Boron Stress Responsive MicroRNAs and Their Targets in Barley

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Ozhuner, Esma ^a   Eldem, Vahap ^a,b   Ipek, Arif ^a   Okay, Sezer ^a   Sakcali, Serdal ^c   Zhang, Baohong ^d   Boke, Hatice ^a   Unver, Turgay ^a  

^a CANKIRI KARATEKIN UNIVERSITY   (Turkey)

^b ISTANBUL UNIVERSITY   (Turkey)

^c SULEYMAN DEMIREL UNIVERSITY   (Turkey)

^d EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 156; MICRORNA 156A; MICRORNA 156B; MICRORNA 156C; MICRORNA 156D; MICRORNA 156R; MICRORNA 157; MICRORNA 159; MICRORNA 160; MICRORNA 160A; MICRORNA 160O; MICRORNA 165; MICRORNA 166; MICRORNA 168; MICRORNA 169; MICRORNA 169C; MICRORNA 171; MICRORNA 171A; MICRORNA 172; MICRORNA 319; MICRORNA 319A; MICRORNA 319C; MICRORNA 397; MICRORNA 399; MICRORNA 408; MICRORNA 444A; MICRORNA 444B; MICRORNA 444C; UNCLASSIFIED DRUG;

ARTICLE; BARLEY; BORON STRESS; CHEMICAL STRESS; DOWN REGULATION; GENE TARGETING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GROWTH; PLANT LEAF; PLANT RESPONSE; PLANT ROOT; PLANT STRESS; PROMOTER REGION; PROTEIN RNA BINDING; REAL TIME POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SEEDLING; SIGNAL TRANSDUCTION; TISSUE SPECIFICITY; UPREGULATION;

BASE SEQUENCE; BORON; DOSE-RESPONSE RELATIONSHIP, DRUG; GENE EXPRESSION REGULATION, PLANT; HORDEUM; MICRORNAS; ORGAN SPECIFICITY; RNA STABILITY; RNA, MESSENGER; STRESS, PHYSIOLOGICAL;

HORDEUM;

EID: 84875478074     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059543     Document Type: Article

References (61)

1. Llave C, Kasschau KD, Rector MA, Carrington JC, (2002) Endogenous and silencing associated small RNAs in plants. Plant Cell 14: 1605-1619.
2. Carrington J, Ambros V, (2003) Role of microRNAs in plant and animal development. Science 301: 336-338.
3. Bartel D, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Jones-Rhoades MW, Bartel DP, Bartel B, (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
5. Zhang BH, Wang QL, Pan XP, (2007) MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210(2): 279-289.
6. Sunkar R, Chinnusamy V, Zhu JH, Zhu JK, (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12: 301-309.
7. Shukla LI, Chinnusamy V, Sunkar R, (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim Biophys Acta-Gene Regul Mech 1779: 743-748.
8. Eldem V, Okay S, Unver T, (2013) Plant microRNAs: new players in functional genomics. Turk J Agric For 37: 1-21.
9. Miwa K, Fujiwara T, (2010) Boron transport in plants: co-ordinated regulation of transporters. Ann Bot 105: 1103-1108.
10. Nable RO, Banuelos GS, Paull JG, (1997) Boron toxicity. Plant and Soil 193: 181-198.
11. Stangoulis JCR, Reid RJ (2002) Boron toxicity in plants and animals. In: Goldbach HEet al (eds) Boron in plant and animal nutrition. Kluwer Academic Press, New York 227-240.
12. Reid RJ, Hayes JE, Post A, Stagoulis JCR, Graham RD, (2004) A critical analysis of the causes of boron toxicity in plants. Plant Cell Environ 25: 1405-1414.
13. Wang BL, Shi L, Li YX, Zhang WH, (2010) Boron toxicity is alleviated by hydrogen sulfide in cucumber (Cucumis sativus L.) seedlings. Planta 231: 1301-1309.
14. Zhou ZS, Huang SQ, Yang ZM, (2008) Bioinformatic identification and expression analysis of new microRNAs from Medicago truncatula. Biochem Biophys Res Commun 374: 538-542.
15. Zhou ZS, Song JB, Yang ZM, (2012) Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium. J Exp Bot 63(12): 4597-4613.
16. Mendoza-Soto AB, Sánchez F, Hernández G, (2012) MicroRNAs as regulators in plant metal toxicity response. Front Plant Sci 3: 105.
17. Schulte D, Timothy JC, Andreas G, Langridge P, Matsumoto T, et al. (2009) The international barley sequencing consortium-At the threshold of efficient access to the barley genome. Plant Physiol 149: 142-147.
18. Sreenivasulu N, Graner A, Wobus U (2008) Barley genomics: An overview. Int J Plant Genomics 2008, 486258.
19. Kantar M, Unver T, Budak H, (2010) Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Funct Integr Genomics 10: 493-507.
20. Dryanova A, Zakharov A, Gulick PJ, (2008) Data mining for miRNAs and their targets in the Triticeae. Genome 51: 433-443.
21. Schreiber AW, Jun Shi B, Yuan Huang C, Langridge P, Baumann U, (2011) Discovery of barley miRNAs through deep sequencing of short reads. BMC Genomics 12: 129.
22. Lv S, Nie X, Wang L, Du X, Biradar SS, et al. (2012) Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing. Int J Mol Sci 13: 2973-2984.
23. Mao W, Li Z, Xia X, Li Y, Yu J, (2012) A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber. PLoS ONE 7(3): e33040.
24. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652.
25. Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
26. Zhang BH, Pan XP, Cox SB, Cobb GP, Anderson TA, (2006) Evidence that miRNAs are different from other RNAs. Cell Mol Life Sci 63(2): 246-254.
27. Zhang B, Pan XP, Cobb GP, Anderson TA, (2006) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289: 3-16.
28. Zhang B, Wang QL, Wang K, Pan X, Liu F, et al. (2007) Identification of cotton microRNAs and their targets. Gene 397: 26-37.
29. Yin Z, Li C, Han X, Shen F, (2008) Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene 414: 60-66.
30. Unver T, Budak H, (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 230: 659-669.
31. Zhang Y (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33 (Web Server issue), W701-4.
32. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the blast2go suite. Nucleic Acids Res 36: 3420-3435.
33. Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP, (2007) Protocol: a highly sensitive RT-PCR method for detection and quantifi cation of microRNAs. Plant Method 3: 12.
34. Unver T, Covert DN, Budak H (2009) Review of current methodological approaches for characterizing microRNAs in plants. Int J Plant Genomics 262463.
35. Unver T, Bozkurt O, Akkaya MS, (2008) Identification of differentially expressed transcripts from leaves of the boron tolerant plant Gypsophila perfoliata L. Plant Cell Rep. 27(8): 1411-1422.
36. Unver T, Parmaksi{dotless}z I, Dündar E, (2010) Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.). Plant Cell Rep 29: 757-769.
37. Unver T, Bakar M, Shearman RC, 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.
38. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA, (2006) Conservation and divergence of plant microRNA genes. Plant J 46(2): 243-259.
39. Zhang B, Pan X, Stellwag EJ, (2008) Identification of soybean microRNAs and their targets. Planta 229(1): 161-182.
40. Zhou L, Liu Y, Liu Z, Kong D, Duan M, et al. (2010) Genome-wide dentification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61: 4157-4168.
41. Li H, Dong Y, Yin H, Wang N, Yang J, et al. (2011) Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biol 11: 170.
42. Song QX, Liu YF, Hu XY, Zhang WK, Ma B, et al. (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol 11: 5.
43. Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, et al. (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10: 3.
44. Chi X, Yang Q, Chen X, Wang J, Pan L, et al. (2011) Identification and Characterization of microRNAs from Peanut (Arachis hypogaea L.) by High-Throughput Sequencing. PLoS ONE 6: 11.
45. Colaiacovo M, Subacchi A, Bagnaresi P, Lamontanara A, Cattivelli L, et al. (2010) A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.). BMC Genomics 11: 595.
46. Li B, Qin Y, Duan H, Yin W, Xia X, (2011) Genome-wide characterization of new and drought stres responsive microRNAs in Populus euphratica. J Exp Bot 62: 3765-3779.
47. Donaire L, Pedrola L, de la Rosa R, Llave C, (2011) High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.). PLoS ONE 6: 11.
48. Wang T, Chen L, Zhao M, Qiuying Tian Q, Hao Zhang W, (2011) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 12: 367.
49. Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, et al. (2010) Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J 62: 960-976.
50. Li YF, Zheng Y, Addo Quaye C, Zhang L, Sain A, et al. (2010) Transcriptome-wide identification of microRNA targets in rice. Plant J 62: 742-759.
51. Xin M, Wang Y, Yao Y, Xie C, Peng H, et al. (2010) Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.). BMC Plant Biol 10: 123.
52. Ando S, Takumi S, Ueda Y, Ueda T, Mori N, et al. (2000) Nicotiana tabacum cDNAs encoding alpha and beta subunits of a heterotrimeric GTP-binding protein isolated from hairy root tissues. Genes Genet Syst 75: 211-221.
53. Bussemer J, Chigri FC, Vothknecht U, (2009) Arabidopsis ATPase family gene 1-like protein 1 is a calmodulin-binding AAA+-ATPase with a dual localization in chloroplasts and mitochondria. FEBS Journal 276: 3870-3880.
54. Buchanan-Wollaston V, Page T, Harrison E, Breeze E, Lim PO, et al. (2005) Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis. Plant J 42: 567-585.
55. Fujisawa Y, Kato T, Ohki S, Ishikawa A, Kitano H, et al. (1999) Suppression of the heterotrimeric G protein causes abnormal morphology, including dwarfism, in rice. Proc Natl Acad Sci USA 96: 7575-7580.
56. Trindade I, Capitao C, Dalmay T, Fevereiro MP, Santos DM, (2009) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231: 705-16.
57. Sunkar R, (2010) MicroRNAs with macro-effects on plant stress responses. Semin Cell Dev Biol 21: 805-811.
58. Yanik H, Türktaş M, Dundar E, Hernandez P, Dorado G, et al. (2013) Genome-wide identification of alternate bearing-associated miRNA in the olive tree (Olea europaea). BMC Plant Biol 13: 10.
59. Khraiwesh B, Zhu JK, Zhu J, (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819: 137-48.
60. Eldem V, Akcay CU, Ozhuner E, Bakir Y, Uranbey S, et al. (2012) Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by highthroughput deep sequencing. PLoS ONE 7(12): e50298.
61. Ma L, Nie L, Liu J, Zhang B, Song S, et al. (2012) An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells. Genomics Proteomics Bioinformatics 10(6): 326-335.