Identification and Characterization of ABA-Responsive MicroRNAs in Rice

Caijuan Tian^{a, b, #},
Zhangli Zuo^{a, b, #},
Jin-Long Qiu^{a
, ,}

a.
State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
b.
University of Chinese Academy of Sciences, Beijing 100049, China

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Corresponding author: E-mail address: qiujl@im.ac.cn (Jin-Long Qiu)

These authors contributed equally to this work. The names are in alphabetic order.

摘要

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Abstract: MicroRNAs (miRNAs) are endogenous non-coding small RNAs that silence genes through mRNA degradation or translational inhibition. The phytohormone abscisic acid (ABA) is essential for plant development and adaptation to abiotic and biotic stresses. In Arabidopsis, miRNAs are implicated in ABA functions. However, ABA-responsive miRNAs have not been systematically studied in rice. Here high throughput sequencing of small RNAs revealed that 107 miRNAs were differentially expressed in the rice ABA deficient mutant, Osaba1. Of these, 13 were confirmed by stem-loop RT-PCR. Among them, miR1425-5P, miR169a, miR169n, miR390-5P, miR397a and miR397b were up-regulated, but miR162b reduced in expression in Osaba1. The targets of these 13 miRNAs were predicted and validated by gene expression profiling. Interestingly, the expression levels of these miRNAs and their targets were regulated by ABA. Cleavage sites were detected on 7 of the miRNA targets by 5′-Rapid Amplification of cDNA Ends (5′-RACE). Finally, miR162b and its target OsTRE1 were shown to affect rice resistance to drought stress, suggesting that miR162b increases resistance to drought by targetingOsTRE1. Our work provides important information for further characterization and functional analysis of ABA-responsive miRNAs in rice.
- Rice /
- Abscisic acid /
- High throughput sequencing /
- MicroRNA /
- Target gene
These authors contributed equally to this work. The names are in alphabetic order.
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参考文献(53)

[1]	Addo-Quaye, C., Miller, W., Axtell, M.J. CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets Bioinformatics, 25 (2009),pp. 130-131
[2]	Anders, S., Huber, W. Differential expression analysis for sequence count data Genome Biol., 11 (2010),p. R106
[3]	Barrera-Figueroa, B.E., Gao, L., Wu, Z.G. et al. High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice BMC Plant Biol., 12 (2012),p. 132
[4]	Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M. et al. Widespread translational inhibition by plant miRNAs and siRNAs Science, 320 (2008),pp. 1185-1190
[5]	Carrington, J.C., Ambros, V. Role of microRNAs in plant and animal development Science, 301 (2003),pp. 336-338
[6]	Chen, C.F., Ridzon, D.A., Broomer, A.J. et al. Real-time quantification of microRNAs by stem-loop RT-PCR Nucleic Acids Res., 33 (2005),p. e179
[7]	Chen, X.M. MicroRNA biogenesis and function in plants FEBS Lett., 579 (2005),pp. 5923-5931
[8]	Dai, X.B., Zhao, P.X. psRNATarget: a plant small RNA target analysis server Nucleic Acids Res., 39 (2011),pp. W155-W159
[9]	Dugas, D.V., Bartel, B. MicroRNA regulation of gene expression in plants Curr. Opin. Plant Biol., 7 (2004),pp. 512-520
[10]	Fujita, Y., Fujita, M., Shinozaki, K. et al. ABA-mediated transcriptional regulation in response to osmotic stress in plants J. Plant Res., 124 (2011),pp. 509-525
[11]	Gao, S.P., Fang, J., Xu, F. et al. Plant Physiol., 165 (2014),pp. 1035-1046
[12]	Gavnholt, B., Larsen, K. Molecular biology of plant laccases in relation to lignin formation Physiol. Plant., 116 (2002),pp. 273-280
[13]	Goddijn, O.J.M., Verwoerd, T.C., Voogd, E. et al. Inhibition of trehalase activity enhances trehalose accumulation in transgenic plants Plant Physiol., 113 (1997),pp. 181-190
[14]	Griffiths-Jones, S., Hui, J.H.L., Marco, A. et al. MicroRNA evolution by arm switching EMBO Rep., 12 (2011),pp. 172-177
[15]	Hiei, Y., Ohta, S., Komari, T. et al. Plant J., 6 (1994),pp. 271-282
[16]	Jain, M., Nijhawan, A., Tyagi, A.K. et al. Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR Biochem. Biophys. Res. Commun., 345 (2006),pp. 646-651
[17]	Kazama, T., Nakamura, T., Watanabe, M. et al. Suppression mechanism of mitochondrial ORF79 accumulation by Rf1 protein in BT-type cytoplasmic male sterile rice Plant J., 55 (2008),pp. 619-628
[18]	Khraiwesh, B., Zhu, J.K., Zhu, J. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants Biochim. Biophys. Acta, 1819 (2012),pp. 137-148
[19]	Kim, V.N. MicroRNA biogenesis: coordinated cropping and dicing Nat. Rev. Mol. Cell Biol., 6 (2005),pp. 376-385
[20]	Klie, S., Nikoloski, Z. The choice between Mapman and Gene Ontology for automated gene function prediction in plant science Front. Genet., 3 (2012),p. 115
[21]	Kozomara, A., Griffiths-Jones, S. miRBase: integrating microRNA annotation and deep-sequencing data Nucleic Acids Res., 39 (2011),pp. D152-D157
[22]	Kozomara, A., Griffiths-Jones, S. miRBase: annotating high confidence microRNAs using deep sequencing data Nucleic Acids Res., 42 (2014),pp. D68-D73
[23]	Kurihara, Y., Watanabe, Y. Proc. Natl. Acad. Sci. USA, 101 (2004),pp. 12753-12758
[24]	Lee, S.C., Luan, S. ABA signal transduction at the crossroad of biotic and abiotic stress responses Plant Cell Environ., 35 (2012),pp. 53-60
[25]	Li, R.Q., Yu, C., Li, Y.R. et al. SOAP2: an improved ultrafast tool for short read alignment Bioinformatics, 25 (2009),pp. 1966-1967
[26]	Li, Y.F., Zheng, Y., Addo-Quaye, C. et al. Transcriptome-wide identification of microRNA targets in rice Plant J., 62 (2010),pp. 742-759
[27]	Liang, C.Z., Wang, Y.Q., Zhu, Y.N. et al. OsNAP connects abscisic acid and leaf senescence by fine-tuning abscisic acid biosynthesis and directly targeting senescence-associated genes in rice Proc. Natl. Acad. Sci. USA, 111 (2014),pp. 10013-10018
[28]	Lunn, J.E. Gene families and evolution of trehalose metabolism in plants Funct. Plant Biol., 34 (2007),pp. 550-563
[29]	Marco, A., Hui, J.H.L., Ronshaugen, M. et al. Functional shifts in insect microRNA evolution Genome Biol. Evol., 2 (2010),pp. 686-696
[30]	Meng, Y.J., Gou, L.F., Chen, D.J. et al. High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism J. Exp. Bot., 61 (2010),pp. 3833-3837
[31]	Morin, R.D., Aksay, G., Dolgosheina, E. et al. Genome Res., 18 (2008),pp. 571-584
[32]	Nemhauser, J.L., Hong, F.X., Chory, J. Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses Cell, 126 (2006),pp. 467-475
[33]	Okamura, K., Phillips, M.D., Tyler, D.M. et al. The regulatory activity of microRNA star species has substantial influence on microRNA and 3' UTR evolution Nat. Struct. Mol. Biol., 15 (2008),pp. 354-363
[34]	Qiu, J.L., Zhou, L., Yun, B.W. et al. Plant Physiol., 148 (2008),pp. 212-222
[35]	Reyes, J.L., Chua, N.H. Plant J., 49 (2007),pp. 592-606
[36]	Romero, C., Belles, J.M., Vaya, J.L. et al. Planta, 201 (1997),pp. 293-297
[37]	Sato, Y., Antonio, B.A., Namiki, N. et al. Nucleic Acids Res., 39 (2011),pp. D1141-D1148
[38]	Schwab, R., Palatnik, J.F., Riester, M. et al. Specific effects of microRNAs on the plant transcriptome Dev. Cell, 8 (2005),pp. 517-527
[39]	Shima, S., Matsui, H., Tahara, S. et al. Biochemical characterization of rice trehalose-6-phosphate phosphatases supports distinctive functions of these plant enzymes FEBS J., 274 (2007),pp. 1192-1201
[40]	Song, J.B., Gao, S., Sun, D. et al. BMC Plant Biol., 13 (2013),p. 210
[41]	Sunkar, R., Chinnusamy, V., Zhu, J.H. et al. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation Trends Plant Sci., 12 (2007),pp. 301-309
[42]	Sunkar, R., Zhou, X.F., Zheng, Y. et al. Identification of novel and candidate miRNAs in rice by high throughput sequencing BMC Plant Biol., 8 (2008),p. 25
[43]	Thimm, O., Blasing, O., Gibon, Y. et al. Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes Plant J., 37 (2004),pp. 914-939
[44]	Thirumurugan, T., Ito, Y., Kubo, T. et al. Mol. Genet. Genomics, 279 (2008),pp. 279-289
[45]	Valencia-Sanchez, M.A., Liu, J.D., Hannon, G.J. et al. Control of translation and mRNA degradation by miRNAs and siRNAs Genes Dev., 20 (2006),pp. 515-524
[46]	Verrier, P.J., Bird, D., Buria, B. et al. Plant ABC proteins - a unified nomenclature and updated inventory Trends Plant Sci., 13 (2008),pp. 151-159
[47]	Wu, H.J., Ma, Y.K., Chen, T. et al. PsRobot: a web-based plant small RNA meta-analysis toolbox Nucleic Acids Res., 40 (2012),pp. W22-W28
[48]	Xu, G., Wu, J.Y., Zhou, L.L. et al. Characterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer cell line by deep sequencing PLoS One, 5 (2010),p. e15519
[49]	Yan, J., Gu, Y.Y., Jia, X.Y. et al. Plant Cell, 24 (2012),pp. 415-427
[50]	Yang, J.S., Phillips, M.D., Betel, D. et al. Widespread regulatory activity of vertebrate microRNA* species RNA, 17 (2011),pp. 312-326
[51]	Zhang, B.H., Pan, X.P., Cobb, G.P. et al. Plant microRNA: a small regulatory molecule with big impact Dev. Biol., 289 (2006),pp. 3-16
[52]	Zhang, Y., Zhu, X.J., Chen, X. et al. BMC Plant Biol., 14 (2014),p. 271
[53]	Zhu, J.K. Salt and drought stress signal transduction in plants Annu. Rev. Plant Biol., 53 (2002),pp. 247-273