRNA; Peach; QRT PCR; Target

Indexed keywords

COMPLEMENTARY DNA; MICRORNA; RNA LIGASE; TRANSCRIPTION FACTOR;

ARTICLE; GENE REGULATORY NETWORK; GENE TARGETING; INTERACTIONS WITH RNA; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID ANALYSIS; PEACH; PROTEIN EXPRESSION; PROTEIN SECONDARY STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA CLEAVAGE; RNA EXTRACTION; RNA SEQUENCE; RNA STRUCTURE;

BASE SEQUENCE; CONSERVED SEQUENCE; DNA, COMPLEMENTARY; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; MOLECULAR SEQUENCE DATA; PRUNUS; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION FACTORS;

PRUNUS PERSICA;

EID: 84870316228     PISSN: 10168478     EISSN: 02191032     Source Type: Journal    
DOI: 10.1007/s10059-012-0004-7     Document Type: Article

References (50)

1. Adai, A., Johnson, C., Mlotshwa, S., Archer-Evans, S., Manocha, V., Vance, V., and Sundaresan, V. (2005). Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 15, 78-91.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Ambros, V. (2004). The functions of animal microRNAs. Nature 431, 350-355.
4. 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 Online 15, 2730-2741.
5. Bartel, D.P. (2004). MicroRNAs:: Genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
6. Carrington, J.C., and Ambros, V. (2003). Role of microRNAs in plant and animal development. Science 301, 336.
7. Chen, X. (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022.
8. Chiou, T.J. (2006). Regulation of Phosphate Homeostasis by Micro-RNA in Arabidopsis. Plant Cell Online 18, 412-421.
9. Debernardi, J.M., Rodriguez, R.E., Mecchia, M.A., and Palatnik, J.F. (2012). Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions. PLoS Genet. 8, e1002419.
10. Design, R.T.P.C.R.P. (2005). Facile means for quantifying micro-RNA expression by real-time PCR. Biotechniques 39, 519-525.
11. Dezulian, T., Remmert, M., Palatnik, J.F., Weigel, D., and Huson, D.H. (2006). Identification of plant microRNA homologs. Bioinformatics 22, 359-360.
12. Dhandapani, V., Ramchiary, N., Paul, P., Kim, J., Choi, S.H., Lee, J., Hur, Y., and Lim, Y.P. (2011). Identification of potential micro-RNAs and their targets in Brassica rapa L. Mol. Cells 32, 21-37.
13. Feng, J., Wang, K., Liu, X., Chen, S., and Chen, J. (2009). The quantification of tomato microRNAs response to viral infection by stem-loop real-time RT-PCR. Gene 437, 14-21.
14. German, M.A., Pillay, M., Jeong, D.H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L.A., Nobuta, K., German, R., et al. (2008). Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotech. 26, 941-946.
15. Griffiths-Jones, S.M. (2006). The microRNA sequence database. Methods Mol. Biol. 342, 129-138.
16. Griffiths-Jones, S., Saini, H.K., Van Dongen, S., and Enright, A.J. (2008). miRBase: Tools for microRNA genomics. Nucleic Acids Res. 36, D154.
17. 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. Monatshefte für Chemie/Chemical Monthly 125, 167-188.
18. Jeong, D.H., Park, S., Zhai, J., Gurazada, S.G., De Paoli, E., Meyers, B.C., and Green, P.J. (2011). Massive analysis of rice small RNAs: Mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 23, 4185-4207.
19. Jian, X., Zhang, L., Li, G., Wang, X., Cao, X., Fang, X., and Chen, F. (2010). Identification of novel stress-regulated microRNAs from Oryza sativa L. Genomics 95, 47-55.
20. 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.
21. Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B. (2006). MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57, 19-53.
22. 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.
23. Lindow, M., and Krogh, A. (2005). Computational evidence for hundreds of non-conserved plant microRNAs. BMC Genomics 6, 119.
24. Livak, K.J., and Schmittgen, T.D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2-[Delta][Delta] CT method. Methods 25, 402-408.
25. 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.
26. Meng, Y., Wu, P., and Chen, M. (2011). MicroRNAs in plant roots: Current understanding and future perspectives. Non Coding RNAs in Plants 269-284.
27. Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant microRNA targets. Cell 110, 513-520.
28. Ro, S., Park, C., Jin, J., Sanders, K.M., and Yan, W. (2006). A PCRbased method for detection and quantification of small RNAs. Biochem. Biophys. Res. Commun. 351, 756-763.
29. 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.
30. Schwab, R., Palatnik, J.F., Riester, M., Schommer, C., Schmid, M., and Weigel, D. (2005). Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8, 517-527.
31. 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.
32. Smith, T.F., and Waterman, M.S. (1981). Identification of common molecular subsequences. J. Mol. Biol 147, 195-197.
33. Song, C., Fang, J., Li, X., Liu, H., and Thomas Chao, C. (2009). Identification and characterization of 27 conserved microRNAs in citrus. Planta 230, 671-685.
34. Song, C., Fang, J., Wang, C., Guo, L., Nicholas, K.K., and Ma, Z. (2010a). MiR-RACE, a new efficient approach to determine the precise sequences of computationally identified trifoliate orange (Poncirus trifoliata) microRNAs. PloS One 5, e10861.
35. Song, C., Wang, C., Zhang, C., Korir, N.K., Yu, H., Ma, Z., and Fang, J. (2010b). Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11, 431.
36. Sun, Y.H., Shi, R., Zhang, X.H., Chiang, V.L., and Sederoff, R.R. (2011). MicroRNAs in trees. Plant Mol. Biol. 1-17.
37. Sunkar, R., Girke, T., Jain, P.K., and Zhu, J.K. (2005). Cloning and characterization of microRNAs from rice. Plant Cell Online 17, 1397-1411.
38. Tong, Z., Gao, Z., Wang, F., Zhou, J., and Zhang, Z. (2009). Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol. Biol. 10, 71.
39. Wang, X.W., Xiong, A.S., Yao, Q.H., Zhang, Z., and Qiao, Y.S. (2010). Direct isolation of high-quality low molecular weight RNA of pear peel from the extraction mixture containing nucleic acid. Mol. Biotechnol. 44, 61-65.
40. Wang, C., Han, J., Liu, C., Kibet, K.N., Kayesh, E., Shangguan, L., Li, X., and Fang, J. (2012). Identification of microRNAs from Amur grape (vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics 13, 122.
41. Wightman, B., Ha, I., and Ruvkun, G. (1993). Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855-862.
42. Yao, Y., Guo, G., Ni, Z., Sunkar, R., Du, J., Zhu, J.K., and Sun, Q. (2007). Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol. 8, R96.
43. Yu, H., Song, C., Jia, Q., Wang, C., Li, F., Nicholas, K.K., Zhang, X., and Fang, J. (2011). Computational identification of microRNAs in apple expressed sequence tags and validation of their precise sequences by miR-RACE. Physiol. Plant. 141, 56-70.
44. Zhang, B., Pan, X., and Anderson, T.A. (2006a). Identification of 188 conserved maize microRNAs and their targets. FEBS Lett. 580, 3753-3762.
45. Zhang, B., Pan, X., Wang, Q., Cobb, G.P., and Anderson, T.A. (2006b). Computational identification of microRNAs and their targets. Comput. Biol. Chem. 30, 395-407.
46. Zhang, B.H., Pan, X.P., Cox, S.B., Cobb, G.P., and Anderson, T.A. (2006c). Evidence that miRNAs are different from other RNAs. Cellular and molecular life sciences. Cell. Mol. Life Sci. 63, 246-254.
47. Zhang, B., Pan, X., and Stellwag, E.J. (2008). Identification of soybean microRNAs and their targets. Planta 229, 161-182.
48. Zhang, Y., Yu, M., Yu, H., Han, J., Song, C., Ma, R., and Fang, J. (2011). Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE. Mol. Biol. Rep. 39, 1975-1987.
49. Zhao, C.Z., Xia, H., Frazier, T.P., Yao, Y.Y., Bi, Y.P., Li, A.Q., Li, M.J., Li, C.S., Zhang, B.H., and Wang, X.J. (2010). Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol. 10, 3.
50. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406.