Plant micrornas: New players in functional genomics

Turkish Journal of Agriculture and Forestry

Volumn 37, Issue 1, 2013, Pages 1-21

  Eldem, Vahap ^a,b   Okay, Sezer ^a   Ünver, Turgay ^a  

^a CANKIRI KARATEKIN UNIVERSITY   (Turkey)

^b ISTANBUL UNIVERSITY   (Turkey)

Author keywords

High throughput next generation sequencing; Plant development; Stress response

Indexed keywords

GENE EXPRESSION; GENETIC ENGINEERING; NUCLEIC ACIDS; THROUGHPUT;

BIOINFORMATICS ANALYSIS; ENVIRONMENTAL FACTORS; ENVIRONMENTAL STIMULI; HIGH-THROUGHPUT SEQUENCING; NEXT-GENERATION SEQUENCING; PLANT DEVELOPMENT; POST-TRANSCRIPTIONAL; STRESS RESPONSE;

RNA;

BIOINFORMATICS; BIOTIC FACTOR; CLONE; ENVIRONMENTAL FACTOR; FLOWER; GENE EXPRESSION; GENOMICS; LEAF MORPHOLOGY; PHYSIOLOGICAL RESPONSE; PLANT; RNA;

EUKARYOTA;

EID: 84870772243     PISSN: 1300011X     EISSN: None     Source Type: Journal    
DOI: 10.3906/tar-1206-50     Document Type: Review

References (231)

1. Abdel-Ghany SE, Pilon M (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J Biochem 283: 15932- 15945.
2. Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008) Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr Biol 18: 758-762.
3. Allen RS, Li J, Stahle MI, Dubroue A, Gubler F, Millar AA (2007) Genetic analysis reveals functional redundancy and the major target genes of the Arabidopsis miR159 family. Proc Natl Acad Sci USA 104: 16371-16376.
4. Alonso-Peral MM, Sun C, Millar AA (2012) MicroRNA159 can act as a switch or tuning microRNA independently of its abundance in Arabidopsis. PLoS ONE 7(4): e34751.
5. Amiteye S, Corral JM, Vogel H, Sharbel TF (2011) Analysis of conserved microRNAs in floral tissues of sexual and apomictic Boechera species. BMC Genomics 12: 500.
6. An FM, Hsiao SR, Chan MT (2011) Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in phalaenopsis orchid. PLoS One 6(5): e18937.
7. Arenas-Huertero C, Pérez B, Rabanal F, Blanco-Melo D, De la Rosa C, Estrada-Navarrete G, Sanchez F, Covarrubias AA, Reyes JL (2009) Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress. Plant Mol Biol 70: 385-401.
8. Ashelford K, Eriksson ME, Allen CM, D'Amore R, Johansson M, Gould P, Kay S, Millar AJ, Hall N, Hall A (2011) Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol 12(3): R28.
9. Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, Wittbrodt J, Antin PB, Plasterk RH (2006) Differences in vertebrate microRNA expression. Proc Natl Acad Sci USA 103: 14385-14389.
10. Aukerman MJ, Sakai H (2003) Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 15: 2730-2741.
11. Axtell MJ, Westholm JO, Lai EC (2011) Vive la difference: Biogenesis and evolution of microRNAs in plants and animals. Genome Biology 12: 221.
12. Baker CC, Sieber P, Wellmer F, Meyerowitz EM (2005) The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis. Curr Biol 15: 303-315.
13. Balcells I, Cirera S, Busk PK (2012) Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol 11: 70-81.
14. Barrera-Figueroa BE, Gao L, Diop NN, Wu Z, Ehlers JD, Roberts PA, Close TJ, Zhu JK, Liu R (2011) Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC Plant Biol 11: 127.
15. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
16. Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci USA 102: 11928-11933.
17. Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW (2010) mRNA and microRNA quality control for RT-qPCR analysis. Methods 50: 237-243.
18. Bednarek P, Kwon C, Schulze-Lefert P (2010) Not a peripheral issue: secretion in plant microbe interactions. Curr Opin Plant Biol 13: 378-387.
19. Benes V, Castoldi M (2010) Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available. Methods 50: 244-249.
20. Bollman KM, Aukerman MJ, Park MY, Hunter C, Berardini TZ, Poethig RS (2003) HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 130: 1493-1504.
21. Bowman JL, Floyd SK (2008) Patterning and polarity in seed plant shoots. Annu Rev Plant Biol 59: 67-88.
22. Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301: 336-338.
23. Castoldi M, Benes V, Hentze MW, Muckenthaler MU (2007) miChip: A microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes. Methods 43: 146-152.
24. Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE, Hentze MW, Muckenthaler MU (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12: 913-920.
25. Cerutti L, Mian N, Bateman A (2000) Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the PIWI domain. Trends Biochem Sci 25: 481-482.
26. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179.
27. Chen J, April CS, Fan JB (2012) miRNA expression profiling using Illumina Universal BeadChips. Methods Mol Biol 822: 103-16.
28. Chen X (2005) microRNA biogenesis and function in plants. FEBS Lett 579: 5923-5931.
29. Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303: 2022-2025.
30. Chi X, Yang Q, Chen X, Wang J, Pan L, Chen M, Yang Z, He Y, Liang X, Yu S (2011) Identification and characterization of microRNAs from peanut (Arachis hypogaea L.) by highthroughput sequencing. PLoS One 6: e27530.
31. Chuck G, Meeley R, Hake S (2008) Floral meristem initiation and meristem cell fate are regulated by the maize AP2 genes ids1 and sid1. Development 135: 3013-3019.
32. Chuck G, Meeley R, Irish E, Sakai H, Hake S (2007) The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/ in determinate spikelet1. Nat Genet 39: 1517-1521.
33. Combier J, Frugier F, de Billy F, Boualem A, El-Yahyaoui F, Moreau S, Vernie T, Ott T, Gamas P, Crespi M, Niebel A (2006) MtHAP2-1 is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 in Medicago truncatula. Genes Dev 20: 3084-3088.
34. Crawford BC, Nath U, Carpenter R, Coen ES (2004) CINCINNATA controls both cell differentiation and growth in petal lobes and leaves of Antirrhinum. Plant Physiol 135: 244-253.
35. D'Andrade PN, Fulmer-Smentek S (2012) Agilent microRNA microarray profiling system. Methods Mol Biol 822: 85-102.
36. Davison TS, Johnson CD, Andruss BF (2006) Analyzing micro-RNA expression using microarrays. Methods Enzymol 411: 14-34.
37. Dee S, Getts RC (2012) MicroRNA expression analysis using the Affymetrix Platform. Methods Mol Biol 822: 117-129.
38. Deo M, Yu JY, Chung KH, Tippens M, Turner DL (2006) Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides. Dev Dyn 235: 2538-2548.
39. 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 (Lond) 103: 29-38.
40. Ding Y, Chen Z, Zhu C (2011) Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa). J Exp Bot 62: 3563-73.
41. Dong Z, Han M, Fedoroff N (2008) The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1. Proc Natl Acad Sci USA 105: 9970-9975.
42. Dongdong L, Zheng Y, Wan L, Zhu X, Wang Z (2009) Differentially expressed microRNAs during solid endosperm development in coconut (Cocos nucifera L.). Scientia Horticulturae 122: 666-669.
43. Donner TJ, Sherr I, Scarpelia E (2009) Regulation of preprocambial cell state acquisition by auxin signaling in Arabidopsis leaves. Development 136: 3235-3246.
44. Du P, Wu J, Zhang J, Zhao S, Zheng H, Gao G, Wei L, Li Y (2011) Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog 7(8): e1002176.
45. Dugas DV, Bartel B (2004) MicroRNA regulation of gene expression in plants. Curr Opin Plant Biol 7: 512-520.
46. Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 15: 2219-2235.
47. Efroni I, Blum E, Goldshmidt A, Eshed Y (2008) A protracted and dynamic maturation schedule underlies Arabidopsis leaf development. Plant Cell 20: 2293-2306.
48. Egan AN, Schlueter J, Spooner DM (2012) Applications of nextgeneration sequencing in plant biology. Am J Bot 99: 175-85.
49. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2: e219.
50. Fang Y, Spector DL (2007) Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants. Curr Biol 17: 818-823.
51. Fehniger TA, Wylie T, Germino E, Leong JW, Magrini VJ, Koul S, Keppel CR, Schneider SE, Koboldt DC, Sullivan RP, Heinz ME, Crosby SD, Nagarajan R, Ramsingh G, Link DC, Ley TJ, Mardis ER (2010) Next-generation sequencing identifies the natural killer cell microRNA transcriptome. Genome Res 20: 1590-604.
52. Frazier TP, Sun G, Burklew CE, Zhang B (2011) Salt and drought stresses induce the aberrant expression of microRNA genes in tobacco. Mol Biotechnol 49: 159-165.
53. Fujioka Y, Utsumi M, Ohba Y, Watanabe Y (2007) Location of a possible miRNA processing site in SmD3/SmB nuclear bodies in Arabidopsis. Plant Cell Physiol 48: 1243-1253.
54. Gandikota M, Birkenbihl RP, Hohmann S, Cardon GH, Saedler H, Huijser P (2007) The miRNA156/157 recognition element in the 30 UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 49: 683-693.
55. German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ (2008) Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 26: 941-946.
56. Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD (2008) Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci USA 105: 803-808.
57. Gonzalez-Ibeas D, Blanca J, Donaire L, Saladie M, Mascarell-Creus A, Cano-Delgado A, Garcia-Mas J, Llave C, Aranda MA (2011) Analysis of the melon (Cucumis melo) small RNAome by highthroughput pyrosequencing. BMC Genomics 12: 393.
58. 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. Plant Cell 17: 1376-1386.
59. Guo L, Lu Z (2010) The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule? PLoS One, 5(6): e11387.
60. Guo N, Ye WW, Wu XL, Shen DY, Wang YC, Xing H, Dou DL (2011) Microarray profiling reveals microRNAs involving soybean resistance to Phytophthora sojae. Genome 54: 954-58.
61. Gutierrez L, Bussell JD, Pacurar DI, Schwambach J, Pacurar M, Bellini C (2009) Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSEFACTOR transcripts and microRNA abundance. Plant Cell 21: 3119-3132.
62. Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Buell CR (2012) Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PLoS One 7(3): e33071.
63. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5: 522-531.
64. Hiraguri A, Itoh R, Kondo N, Nomura Y, Aizawa D, Murai Y, Koiwa H, Seki M, Shinozaki K, Fukuhara T (2005) Specific interactions between Dicer-like proteins and HYL1/DRBfamily dsRNAbinding proteins in Arabidopsis thaliana. Plant Mol Biol 57: 173-188.
65. Houbaviy HB, Dennis L, Jaenisch R, Sharp PA (2005) Characterization of a highly variable eutherian microRNA gene. RNA 11: 1245- 1257.
66. Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ (2009) Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiol 151: 2120-2132.
67. Hsieh TF, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D (2009) Genome-wide demethylation of Arabidopsis endosperm. Science 324: 1451-1454.
68. Huang SQ, Xiang AL, Che LL, Chen S, Li H, Song JB, Yang ZM (2010) A set of miRNAs from Brassica napus in response to sulphate deficiency and cadmium stress. Plant Biotechnol J 8: 887-899.
69. International Brachypodium Initiative. Vogel etal. (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature: 463: 763-768.
70. Jagadeeswaran G, Saini A, Sunkar R (2009) Biotic and abiotic stress down-regulate miR398 expression in Arabidopsis. Planta 229: 1009-1014.
71. Jin H, Vacic V, Girke T, Lonardi S, Zhu JK (2008) Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol Biol 9: 6.
72. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
73. Juarez MT, Kui JS, Thomas J, Heller BA, Timmermans MC (2004) MicroRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428: 84-88.
74. Judson RL, Babiarz JE, Venere M, Blelloch R (2009) Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat Biotechnol 27(5): 459-461.
75. Jung JH, Seo PJ, Park CM (2009) MicroRNA biogenesis and function in higher plants. Plant Biotechnol Rep 3: 111-126.
76. Jung JH, Seo YH, Seo PJ, Reyes JL, Yun J, Chua NH, Park CM (2007) The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell 19: 2736-2748.
77. 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.
78. Katiyar-Agarwal S, Jin H (2010) Role of small RNAs in host-microbe interactions. Annu Rev Phytopathol 4: 225-246.
79. Kaufmann K, Muino JM, Osteras M, Farinelli L, Krajewski P, Angenent GC (2010) Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat Protocols 5(3): 457-472.
80. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115: 209-216.
81. Kidner C, Timmermans M (2006) In situ hybridisation as a tool to study the role of miRNAs in plant development. Meth Mol Biol 342: 159-179.
82. Kidner CA, Martienssen RA (2004) Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428: 81-84.
83. Kidner CA, Martienssen RA (2005) The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev Biol 280: 504-517.
84. Kim J, Jung JH, Reyes JL, Kim YS, Kim SY, Chung KS, Kim JA, Lee M, Lee Y, Narry Kim V, Chua NH, Park CM (2005) microRNAdirected cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J 42: 84-94.
85. Kim JJ, Lee JH, Kim W, Jung SH, Huijser P, Ahn JH (2012) The microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module regulates ambient temperatureresponsive flowering via FLOWERING LOCUS T in Arabidopsis. Plant Phys 159: 461-478.
86. Kloosterman WP, Wienholds E, de Bruijn E, Kauppinen S, Plasterk RH (2006) In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods 3: 27-29.
87. Koscianska E, Starega-Roslan J, Czubala K, Krzyzosiak WJ (2011) High-resolution northern blot for a reliable analysis of microRNAs and their precursors. ScientificWorldJournal 11: 102-117.
88. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157.
89. Kurihara Y, Takashi Y, Watanabe Y (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12: 206-212.
90. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
91. Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Ratsch G, Weigel D (2008) Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci USA 105: 8795-8800.
92. Laufs P, Peaucelle A, Morin H, Traas J (2004) MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131: 4311-4322.
93. Lauter N, Kampani A, Carlson S, Goebel M, Moose SP (2005) microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proc Natl Acad Sci USA 102: 9412- 9417.
94. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek HS, Kim NV (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23: 4051-4060.
95. Lelandais-Briere C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M (2009) Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. Plant Cell 21: 2780-2796.
96. Li B, Qin Y, Duan H, Yin W, Xia X (2011a) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot 62: 3765-3779.
97. Li H, Dong Y, Yin H, Wang N, Yang J, Liu X, Wang Y, Wu J, Li X (2011b) Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biol 11: 170.
98. Li J, Yang Z, Yu B, Liu J, Chen X (2005). Methylation protects miRNAs and siRNAs from a 30-end uridylation activity in Arabidopsis. Curr Biol 15: 1501-1507.
99. 2 -responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica) Nucleic Acids Res 39: 2821-2833.
100. Li WX, Oono Y, Zhu J, He XJ, Wu JM, Iida K, Lu XY, Cui X, Jin H, Zhu JK (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell 20: 2238-2251.
101. Li Y, Zhang Q, Zhang J, Wu L, Qi Y, Zhou JM (2010a) Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiol 152: 2222-223.
102. Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R (2010b) Transcriptome-wide identification of microRNA targets in rice. Plant J 62: 742-759.
103. Liang G, Yang F, Yu D (2010) MicroRNA395 mediates regulation of sulfate accumulation and allocation in Arabidopsis thaliana. Plant J 62: 1046-1057.
104. Lima JC, Arenhart RA, Margis-Pinheiro M, Margis R (2011) Aluminum triggers broad changes in microRNA expression in rice roots. Genet Mol Res 10: 2817-2832.
105. Liu CG, Calin GA, Volinia S, Croce CM (2008) MicroRNA expression profiling using microarrays. Nat Protoc 3(4): 563-78.
106. Liu D, Song Y, Chen Z, Yu D (2009) Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. Physiol Plant 136: 223-236.
107. 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.
108. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ, Hammond SM, Joshua-Tor L, Hannon GJ (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437- 1441.
109. Lobbes D, Rallapalli G, Schmidt DD, Martin C, Clarke J (2006) SERRATE: a new player on the plant microRNA scene. EMBO Rep 7: 1052-1058.
110. López-Gomollón S (2011) Detecting sRNAs by Northern blotting. Methods Mol Biol 732: 25-38.
111. Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55: 131-151.
112. Lv DK, Bai X, Li Y, Ding XD, Ge Y, Cai H, Ji W, Wu N, Zhu YM. (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459: 39-47.
113. Mallory AC, Reinhart BJ, Jones-Rhoades MW, Tang G, Zamore PD, Barton MK, Bartel DP (2004) MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO J 23: 3356-3364.
114. Mallory AC, Bartel DP, Bartel B (2005) MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17: 1360-1375.
115. 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.
116. Marin E, Jouannet V, Herz A, Lokerse AS, Weijers D, Vaucheret H, Nussaume L, Crespi MD, Maizel A (2010) miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth. Plant Cell 22: 1104-1117.
117. Martin RC, Asahina M, Liu PP, Kristof JR, Coppersmith JL, Pluskota WE, Bassel GW, Goloviznina NA, Nguyen TT, Martinez-Andujar C, Kumar AMB, Pupel P, Nonogaki H (2010) The microRNA156 and microRNA172 gene regulation cascades at post-germinative stages in Arabidopsis. Seed Sci Res 20: 79-87.
118. Megraw M, Baev V, Rusinov V, Jensen S, Kalantidis K, Hatzigeorgiou AG (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 16: 1612-1619.
119. Meng Y, Gou L, Chen D, Wu P, Chen M (2010) High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism. J Exp Bot 61: 3833-3837.
120. Mestdagh P, Feys T, Bernard N, Guenther S, Chen C, Speleman F, Vandesompele J (2008) High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Res 36: e143.
121. Metzker ML (2010) Sequencing technologies - The next generation. Nature Reviews Genetics 11: 31-46.
122. Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell 133(1): 116-127.
123. Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del Fabbro C, Valle G, Policriti A, Morgante M et al. (2009) High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics 10: 558.
124. Millar AA, Waterhouse PM (2005) Plant and animal microRNAs: Similarities and differences. Funct Integr Genomics 5: 129- 135.
125. Miyoshi K, Tsukumo H, Nagami T, Siomi H, Siomi MC (2005) Slicer function of Drosophila argonautes and its involvement in RISC formation. Genes Dev 19: 2837-2848.
126. Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133: 128-141.
127. Moreno-Risueno MA, Norman JMV, Moreno A, Zhang J, Ahnert SE, Benfey PN (2010) Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science 329: 1306-1311.
128. Mutasa-Gottgens ES, Joshi A, Holmes HF, Hedden P, Gottgens B (2012) A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. BMC Genomics 13: 99.
129. Nath U, Crawford BC, Carpenter R, Coen E (2003) Genetic control of surface curvature. Science 299: 1404-1407.
130. Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones JD (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312: 436-439.
131. Nelson PT, Baldwin DA, Kloosterman WP, Kauppinen S, Plasterk RH, Mourelatos Z (2006) RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 12: 187-191.
132. Ni FT, Chu LY, Shao HB, Liu ZH (2009) Gene expression and regulation of higher plants under soil water stress. Curr Genomics 10: 269-280.
133. Nikovics K, Blein T, Peaucelle A, Ishida T, Morin H, Aida M, Laufs P (2006) The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis. Plant Cell 18: 2929-2945.
134. Nodine MD, Bartel DP (2010) MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis. Genes Dev 24: 2678-2692.
135. Nuovo G, Lee EJ, Lawler S, Godlewski J, Schmittgen T (2009) In situ detection of mature microRNAs by labeled extension on ultramer templates. Methods 46: 115-126.
136. Ori N, Cohen AR, Etzioni A, Brand A, Yanai O, Shleizer S, Menda N, Amsellem Z, Efroni I, Pekker I, Alvarez JP, Blum E, Zamir D, Eshed Y (2007) Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nat Genet 39: 787-791.
137. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263.
138. Pall GS, Hamilton AJ (2008) Improved northern blot method for enhanced detection of small RNA. Nat Protoc 3: 1077-1084.
139. Pant BD, Buhtz A, Kehr J, Scheible WR (2008) MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J 53: 731-738.
140. Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyán J (2010) Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis. Plant J 62(6): 960-976.
141. Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Poethig RS (2005). Nuclear processing and export of microRNAs in Arabidopsis. Proc Natl Acad Sci USA 102: 3691-3696.
142. Park W, Li J, Song R, Messing J, Chen X (2002) CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 12: 1484-1495.
143. Parker JS, Roe SM, Barford D (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 23: 4727-4737.
144. Pearson BJ, Eisenhoffer GT, Gurley KA, Rink JC, Miller DE, Sanchez AA (2009) Formaldehyde-based whole-mount in situ hybridization method for planarians. Dev Dyn 238: 443-50.
145. Peng H, Chun J, Ai TB, Tong YA, Zhang R, Zhao MM, Chen F, Wang SH (2012) MicroRNA profiles and their control of male gametophyte development in rice. Plant Mol Biol DOI: 10.1007/s11103-012-9898-x
146. Ramachandran V, Chen X (2008). Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321: 1490- 1492.
147. Rausch T, Wachter A (2005) Sulfur metabolism: a versatile platform for launching defence operations. Trends Plant Sci 10: 503-509.
148. Raymond CK, Roberts BS, Garrett-Engele P, Lim LP, Johnson JM (2005) Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 1: 1737-1744.
149. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16, 1616-1626.
150. Reyes JL, Chua NH (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49: 592-606.
151. Rhoades JMW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14: 787-799.
152. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110: 513- 520.
153. Rodriguez RE, Mecchia MA, Debernardi JM, Schommer C, Weigel D, Palatnik JF (2010) Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development 137: 103-112.
154. Ronemus M, Vaughn MW, Martienssen RA (2006) MicroRNA targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNAdependent RNA polymerase in Arabidopsis. Plant Cell 18: 1559-1574.
155. Rubio-Somoza I, Cuperus JT, Weigel D, Carrington JC (2009) Regulation and functional specialization of smallRNA-target nodes during plant development. Curr Opin Plant Biol 12: 622-627.
156. Schadt EE, Turner S, Kasarskis A (2011) A window into third generation sequencing. Hum Mol Genet 19: R227?R240; erratum/corrigendum 20: 853 (2011).
157. Schmittgen TD, Lee EJ, Jiang J, Sarkar A, Yang L, Elton TS, Chen C (2008) Real-time PCR quantification of precursor and mature microRNA. Methods 44: 31-38.
158. Schommer C, Palatnik JF, Aggarwal P, Chetelat A, Cubas P, Farmer EE, Nath U, Weigel D (2008) Control of jasmonate biosynthesis and senescence by miR319 targets. PLoS Biol 6(9): e230.
159. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517-527.
160. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115: 199-208.
161. Sharbati-Tehrani S, Kutz-Lohroff B, Bergbauer R, Scholven J, Einspanier R (2008) miR-Q: a novel quantitative RT-PCR approach for the expression profiling of small RNA molecules such as miRNAs in a complex sample. BMC Mol Biol 9: 34.
162. Shikata M, Koyama T, Mitsuda N, Ohme-Takagi M (2009) Arabidopsis SBP-box genes SPL10, SPL11 and SPL2 control morphological change in association with shoot maturation in the reproductive phase. Plant Cell Physiol 50: 2133-2145.
163. Shleizer-Burko S, Burko Y, Ben-Herzel O, Ori N (2011) Dynamic growth program regulated by LANCEOLATE enables flexible leaf patterning. Development 138: 695-704.
164. Shukla Ll, Chinnusamy V, Sunkar R (2008) The role of microRNAs and other endogenous small RNAs in plant stress responses. Biochim Biophys Acta 1779: 743-748.
165. Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J (2011) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11: 431.
166. Song QX, Liu YF, Hu XY, Zhang WK, Ma B, Chen SY, Zhang JS (2011) Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol 11: 5.
167. Sorin C, Bussell JD, Camus I, Ljung K, Kowalczyk M, Geiss G, McKhann H, Garcion C, Vaucheret H, Sandberg G, Bellini C (2005) Auxin and light control of adventitious rooting in Arabidopsis require ARGONAUTE1. Plant Cell 17: 1343-1359.
168. Sunkar R (2010) MicroRNAs with macro-effects on plant stress responses. Semin Cell Dev Biol 21: 805-811.
169. 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.
170. Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17: 196-203.
171. Sunkar R, Zhu J (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019.
172. Sweetman D (2011) In situ detection of microRNAs in animals. Methods Mol Biol 732: 1-8.
173. Sweetman, D, Goljanek K, Rathjen T, Oustanina S, Braun T, Dalmay T, Munsterberg A (2008) Specific requirements of MRFs for the expression of muscle specific microRNAs, miR-1, miR-206 and miR-133 Dev Biol 321: 491-499.
174. Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y (2008) The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol 49: 493-500.
175. Thiebaut F, Rojas CA, Almeida KL, Grativol C, Domiciano GC, Lamb CR, Engler JDEA, Hemerly AS, Ferreira PC (2012) Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ 35: 502-512.
176. Thompson RC, Deo M, Turner DL (2007) Analysis of microRNA expression by in situ hybridization with RNA oligonucleotide probes. Methods 43: 153-161.
177. Trindade I, Capitão C, Dalmay T, Fevereiro MP, Santos DM (2010) miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula. Planta 231: 705-716.
178. Unver T, Bakar M, Shearman R, Budak H (2010a) Genome-wide profiling and analysis of Festuca arundinacea miRNAs and transcriptomes in response to foliar glyphosate application. Mol Genet Genomics 283: 397-413.
179. Unver T, Budak H (2009) Conserved microRNAs and their targets in model grass species Brachypodium distachyon. Planta 230: 659-669.
180. Unver T, Covert DN, Budak H (2009) Review of current methodological approaches for characterizing microRNAs in plants. Int J Plant Genomics 262463.
181. Unver T, Parmaksiz I, Dündar E (2010b) Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.). Plant Cell Rep 29: 757-769.
182. Válóczi, A, Hornyik C, Varga N, Burgyán J, Kauppinen S, Havelda Z (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 32: e175-82.
183. Varallyay E, Burgyán J, Havelda Z (2008) MicroRNA detection by northern blotting using locked nucleic acid probes. Nat Protoc 3: 190-196.
184. Várallyay E, Havelda Z (2011) Detection of microRNAs in plants by in situ hybridization. Methods Mol Biol 732: 9-23.
185. Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Method 3: 12.
186. Vaucheret H, Vazquez F, Crete P, Bartel DP (2004) The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18: 1187-1197.
187. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus domestica Borkh). Nature Genetics 42: 833-839.
188. Vester B, Wengel J (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43: 13233-13241.
189. Vidal EA, Araus V, Lu C, Parry G, Green PJ, Coruzzi GM, Gutierrez RA (2010) Nitrate responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci USA 107: 4477-4482.
190. Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136: 669-687.
191. Wang JW, Park MY, Wang LJ, Koo Y, Chen XY, Weigel D, Poethig RS (2011a) miRNA control of vegetative phase change in trees. PLoS Genet 7: e1002012.
192. Wang JW, Schwab R, Czech B, Mica E, Weigel D (2008) Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell 20: 1231-1243.
193. Wang JW, Wang LJ, Mao YB, Cai WJ, Xue HW, Chen XY (2005) Control of root cap formation by microRNA-targeted auxin response factors in Arabidopsis. Plant Cell 17: 2204-2216.
194. Wang T, Chen L, Zhao M, Tian Q, Zhang WH (2011b) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genomics 12: 367.
195. Wang Y, Blelloch R (2009) Cell cycle regulation by MicroRNAs in embryonic stem cells. Cancer Res 69: 4093-4096.
196. Wang Z, Yang B (2010) MicroRNA Expression Detection Methods, Springer-Verlag Berlin Heidelberg, Chapter 5: End-Point Stem-Loop Real-Time RT-PCR for miRNA Quantification 131-140.
197. Wei LQ, Yan LF, Wang T (2011) Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa. Genome Biol 12(6): R53.
198. Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, X. (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12: 451.
199. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH (2005) MicroRNA expression in zebrafish embryonic development. Science 309: 310-311.
200. Williams L, Grigg SP, Xie M, Christensen S, Fletcher JC (2005) Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development 132: 3657-3668.
201. Willmann MR, Mehalick AJ, Packer RL, Jenik PD (2011) MicroRNAs regulate the timing of embryo maturation in Arabidopsis. Plant Physiol 155: 1871-1884.
202. Wu G, Poethig RS (2006) Temporal regulation of shoot developmentin Arabidopsis thaliana by miR156 and its target SPL3. Development 133: 3539-3547.
203. 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.
204. Wu XM, Liu MY, Ge XX, Xu Q, Guo WW (2011) Stage and tissuespecific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange. Planta 233: 495-505.
205. Wulczyn FG, Smirnova L, Rybak A, Brandt C, Kwidzinski E, Ninnemann O, Strehle M, Seiler A, Schumacher S, Nitsch R (2007) Post-transcriptional regulation of the let-7 microRNA during neural cell specification. FASEB J 21: 415-426.
206. Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of Arabidopsis MIRNA Genes. Plant Physiol 138: 2145-2154.
207. Xin M, Wang Y, Yao Y, Song N, Hu Z, Qin D, Xie C, Peng H, Ni Z, Sun Q (2008) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol 11: 61.
208. Xing S, Salinas M, Hohmann S, Berndtgen R, Huijser P (2010) miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis. Plant Cell 22: 3935-3950.
209. Xue LJ, Zhang JJ, Xue HW (2009) Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res 37: 916- 930.
210. Yamasaki H, Abdel-Ghany SE, Cohu CM, Kobayashi Y, Shikanai T, Pilon M (2007) Regulation of copper homeostasis by microRNA in Arabidopsis. J Biol Chem 282: 16369-16378.
211. Yang L, Conway SR, Poethig RS (2011) Vegetative phase change is mediated by a leaf-derived signal that represses the transcription of miR156. Development 138: 245-249.
212. Yang L, Liu Z, Lu F, Dong A, Huang H (2006) SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis. Plant J 47: 841-850.
213. Yang T, Xue L, An L (2007) Functional diversity of miRNA in plants. Plant Sci 172: 423-432.
214. Yang Z, Ebright YW, Yu B, Chen X (2006) HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res 34: 667-675.
215. Yant L, Mathieu J, Dinh TT, Ott F, Lanz C, Wollmann H, Chen X, Schmid M (2010) Orchestration of the floral transition and floral development in Arabidopsis by the bifunctional transcription factor APETALA2. Plant Cell 22: 2156-2170.
216. Yin JQ, Zhao RC, Morris KV (2008) Profiling microRNA expression with microarrays. Trends Biotechnol 26: 70-76.
217. Yoon EK, Yang JH, Lim J, Kim SH, Kim SK, Lee WS (2010) Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Res 38: 1382-1391.
218. Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M, Ramachandran V, Li W, Lagrange T, Walker JC, Chen X (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci USA 105: 10073- 10078.
219. Yu B, Yang Z, Li J, Minakhina S, Yang M, Padgett RW, Steward R, Chen X (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307: 932-935.
220. Yu L, Yu X, Shen R, He Y (2005) HYL1 gene maintains venation and polarity of leaves. Planta 221: 231-242.
221. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006a) Conservation and divergence of plant microRNA genes. Plant J 46(2): 243-259.
222. Zhang B, Pan X, Cobb GP, Anderson TA (2006b) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289: 3-16.
223. Zhang J, Xu Y, Huan Q, Chong K (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genomics 10: 449.
224. Zhang J, Zhang S, Han S, Wu T, Li X, Li W, Qi L (2012) Genomewide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis. Planta DOI: 10.1007/s00425-012-1643-9.
225. Zhang W, Gao S, Zhou X, Chellappan P, Chen Z, Zhou X, Zhang X, Fromuth N, Coutino G, Coffey M, Jin H (2011a) Bacteriaresponsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol Biol 75: 93- 105.
226. Zhang X, Zhao H, Gao S, Wang WC, Katiyar-Agarwal S, Huang HD, Raikhel N, Jin H (2011b) Arabidopsis Argonaute 2 regulates innate immunity via miRNA393*- mediated silencing of aGolgi-localized SNARE gene, MEMB12. Cell 42: 356-366.
227. Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10: 3.
228. Zhou M, Gu LF, Li PC, Song XW, Wei LY, Chen ZY, Cao XF (2010) Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica). Front Biol. 5: 67-90.
229. Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W (2008) Identification of cold-inducible microRNAs in plants by transcriptome analysis. Biochim Biophys Acta 1779: 780-788.
230. Zhou X, Zhu Q, Eicken C, Sheng N, Zhang X, Yang L, Gao X (2012) MicroRNA profiling using μParaflo Microfluidic Array Technology. Methods Mol Biol 822: 153-82.
231. Zhu C, Ding Y, Liu H (2011) MiR398 and plant stress responses. Physiol Plant 143: 1-9.