Dehydration stress-responsive mirna in brachypodium distachyon: Evident by genome-wide screening of micrornas expression

OMICS A Journal of Integrative Biology

Volumn 15, Issue 11, 2011, Pages 791-799

  Budak, Hikmet ^a   Akpinar, Ani ^a  

^a SABANCI UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PLANT RNA;

ARTICLE; BRACHYPODIUM; DEHYDRATION; DROUGHT TOLERANCE; GENE EXPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PLANT GENOME; PLANT LEAF; PLANT ROOT; PLANT STRESS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS;

BRACHYPODIUM; GENOME, PLANT; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, PLANT; STRESS, PHYSIOLOGICAL; WATER;

EID: 82355186184     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2011.0073     Document Type: Article

References (47)

1. Achard, P., Herr, A., Baulcombe, D.C., and Harberd, N.P. (2004). Modulation of floral development by a gibberellin-regulated microRNA. Development 131, 3357-3365. (Pubitemid 39139882)
2. Arenas-Huertero, C., Pérez, B., Rabanal, F., Blanco-Melo, D., De la Rosa, C., Estrada-Navarrete, G., et al. (2009). Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress. Plant Mol Biol 70, 385-401.
3. Bao, N., Lye, K.W., and Barton, M.K. (2004). MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev Cell 7, 653-662. (Pubitemid 39462686)
4. Bartel, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
5. Bonnet, E., Wuyts, J., Rouze, P., and van de Peer, Y. (2004). Detection of 91 potential in plant conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci USA 101, 11511-11516. (Pubitemid 39038378)
6. Cebec?, O., and Budak, H. (2009). Global expression patterns of three Festuca species exposed to different doses of glyphosate using the affymetrix genechip wheat genome array. Comp Funct Genomics 505701.
7. Chen, X. (2005). MicroRNA biogenesis and function in plants. FEBS Lett 579, 5923-5931. (Pubitemid 41484137)
8. Covarrubias, A.A., and Reyes, J.L. (2010). Post-transcriptional gene regulation of salinity and drought responses by plant microRNAs. Plant Cell Environ 33, 481-489.
9. Draper, J., Mur, L.A.J., Jenk?ns, G., Ghosh-B?swas, G.C., Bablak, P., Hasterok, R., Routledge, A.P.M. (2001). Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol 127, 1539-1555. (Pubitemid 34050024)
10. Ergen, N.Z., and Budak, H. (2009). Sequencing over 13000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress. Plant Cell Environ 32, 220-236.
11. Ergen, N.Z., Dinler, G., Shearman, R.C., and Budak, H. (2007). Identifying, cloning and structural analysis of differentially expressed genes upon Puccinia infection of Festuca rubra var. rubra. Gene 393, 145-152. (Pubitemid 46566481)
12. Ergen, N.Z., Thimmapuram, J., Bohnert, H.J., and Budak, H. (2009). Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Funct Integr Genomics 9, 377-396.
13. Filiz, E., Ozdemir, B.S., Budak, F., Vogel, J.P., Tuna, M., and Budak, H. (2009a). Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome 52, 876-890.
14. Filiz, E., Ozdemir, B.S., Tuna, M., and Budak, H. (2009b). Diploid Brachypodium distachyon of Turkey: molecular and morphologic analysis. Proceedings of the 5th International Symposium on the Molecular Breeding of Forage and Turf. T. Yamada, and G. Spangenberg, eds. (Springer, Berlin), pp. 83-89.
15. Guo, H.S., X?e, Q., Fe?, 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.
16. International Brachypodium ntatve. (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763-768.
17. 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. (Pubitemid 38780852)
18. Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B. (2006). Micro-RNAs and their regulatory roles in plants. Annu Rev Plant Biol 57, 19-53. (Pubitemid 44061017)
19. Kantar, M., Unver, T., and Budak, H. (2010). Regulation of barley miRNA upon dehydration stress correlated with target gene expression. Funct Integr Genomics 10, 493-507.
20. Kantar, M., Lucas, S.J., and Budak, H. (2011). miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 233, 471-484.
21. Kasschau, K.D., X?e, Z., Allen, E., Llave, C., Chapman, E.J., Kr?zan, K.A., and Carr?ngton, J.C. (2003). P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev Cell 4, 205-217. (Pubitemid 36221797)
22. K?m, J., Jung, J.H., Reyes, J.L., K?m, Y.S., K?m, S.Y., and Chung, K.S., et al. (2005). MicroRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J 42, 84-94.
23. Laufs, P., Peaucelle, A., Mor?n, H., and Traas, J. (2004).MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131, 4311-4322. (Pubitemid 39276198)
24. Li, W.X., Oono, Y., Zhu, J., He, X.J., Wu, J.M., Iida, K., et al. (2008). The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell 20, 2238-2251. (Pubitemid 352844522)
25. Liu, H.H., Tian, X., Li, Y.J., Wu, C.A., and Zheng, C.C. (2008). Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14, 836-843. (Pubitemid 351574905)
26. Llave, C., Kasschau, K.D., Rector, M.A., and Carrington, J.C. (2002). Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605-1619. (Pubitemid 34817147)
27. Lu, S., Sun, Y.H., and Ch?ang, V.L. (2008). Stress-responsive microRNAs in Populus. Plant J 55, 131-151. (Pubitemid 351990939)
28. Mallory, A.C., Bartel, D.P., and Bartel, B. (2005). MicroRNAdirected regulation of Arabidopsis Auxin response factor 17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17, 1360-1375. (Pubitemid 43138190)
29. Nishimura, N., Kitahata, N., Seki, M., Narusaka, Y., Narusaka, M., and Kuromori, T., et al. (2005). Analysis of ABA Hypersensitive Germination2 revealed the pivotal functions of PARN in stress response in Arabidopsis. Plant J 44, 972-984. (Pubitemid 43906726)
30. Ozdem?r, B.S., Hernandez, P., F?l?z, E., and Budak, H. (2008). Brachypodium genomics. Int J Plant Genomics 2008, 536104.
31. Ph?ll?ps, J.R., Dalmay, T., and Bartels, D. (2007). The role of small RNAs in abiotic stress. FEBS Lett 581, 3592-3597. (Pubitemid 47081000)
32. Rhoades, M., Re?nhart, B.J., L?m, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. (2002). Prediction of plant microRNA targets. Cell 110, 513-520. (Pubitemid 35232294)
33. Schwab, R., Palatn?k, J.F., R?ester, M., Schommer, C., Schm?d, M., and We?gel, D. (2005). Specific effects of microRNAs on the plant transcriptome. Dev Cell 8, 517-527. (Pubitemid 40450741)
34. Sunkar, R., and Zhu, J.K. (2004). Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16, 2001-2019. (Pubitemid 39059724)
35. Sunkar, R., Kapoor, A., and Zhu, J.K. (2006). Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miRNA398 and important for oxidative stress tolerance. Plant Cell 18, 2051-2065. (Pubitemid 44260196)
36. Thomson, J.M., Parker, J., Perou, C.M., and Hammond, S.M. (2004). A custom microarray platform for analysis of micro-RNA gene expression. Nat Methods 1, 47-53.
37. Unver, T., and Budak, H. (2009). Conserved microRNAs and their targets in model grass species Bracyhpodium distachyon. Planta 230, 659-669.
38. Unver, T., Namuth-Covert, D.M., and Budak, H. (2009). Review of current methodological approaches for characterizing microRNAs in plants. Int J Plant Genomics 2009, 262463.
39. Unver, T., Bakar, M., Shearman, R.C., and Budak, H. (2010). Genome-wide profiling and analysis of Festuca arundinacea miRNAs and transcriptomes in response to foliar glyphosate application. Mol Genet Genomics 283, 397-413.
40. Varkonyi-Gasic, E., Wu, R., Wood, M., Walton, E.F., and Hellens, R.P. (2007). Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3, 12.
41. Wei, B., Cai, T., Zhang, R., Li, A., Huo, N., and Li, S., et al. (2009). Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct Integr Genomics 9, 499-511.
42. Xiong, L., Gong, Z., Rock, C.D., Subramanian, S., Guo, Y., and Xu, W., et al. (2001). Modulation of abscisic acid signal transduction and biosynthesis by an Sm-like protein in Arabidopsis. Dev Cell 1, 771-781. (Pubitemid 33586132)
43. Yin, Z., Li, C., Han, X., and Shen, F. (2008). Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene 414, 60-66.
44. Zhang, B.H., Pan, X.P., Cobb, G.P., and Anderson, T.A. (2006a). Plant microRNA: a small regulatory molecule with a big impact. Dev Biol 289, 3-16. (Pubitemid 41804084)
45. Zhang, B.H., Pan, X.P., Cobb, G.P., and Anderson, T.A. (2006b). Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63, 246-254. (Pubitemid 43100293)
46. Zhang, J., Xu, Y., Huan, Q., and Chong, K. (2009). Deep sequencing of Brachypodium small RNAs at the global genomelevel identifies microRNAs involved in cold stress response. BMC Genomics 10, 449.
47. Zhao, B., Liang, R., Ge, L., Li, W., Xiao, H., and Lin H, et al. (2007). Identification of drought-induced microRNAs in rice. Biochem Biophys Res Commun 354, 585-590. (Pubitemid 46161364)