Characterization of mirnas in response to short-term waterlogging in three inbred lines of Zea mays

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Liu, Zhijie ^a,b   Kumari, Sunita ^b   Zhang, Lifang ^b   Zheng, Yonglian ^a   Ware, Doreen ^b,c  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MIR159; MIR164; MIR167; MIR393; MIR408; MIR528; UNCLASSIFIED DRUG;

ARTICLE; GENE EXPRESSION; GENE REGULATORY NETWORK; GENE TARGETING; HYPOXIA; INBRED STRAIN; MAIZE; MATHEMATICAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT STRESS; PROMOTER REGION; REGULATORY SEQUENCE; ROOT DEVELOPMENT; TRANSCRIPTION REGULATION; WATERLOGGING;

ADAPTATION, PHYSIOLOGICAL; BASE SEQUENCE; CLUSTER ANALYSIS; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; INBREEDING; MICRORNAS; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA LIGASE (ATP); RNA, PLANT; STRESS, PHYSIOLOGICAL; TIME FACTORS; WATER; ZEA MAYS;

ZEA MAYS;

EID: 84863107508     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039786     Document Type: Article

References (122)

1. Maltby E, (1991) Wetlands-their status and role in the biosphere. In: Jackson MB, Davies DD, Lambers H, editors. pp. 3-21 editors. Plant life under oxygen deprivation: Ecology, physiology and biochemistry: The Hague: SPB Academic.
2. Meyer WS, Barrs HD, Mosier AR, Schaefer NL, (1987) Response of maize to three short-term periods of waterlogging at high and low nitrogen levels on undisturbed and repacked soil. Irrigation Science 8: 257-272.
3. Ritter W, Beer C, (1969) Yield reduction by controlled flodding of corn. American Society of Agricultural Engineers Transactions 12: 46-47.
4. Sachs MM, Freeling M, Okimoto R, (1980) The anaerobic proteins of maize. Cell 20: 761-767.
5. Chandel NS, Maltepe E, Goldwasser E, Mathieu CE, Simon MC, et al. (1998) Mitochondrial reactive oxygen species trigger hypoxia-induced transcription. Proceedings of the National Academy of Sciences of the United States of America 95: 11715-11720.
6. Lopez-Barneo J, Pardal R, Ortega-Saenz P, (2001) Cellular mechanism of oxygen sensing. Annual Review of Physiology 63: 259-287.
7. Lopez-Barneo J, del Toro R, Levitsky KL, Chiara MD, Ortega-Saenz P, (2004) Regulation of oxygen sensing by ion channels. Journal of Applied Physiology 96: 1187-1195.
8. Waypa GB, Schumacker PT, (2005) Hypoxic pulmonary vasoconstriction: redox events in oxygen sensing. Journal of Applied Physiology 98: 404-414.
9. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
10. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
11. Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, et al. (2009) A genome-wide characterization of microRNA genes in maize. PLoS Genetics 5: e1000716.
12. Sunkar R, Zhu JK, (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. The Plant Cell 16: 2001-2019.
13. Lu S, Sun YH, Chiang VL, (2008) Stress-responsive microRNAs in Populus. The Plant Journal 55: 131-151.
14. Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W, (2008) Identification of cold-inducible microRNAs in plants by transcriptome analysis. Biochimica et Biophysica Acta 1779: 780-788.
15. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK, (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123: 1279-1291.
16. Ding D, Zhang L, Wang H, Liu Z, Zhang Z, et al. (2009) Differential expression of miRNAs in response to salt stress in maize roots. Annals of Botany 103: 29-38.
17. Reyes JL, Chua NH, (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. The Plant Journal 49: 592-606.
18. 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. The Plant Cell 18: 2051-2065.
19. Katiyar-Agarwal S, Jin H, (2007) Discovery of pathogen-regulated small RNAs in plants. Methods in Enzymology 427: 215-227.
20. Zhang Z, Wei L, Zou X, Tao Y, Liu Z, et al. (2008) Submergence-responsive MicroRNAs are potentially involved in the regulation of morphological and metabolic adaptations in maize root cells. Annals of Botany 102: 509-519.
21. Sunkar R, Chinnusamy V, Zhu J, Zhu JK, (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends in Plant Science 12: 301-309.
22. Dennis ES, Dolferus R, Ellis M, Rahman M, Wu Y, et al. (2000) Molecular strategies for improving waterlogging tolerance in plants. Journal of Experimental Botany 51: 89-97.
23. Zhai L, Liu Z, Zou X, Jiang Y, Qiu F, et al. (2012) Genome-wide identification and analysis of microRNA responding to long-term waterlogging in crown roots of maize seedlings. Physiologia Plantarum 9999.
24. Qiu F, Zheng Y, Zhang Z, Xu S, (2007) Mapping of QTL associated with waterlogging tolerance during the seedling stage in maize. Annals of Botany 99: 1067-1081.
25. Tang W, Zhang Z, Zou X, Zheng Y, (2005) Functional genomics of maize submergence tolerance and cloning of the related gene Sicyp51. Science China Life Sciences 48: 337-345.
26. Liu Y, Tang B, Zheng Y, Ma K, Xu S, et al. (2010) Screening Methods for Waterlogging Tolerance at Maize (Zea mays L.) Seedling Stage. Agricultural Sciences in China 9: 362-369.
27. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
28. Steemers FJ, Gunderson KL, (2005) Illumina, Inc. Pharmacogenomics 6(7): 777-782.
29. Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, et al. (2008) Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proceedings of the National Academy of Sciences of the United States of America 105: 14958-14963.
30. Szittya G, Moxon S, Santos DM, Jing R, Fevereiro MP, et al. (2008) High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics 9: 593.
31. Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, et al. (2010) Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis. Journal of Experimental Botany 61: 165-177.
32. Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research 39: D152-157.
33. t Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, et al. (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Research 36: e141.
34. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research 33: e179.
35. Varkonyi-Gasic E, Hellens RP, (2011) Quantitative Stem-Loop RT-PCR for Detection of MicroRNAs. Methods in Molecular Biology 744: 145-157.
36. Feng J, Wang K, Liu X, Chen S, Chen J, (2009) The quantification of tomato microRNAs response to viral infection by stem-loop real-time RT-PCR. Gene 437: 14-21.
37. Jones-Rhoades MW, Bartel DP, (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular Cell 14: 787-799.
38. Yao X, Wang H, Li H, Yuan Z, Li F, et al. (2009) Two types of cis-acting elements control the abaxial epidermis-specific transcription of the MIR165a and MIR166a genes. FEBS Letter 583: 3711-3717.
39. Wu MF, Tian Q, Reed JW, (2006) Arabidopsis microRNA167 controls patterns of ARF6 and ARF8 expression, and regulates both female and male reproduction. Development 133: 4211-4218.
40. Wang L, Gu X, Xu D, Wang W, Wang H, et al. (2011) miR396-targeted AtGRF transcription factors are required for coordination of cell division and differentiation during leaf development in Arabidopsis. Journal of Experimental Botany 62: 761-773.
41. Sieber P, Wellmer F, Gheyselinck J, Riechmann JL, Meyerowitz EM, (2007) Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness. Development 134: 1051-1060.
42. Raman S, Greb T, Peaucelle A, Blein T, Laufs P, et al. (2008) Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana. The Plant Journal 55: 65-76.
43. Vidal EA, Araus V, Lu C, Parry G, Green PJ, et al. (2010) Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 107: 4477-4482.
44. Gao P, Bai X, Yang L, Lv D, Pan X, et al. (2010) osa-MIR393: a salinity- and alkaline stress-related microRNA gene. Molecular Biology Reports 38: 237-242.
45. Kantar M, Lucas SJ, Budak H, (2010) miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 233(3): 471-484.
46. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, et al. (2010) miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. The Plant Cell 22: 1104-1117.
47. Sunkar R, Girke T, Jain PK, Zhu JK, (2005) Cloning and characterization of microRNAs from rice. The Plant Cell 17: 1397-1411.
48. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC, (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14: 836-843.
49. Lelandais-Briere C, Sorin C, Declerck M, Benslimane A, Crespi M, et al. (2010) Small RNA diversity in plants and its impact in development. Current Genomics 11: 14-23.
50. Ulmasov T, Hagen G, Guilfoyle TJ, (1999) Dimerization and DNA binding of auxin response factors. The Plant Journal 19: 309-319.
51. Kim JH, Choi D, Kende H, (2003) The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. The Plant Journal 36: 94-104.
52. Stracke R, Werber M, Weisshaar B, (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Current Opinion in Plant Biology 4: 447-456.
53. Cardon G, Hohmann S, Klein J, Nettesheim K, Saedler H, et al. (1999) Molecular characterisation of the Arabidopsis SBP-box genes. Gene 237: 91-104.
54. Cubas P, Lauter N, Doebley J, Coen E, (1999) The TCP domain: a motif found in proteins regulating plant growth and development. The Plant Journal 18: 215-222.
55. Zhong KY, Ye MS, Hu XW, Guo JC, (2006) [Role of the transcription factors CBF in plant cold tolerance]. Yi Chuan 28: 249-254.
56. Kobe B, Kajava AV, (2001) The leucine-rich repeat as a protein recognition motif. Current Opinion in Structural Biology 11: 725-732.
57. Yang Y, Fanning L, Jack T, (2003) The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins, APETALA3 and PISTILLATA. The Plant Journal 33: 47-59.
58. de Folter S, Immink RG, Kieffer M, Parenicova L, Henz SR, et al. (2005) Comprehensive interaction map of the Arabidopsis MADS Box transcription factors. The Plant Cell 17: 1424-1433.
59. Nakano T, Suzuki K, Fujimura T, Shinshi H, (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiology 140: 411-432.
60. Tree JJ, Ulett GC, Hobman JL, Constantinidou C, Brown NL, et al. (2007) The multicopper oxidase (CueO) and cell aggregation in Escherichia coli. Environmental Microbiology 9: 2110-2116.
61. Guan L, Scandalios JG, (1993) Characterization of the catalase antioxidant defense gene Cat1 of maize, and its developmentally regulated expression in transgenic tobacco. The Plant Journal 3: 527-536.
62. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, et al. (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320: 1185-1190.
63. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B, (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research 32: D91-94.
64. Webster CI, Packman LC, Pwee KH, Gray JC, (1997) High mobility group proteins HMG-1 and HMG-I/Y bind to a positive regulatory region of the pea plastocyanin gene promoter. The Plant Journal 11: 703-715.
65. Kozaki A, Hake S, Colasanti J, (2004) The maize ID1 flowering time regulator is a zinc finger protein with novel DNA binding properties. Nucleic Acids Research 32: 1710-1720.
66. Johannesson H, Wang Y, Engstrom P, (2001) DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro. Plant Molecular Biology 45: 63-73.
67. Sessa G, Morelli G, Ruberti I, (1993) The Athb-1 and-2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities. The EMBO Journal 12: 3507-3517.
68. Niu X, Helentjaris T, Bate NJ, (2002) Maize ABI4 binds coupling element1 in abscisic acid and sugar response genes. The Plant Cell 14: 2565-2575.
69. Martinez-Garcia JF, Moyano E, Alcocer MJ, Martin C, (1998) Two bZIP proteins from Antirrhinum flowers preferentially bind a hybrid C-box/G-box motif and help to define a new sub-family of bZIP transcription factors. The Plant Journal 13: 489-505.
70. Niu X, Renshaw-Gegg L, Miller L, Guiltinan MJ, (1999) Bipartite determinants of DNA-binding specificity of plant basic leucine zipper proteins. Plant Molecular Biology 41: 1-13.
71. Sato N, Ohshima K, Watanabe A, Ohta N, Nishiyama Y, et al. (1998) Molecular characterization of the PEND protein, a novel bZIP protein present in the envelope membrane that is the site of nucleoid replication in developing plastids. The Plant Cell 10: 859-872.
72. Yanagisawa S, Schmidt RJ, (1999) Diversity and similarity among recognition sequences of Dof transcription factors. The Plant Journal 17: 209-214.
73. Gubler F, Raventos D, Keys M, Watts R, Mundy J, et al. (1999) Target genes and regulatory domains of the GAMYB transcriptional activator in cereal aleurone. The Plant Journal 17: 1-9.
74. Hosoda K, Imamura A, Katoh E, Hatta T, Tachiki M, et al. (2002) Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. The Plant Cell 14: 2015-2029.
75. Solano R, Nieto C, Avila J, Canas L, Diaz I, et al. (1995) Dual DNA binding specificity of a petal epidermis-specific MYB transcription factor (MYB.Ph3) from Petunia hybrida. The EMBO Journal 14: 1773-1784.
76. Huang H, Mizukami Y, Hu Y, Ma H, (1993) Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS. Nucleic Acids Research 21: 4769-4776.
77. Huang H, Tudor M, Weiss CA, Hu Y, Ma H, (1995) The Arabidopsis MADS-box gene AGL3 is widely expressed and encodes a sequence-specific DNA-binding protein. Plant Molecular Biology 28: 549-567.
78. West AG, Causier BE, Davies B, Sharrocks AD, (1998) DNA binding and dimerisation determinants of Antirrhinum majus MADS-box transcription factors. Nucleic Acids Research 26: 5277-5287.
79. Meng Y, Ma X, Chen D, Wu P, Chen M, (2010) MicroRNA-mediated signaling involved in plant root development. Biochemical and Biophysical Research Communications 393: 345-349.
80. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T, (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
81. Achard P, Herr A, Baulcombe DC, Harberd NP, (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131: 3357-3365.
82. He C, Finlayson SA, Drew MC, Jordan WR, Morgan PW, (1996) Ethylene biosynthesis during aerenchyma formation in roots of maize subjected to mechanical impedance and hypoxia. Plant Physiology 112: 1679-1685.
83. Colmer TD, Cox MC, Voesenek LA, (2006) Root aeration in rice (Oryza sativa): evaluation of oxygen, carbon dioxide, and ethylene as possible regulators of root acclimatizations. The New Phytologist 170: 767-777.
84. Muhlenbock P, Plaszczyca M, Mellerowicz E, Karpinski S, (2007) Lysigenous aerenchyma formation in Arabidopsis is controlled by LESION SIMULATING DISEASE1. The Plant Cell 19: 3819-3830.
85. Jackson MB, (2008) Ethylene-promoted elongation: an adaptation to submergence stress. Annals of Botany 101: 229-248.
86. Olsen AN, Ernst HA, Leggio LL, Skriver K, (2005) NAC transcription factors: structurally distinct, functionally diverse. Trends in Plant Science 10: 79-87.
87. Guo HS, Xie Q, Fei JF, Chua NH, (2005) MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development. The Plant Cell 17: 1376-1386.
88. Dharmasiri N, Dharmasiri S, Estelle M, (2005) The F-box protein TIR1 is an auxin receptor. Nature 435: 441-445.
89. Yang JH, Han SJ, Yoon EK, Lee WS, (2006) Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells. Nucleic Acids Research 34: 1892-1899.
90. Adman ET, (1991) Copper protein structures. Advances in Protein Chemistry 42: 145-197.
91. Savelieff MG, Wilson TD, Elias Y, Nilges MJ, Garner DK, et al. (2008) Experimental evidence for a link among cupredoxins: red, blue, and purple copper transformations in nitrous oxide reductase. Proceedings of the National Academy of Sciences of the United States of America 105: 7919-7924.
92. Shigyo M, Hasebe M, Ito M, (2006) Molecular evolution of the AP2 subfamily. Gene 366: 256-265.
93. Webster CI, Packman LC, Gray JC, (2001) HMG-1 enhances HMG-I/Y binding to an A/T-rich enhancer element from the pea plastocyanin gene. European Journal of Biochemistry 268: 3154-3162.
94. Reeves R, (2001) Molecular biology of HMGA proteins: hubs of nuclear function. Gene 277: 63-81.
95. Henriksson E, Olsson AS, Johannesson H, Johansson H, Hanson J, et al. (2005) Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant Physiology 139: 509-518.
96. Olsson AS, Engstrom P, Soderman E, (2004) The homeobox genes ATHB12 and ATHB7 encode potential regulators of growth in response to water deficit in Arabidopsis. Plant Molecular Biology 55: 663-677.
97. Acevedo-Hernandez GJ, Leon P, Herrera-Estrella LR, (2005) Sugar and ABA responsiveness of a minimal RBCS light-responsive unit is mediated by direct binding of ABI4. The Plant Journal 43: 506-519.
98. Colasanti J, Yuan Z, Sundaresan V, (1998) The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell 93: 593-603.
99. Colasanti J, Sundaresan V, (2000) 'Florigen' enters the molecular age: long-distance signals that cause plants to flower. Trends in Biochemical Sciences 25: 236-240.
100. Li H, Sun J, Xu Y, Jiang H, Wu X, et al. (2007) The bHLH-type transcription factor AtAIB positively regulates ABA response in Arabidopsis. Plant Molecular Biology 65: 655-665.
101. Guiltinan MJ, Marcotte WR Jr, Quatrano RS, (1990) A plant leucine zipper protein that recognizes an abscisic acid response element. Science 250: 267-271.
102. Shen Q, Ho TH, (1995) Functional dissection of an abscisic acid (ABA)-inducible gene reveals two independent ABA-responsive complexes each containing a G-box and a novel cis-acting element. The Plant Cell 7: 295-307.
103. Choi H, Hong J, Ha J, Kang J, Kim SY, (2000) ABFs, a family of ABA-responsive element binding factors. The Journal of Biological Chemistry 275: 1723-1730.
104. Uno Y, Furihata T, Abe H, Yoshida R, Shinozaki K, et al. (2000) Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and high-salinity conditions. Proceedings of the National Academy of Sciences of the United States of America 97: 11632-11637.
105. van der Zaal BJ, Droog FN, Pieterse FJ, Hooykaas PJ, (1996) Auxin-sensitive elements from promoters of tobacco GST genes and a consensus as-1-like element differ only in relative strength. Plant Physiology 110: 79-88.
106. Liu F, Vantoai T, Moy LP, Bock G, Linford LD, et al. (2005) Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiology 137: 1115-1129.
107. Yokoyama A, Yamashino T, Amano Y, Tajima Y, Imamura A, et al. (2007) Type-B ARR transcription factors, ARR10 and ARR12, are implicated in cytokinin-mediated regulation of protoxylem differentiation in roots of Arabidopsis thaliana. Plant & Cell Physiology 48: 84-96.
108. Gomez-Cadenas A, Zentella R, Walker-Simmons MK, Ho TH, (2001) Gibberellin/abscisic acid antagonism in barley aleurone cells: site of action of the protein kinase PKABA1 in relation to gibberellin signaling molecules. The Plant Cell 13: 667-679.
109. Zentella R, Yamauchi D, Ho TH, (2002) Molecular dissection of the gibberellin/abscisic acid signaling pathways by transiently expressed RNA interference in barley aleurone cells. The Plant Cell 14: 2289-2301.
110. Dennis ES, Gerlach WL, Walker JC, Lavin M, Peacock WJ, (1988) Anaerobically regulated aldolase gene of maize. A chimaeric origin? Journal of Molecular Biology 202: 759-767.
111. Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K, (1993) An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. The Plant Cell 5: 1529-1539.
112. Lee TG, Jang CS, Kim JY, Kim DS, Park JH, et al. (2007) A Myb transcription factor (TaMyb1) from wheat roots is expressed during hypoxia: roles in response to the oxygen concentration in root environment and abiotic stresses. Physiologia Plantarum 129: 375-385.
113. Li Y, Li C, Ding G, Jin Y, (2011) Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways. BMC Evolutionary Biology 11: 122.
114. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, et al. (2005) Specific effects of microRNAs on the plant transcriptome. Developmental Cell 8: 517-527.
115. Qiu D, Pan X, Wilson IW, Li F, Liu M, et al. (2009) High throughput sequencing technology reveals that the taxoid elicitor methyl jasmonate regulates microRNA expression in Chinese yew (Taxus chinensis). Gene 436: 37-44.
116. Jia H, Nettleton D, Peterson JM, Vazquez-Carrillo G, Jannink JL, et al. (2007) Comparison of transcript profiles in wild-type and o2 maize endosperm in different genetic backgrounds. Crop Science 47: 45-59.
117. Llave C, Xie Z, Kasschau KD, Carrington JC, (2002) Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA. Science 297(5589): 2053-2056.
118. Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE, (2004) Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA 10: 1586-1594.
119. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. The EMBO Journal 23: 4051-4060.
120. Voinnet O, (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
121. Smith AD, Sumazin P, Xuan Z, Zhang MQ, (2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proceedings of the National Academy of Sciences of the United States of America 103: 6275-6280.
122. Schones DE, Smith AD, Zhang MQ, (2007) Statistical significance of cis-regulatory modules. BMC Bioinformatics 8: 19.