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Plant miRNomics: Novel Insights in Gene Expression and Regulation

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PlantOmics: The Omics of Plant Science

Abstract

Advances in transcriptomics have led to the classification of small RNAs (sRNAs) into mainly three categories: miRNAs, siRNAs and piRNAs. However, there are many new types of sRNAs under exploration. Though such sRNAs differ from one another, they collaborate in their mode of action. Among the sRNAs, microRNAs (miRNAs) widely captured the attention of molecular biologists. miRNAs are short, endogenously expressed and non-translated RNAs. Mature plant miRNAs are in general smaller in size (~22 bp) and considered as negative gene regulatory molecules. In general plant miRNAs have the following features: (a) They are coded by miRNA genes with unknown length and are sequentially cleaved from pri-miRNA and pre-miRNA into a short mature miRNA by Dicer -like 1 (dcl1) and several other enzymes. (b) All pre-miRNAs can form a stem-looped hairpin secondary structure with the mature miRNA on one arm and the complementary sequence, termed miRNA*, on the another arm with high negative minimum folding free energy (MFE) and MFE index (MFEI). (c) Typically, miRNAs do negatively regulate target gene expression and the miRNA* sequence is degraded by an unknown mechanism. However, in some cases, the miRNA* sequence also can function to target a specific gene. Over the past few years, microarray technologies, large-scale small RNA and whole genome sequencing projects and data mining have provided a wealth of information about the spectrum of plant miRNAs and their targets. Hitherto identified miRNAs in plant kingdom have shown that they are deeply conserved; nevertheless considerable numbers of species-specific miRNAs also exist. Evidences are gradually mounting to notify that miRNAs have key roles in developmental timing, cell proliferation and cell death, organogenesis, patterning of tissues/organ and more importantly, in response to external environmental stimuli. Thus it is very obvious that plant miRNAs are more numerous and their regulatory impact is more pervasive than was previously suspected.

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References

  • Abdel-Ghany SE, Pilon M (2008) MicroRNA-mediated systemic down-regulation of copper protein expression in response to low copper availability in Arabidopsis. J Biol Chem 283:15932–15945

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Achard P, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131:3357–3365

    Article  CAS  PubMed  Google Scholar 

  • Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet 36:1282–1290

    Article  CAS  PubMed  Google Scholar 

  • Almeida R, Allshire RC (2005) RNA silencing and genome regulation. Trends Cell Biol 15(5):251–258

    Article  CAS  PubMed  Google Scholar 

  • Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9:277–279

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Barad O et al (2004) MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res 14:2486–2494

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Barah P, Winge P, Kusnierczyk A, Tran DH, Bones AM (2013) Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection. PLoS One 8(3):e58987

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  • Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58

    Article  CAS  Google Scholar 

  • Baulcombe D (2004) RNA silencing in plants. Nature 431:356–363

    Article  CAS  PubMed  Google Scholar 

  • Bottino CM et al (2013) High-throughput sequencing of small RNA transcriptome reveals salt stress regulated microRNAs in sugarcane. PLoS One 8(3):e59423

    Article  Google Scholar 

  • Brown JR, Sanseau P (2005) A computational view of microRNAs and their targets. Drug Discov Today 10:595–601

    Article  CAS  PubMed  Google Scholar 

  • Cai Y, Yu X, Hu S, Yu J (2009) A brief review on the mechanisms of miRNA regulation. Genomics Proteomics Bioinformatics 7(4):147–154

    Article  CAS  PubMed  Google Scholar 

  • Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44

    Article  PubMed  Google Scholar 

  • Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460(7254):479–486

    PubMed Central  CAS  PubMed  Google Scholar 

  • Cogoni C, Irelan JT, Schumacher M, Schmidhauser T, Selker EU, Macino G (1996) Transgene silencing of the al-1 gene in vegetative cells of Neurospora is mediated by a cytoplasmic effector and does not depend on DNA-DNA interactions or DNA methylation. EMBO J 15:3153–3163

    PubMed Central  CAS  PubMed  Google Scholar 

  • Cui XJ, Shin HS, Song C, Laosinchai W, Amano Y, Brown RM (2001) A putative plant homolog of the yeast beta-1, 3-glucan synthase subunit FKS1 from cotton (Gossypium hirsutum L.) fibers. Planta 213:223–230

    Article  CAS  PubMed  Google Scholar 

  • De Felippes FF, Schneeberger K, Dezulian T, Huson DH, Weigel D (2008) Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14:2455–2459

    Article  PubMed  Google Scholar 

  • Deans T, Cantor C, Collins J (2007) A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130:363–372

    Article  CAS  PubMed  Google Scholar 

  • Debernardi JM, Rodriguez RE, Mecchia MA, Palatnik JF (2012) Functional specialization of the plant miR396 regulatory network through distinct microRNA–target interactions. PLoS Genet 8(1):e1002419

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ding D et al (2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot 103:29–38

    Article  PubMed Central  CAS  Google Scholar 

  • Du P et al (2011) Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog 7(8):e1002176

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ebert MS, Neilson JR, Sharp PA (2007) MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 4:721–726

    Article  CAS  Google Scholar 

  • 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 14 2(2):e219

    Google Scholar 

  • Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15:2038–2043

    Article  CAS  PubMed  Google Scholar 

  • Gepstein S, Glick BR (2013) Strategies to ameliorate abiotic stress-induced plant senescence. Plant Mol Biol. doi:10.1007/s11103-013-0038-z

  • Gómez-Gómez L, Boller T (2002) Flagellin perception: a paradigm for innate immunity. Trends Plant Sci 6:251–256

    Article  Google Scholar 

  • Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, Wang XJ, Chen ZJ (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci U S A 106:17835–17840

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hannon GJ (2002) RNA interference. Nature 418:244–251

    Article  CAS  PubMed  Google Scholar 

  • He XF, Fang YY, Feng L, Guo HS (2008) Characterization of conserved and novel microRNAs and their targets, including a TuMV-induced TIR-NBS-LRR class R gene-derived novel miRNA in Brassica. FEBS Lett 582(16):2445–2452

    Article  CAS  PubMed  Google Scholar 

  • Hohn T, Vazquez F (2011) RNA silencing pathways of plants: silencing and its suppression by plant DNA viruses. Biochim Biophys Acta 1809(11–12):588–600

    Article  CAS  PubMed  Google Scholar 

  • Hu Q et al (2011) Specific impact of tobamovirus infection on the Arabidopsis small RNA profile. PLoS One 6(5):e19549

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jagadeeswaran G, Saini A, Sunkar R (2009) Biotic and abiotic stress downregulate miR398 expression in Arabidopsis. Planta 229:1009–1014

    Article  CAS  PubMed  Google Scholar 

  • Jia X, Wang WX, Ren LG, Chen QG, Mendu V, Willcut B, Dinkins R, Tang XQ, Tang GL (2009) Differential and dynamic regulation of miR398 in response to ABA and salt stress in Populus tremula and Arabidopsis thaliana. Plant Mol Biol 71:51–59

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW (2012) Conservation and divergence in plant miRNAs. Plant Mol Biol 80:3–16

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  Google Scholar 

  • Kedde M et al (2012) Role of microRNAs and other sRNAs of plants in their changing environments. J Plant Physiol 169(16):1664–1672

    Article  Google Scholar 

  • Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS (2009) Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 27:549–555

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kim VN, Nam JW (2006) Genomics of microRNA. Trends Genet 22(3):165–173

    Article  CAS  PubMed  Google Scholar 

  • Kruszka K et al (2012) Role of microRNAs and other sRNAs of plants in their changing environments. J Plant Physiol 169(16):1664–1672

    Article  CAS  PubMed  Google Scholar 

  • Krutzfeldt J et al (2005) Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438:685–689

    Article  PubMed  Google Scholar 

  • Kulcheski FR et al (2011) Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics 12(1):307

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858

    Article  CAS  PubMed  Google Scholar 

  • Lanet E, Delannoy E, Sormani R, Floris M, Brodersen P, Crété P, Voinnet O, Robaglia C (2009) Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 21:1762–1768

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lang QL et al (2011) Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection. J Zhejiang Univ Sci B 12(2):116–125

    Article  PubMed Central  PubMed  Google Scholar 

  • Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862

    Article  CAS  PubMed  Google Scholar 

  • Laufs P et al (2004) MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems. Development 131:4311–4322

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862–864

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854

    Article  CAS  PubMed  Google Scholar 

  • Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M (2009) Genome-wide small RNA analysis revealed differentially regulated miRNA isoforms in Medicago truncatula roots and nodules. Plant Cell 21:2780–2796

    Article  PubMed Central  PubMed  Google Scholar 

  • Li WX et al (2008) The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and post-transcriptionally to promote drought resistance. Plant Cell 20:2238–2251

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Li H, Deng Y, Wu T, Subramanian S, Yu O (2010a) Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiol 153:1759–1770

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Li L, Xu J, Yang D, Tan X, Wang H (2010b) Computational approaches for microRNA studies: a review. Mamm Genome 21:1–12

    Article  CAS  PubMed  Google Scholar 

  • Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297:2053–2056

    Article  CAS  PubMed  Google Scholar 

  • Lu J et al (2005a) MicroRNA expression profiles classify human cancers. Nature 435:834–838

    Article  CAS  PubMed  Google Scholar 

  • Lu SF et al (2005b) Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell 17:2186–2203

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lu S, Sun YH, Chiang VL (2008) Stress-responsive microRNAs in Populus. Plant J 55(1):131–151

    Article  CAS  PubMed  Google Scholar 

  • Lv DK et al (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459:39–47

    Article  CAS  PubMed  Google Scholar 

  • Ma Z, Coruh C, Axtell MJ (2010) Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 22:1090–1103

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • MacLean D, Elina N, Havecker ER, Heimstaedt SB, Studholme DJ, Baulcombe DC (2010) Evidence for large complex networks of plant short silencing RNAs. PLoS One 5:e9901

    Article  PubMed Central  PubMed  Google Scholar 

  • Mallory AC, Bouché N (2008) MicroRNA-directed regulation: to cleave or not to cleave. Trends Plant Sci 13:359–367

    Article  CAS  PubMed  Google Scholar 

  • Mendoza-Soto AB, Sánchez F, Hernández G (2012) MicroRNAs as regulators in plant metal toxicity response. Front Plant Sci 3:105

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Meng Y, Huang F, Shi Q, Cao J, Chen D, Zhang J, Ni J, Wu P, Chen M (2009) Genome-wide survey of rice microRNAs and microRNA- target pairs in the root of a novel auxin-resistant mutant. Planta 230:883–898

    Article  CAS  PubMed  Google Scholar 

  • Mette MF, van der Winden J, Matzke M, Matzke AJ (2002) Short RNAs can identify new candidate transposable element families in Arabidopsis. Plant Physiol 130:6–9

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Meyers BC, Axtell MJ, Bartel B et al (2008) Criteria for annotation of plant MicroRNAs. Plant Cell 20(12):3186–3190

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Navarro L, Dunoyer P, Jay F, Arnold B, Dharmasiri N, Estelle M, Voinnet O, Jones JDG (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312:436

    Article  CAS  PubMed  Google Scholar 

  • Nozawa M, Miura S, Nei M (2010) Origins and evolution of microRNA genes in Drosophila species. Genome Biol Evol 2:180–189

    Article  PubMed Central  PubMed  Google Scholar 

  • Nozawa M, Miura S, Nei M (2011) Origins and evolution of microRNA genes in plant species. Genome Biol Evol 564:55–7545

    Google Scholar 

  • Pang M, Xinga C, Adamsa N, Rodriguez-Uribea L, Hughsc SE, Hansonb SF, Zhang J (2011) Comparative expression of miRNA genes and miRNA-based AFLP marker analysis in cultivated tetraploid cottons. J Plant Physiol 168:824–830

    Article  CAS  PubMed  Google Scholar 

  • Parizotto EA, Dunoyer P, Rahm N, Himber C, Voinnet O (2004) In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of plant miRNA. Genes Dev 18(18):2237–2242

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Piriyapongsa J, Jordan IK (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14:814–821

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20:3407–3425

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18(5):1121–1133

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos B, Baulcombe DC (2012) MicroRNA superfamily regulates nucleotide binding site–leucine-rich repeats and other mRNAs. Plant Cell 24:859–874

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Song C, Fang J, Li X, Liu H, Thomas Chao C (2009) Identification and characterization of 27 conserved microRNAs in citrus. Planta 230(4):671–685

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sun G (2011) MicroRNAs and their diverse functions in plants. Plant Mol Biol 80(1):17–36

    Article  PubMed  Google Scholar 

  • Sun W, Li YSJ, Huang HD, Shyy JYJ, Chien S (2010) microRNA: a master regulator of cellular processes for bioengineering systems. Annu Rev Biomed Eng 12:1–27

    Article  CAS  PubMed  Google Scholar 

  • Sun YH, Shi R, Zhang XH, Chiang VL, Sederoff RR (2012) MicroRNAs in trees. Plant Mol Biol 80:37–53

    Article  CAS  PubMed  Google Scholar 

  • Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sunkar R, Girke T, Jain PK, Zhu JK (2005) Cloning and characterization of MicroRNAs from rice. Plant Cell 17:1397–1411

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sunkar R, Li YF, Jagadeeswaran G (2012) Functions of microRNAs in plant stress responses. Trends Plant Sci 17(4):196–203

    Article  CAS  PubMed  Google Scholar 

  • Tang G, Reinhart BJ, Bartel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17(1):49–63

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tang G, Galili G, Zhuang X (2007) RNAi and microRNA: breakthrough technologies for the improvement of plant nutritional value and metabolic engineering. Metabolomics 3:357–369

    Article  CAS  Google Scholar 

  • Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75:855–862

    Article  CAS  PubMed  Google Scholar 

  • Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465–475

    Article  CAS  PubMed  Google Scholar 

  • Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol 138:2145–2154

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Yin X, Wang J, Cheng H, Wang X, Yu D (2013) Detection and evolutionary analysis of soybean miRNAs responsive to soybean mosaic virus. Planta 237(5):1213–1225

    Article  CAS  PubMed  Google Scholar 

  • Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15:336–360

    Article  PubMed  Google Scholar 

  • Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006a) Conservation and divergence of plant microRNA genes. Plant J 46:243–259

    Article  CAS  PubMed  Google Scholar 

  • Zhang B, Pan X, Cobb GP, Anderson TA (2006b) Plant microRNA: a small regulatory molecule with big impact. Dev Biol 289:3–16

    Article  CAS  PubMed  Google Scholar 

  • Zhang B, Wang Q, Pan X (2007) MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210:279–289

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z et al (2008) Submergence-responsive microRNAs are potentially involved in the regulation of morphological and metabolic adaptations in Maize Root Cells. Ann Bot 102:509–519

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang L, Zheng Y, Jagadeeswaran G, Li Y, Gowdu K et al (2011a) Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum. Genomics 98(6):460–468

    Article  CAS  PubMed  Google Scholar 

  • Zhang W, Gao S, Zhou X, Chellappan P (2011b) Bacteria-responsive microRNAs regulates plant innate immunity by modulating plant hormone networks. Plant Mol Biol 75:93–105

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhou X et al (2008) Identification of cold-inducible micro RNAs in plants by transcriptome analysis. Biochim Biophys Acta 1779(11):780–788

    Article  CAS  PubMed  Google Scholar 

  • Zhou L et al (2010) Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa. J Exp Bot 61:4157–4168

    Article  CAS  PubMed  Google Scholar 

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Acknowledgement

I wish to thank DBT, India and BMZ-GIZ, Germany, for funding which helped in setting up pilot studies in miRNA. I sincerely apologise to colleagues whose work I could not cite because of space limitations.

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Authors and Affiliations

  1. Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India

    N. Manikanda Boopathi Ph.D.

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  1. N. Manikanda Boopathi Ph.D.
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Correspondence to N. Manikanda Boopathi Ph.D. .

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Editors and Affiliations

  1. Department of Genomics, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, West Bengal, India

    Debmalya Barh

  2. University of Agriculture, Centre of Biochemistry and Biotechnology, Faisalabad, Pakistan

    Muhammad Sarwar Khan

  3. Department of Plant Biology, North Carolina State University, Raleigh, North Carolina, USA

    Eric Davies

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Boopathi, N.M. (2015). Plant miRNomics: Novel Insights in Gene Expression and Regulation. In: Barh, D., Khan, M., Davies, E. (eds) PlantOmics: The Omics of Plant Science. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2172-2_7

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