Int. J. Biomol. & Biomed.5(3), 1-12, November 2016
Micro RNAs (miRNAs) are small non-coding RNAs molecules having approximately 18-25 nucleotides, they are present in both plants and animals genomes. MiRNAs have diverse spatial expression patterns and regulate various developmental metabolisms, stress responses and other physiological processes. The dynamic gene expression playing major roles in phenotypic differences in organisms are believed to be controlled by miRNAs. Mutations in regions of regulatory factors, such as miRNA genes or transcription factors (TF) necessitated by dynamic environmental factors or pathogen infections, have tremendous effects on structure and expression of genes. The resultant novel gene products presents potential explanations for constant evolving desirable traits that have long been bred using conventional means, biotechnology or genetic engineering. Rice grain quality, yield, disease tolerance, climate-resilience and palatability properties are not exceptional to miRN Asmutations effects. There are new insights courtesy of high-throughput sequencing and improved proteomic techniques that organisms’ complexity and adaptations are highly contributed by miRNAs containing regulatory networks. This article aims to expound on how rice miRNAs could be driving evolution of traits and highlight the latest miRNA research progress. Moreover, the review accentuates miRNAs grey areas to be addressed and gives recommendations for further studies.
3K RGP. 2014. The 3,000 rice genomes project. Gigascience 3, 7.
Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington J. C.2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics 36, 1282-90.
Aukerman MJ, Sakai H. 2003. Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. The Plant Cell 15, 2730-41.
Baldrich P, San Segundo B. 2016. MicroRNAs in Rice Innate Immunity. Rice (N Y) 9, 6.
Baranauske S, Mickute M, Plotnikova A, Finke A, Venclovas C, Klimasauskas S, Vilkaitis G. 2015. Functional mapping of the plant small RNA methyltransferase: HEN1 physically interacts with HYL1 and DICER-LIKE 1 proteins. Nucleic Acids Research 43, 2802-12.
Bartel DP. 2004. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 116, 281-297.
Baumberger N, Baulcombe DC. 2005. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proceedings of the National Academy of Sciences 102, 11928-11933.
Berezikov E. 2011. Evolution of microRNA diversity and regulation in animals. Nature Reviews Genetics 12, 846-860.
Carbonell A, Fahlgren N, Garcia-Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT, Carrington JC. 2012. Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. The Plant Cell 24, 3613-3629.
Carrington JC, Ambros V. 2003. Role of microRNAs in plant and animal development. Science 301, 336-8.
Chen H, Li Z, Xiong L. 2012. A plant microRNA regulates the adaptation of roots to drought stress. Federation of European Biochemical Societies Letters 586, 1742-1747.
Chen, X.2004. MicroRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science303,2022-2025.
Chen Z, Li F, Yang S, Dong Y, Yuan Q, Wang F, Li W, Jiang Y, Jia S, Pei X. 2013. Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.). PLoS One 8, e82844.
Cuperus JT, Fahlgren N, Carrington JC. 2011. Evolution and functional diversification of MIRNA genes. The Plant Cell 23, 431-442.
Debat HJ, Ducasse DA. 2014. Plant microRNAs: Recent Advances and Future Challenges. Plant Molecular Biology Reporter 32, 1257-1269.
Deleris Al, Gallego-Bartolome J, Bao JD, Kasschau K, Carrington JC, Voinnet O. 2006. Hierarchical Action and Inhibition of Plant Dicer-Like Proteins in Antiviral Defense. Science 313, 68-71.
Deng X, Zhou H, Zhang G, Wang W, Mao L, Zhou X, Yu Y, Lu H. 2015. Sgf73, a subunit of SAGA complex, is required for the assembly of RITS complex in fission yeast. Scientific Reports 5, 14707.
Ding Y, Chen Z, Zhu C. 2011. Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza Sativa). Journal of Experimental Botany 62, 3563-73.
Dugas DV, Bartel B. 2008. Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Molecular Biology 67, 403-17.
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.
Eamens AL, Wook Kim K, Waterhouse PM. 2012. DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana. Plant Signaling and Behavior 7, 1224-1229.
Eamens A, Wang MB, Smith NA, Waterhouse PM. 2008. RNA silencing in plants: yesterday, today, and tomorrow. Plant Physiology 147, 456-468.
Eckardt NA. 2005. MicroRNAs Regulate Auxin Homeostasis and Plant Development. The Plant Cell 17, 1335-1338.
Ehrenreich IM, Purugganan MD. 2008. Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiology 146, 1974-82.
Endo Y, Iwakawa HO, Tomari Y. 2013. Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly. EMBO Reports 14, 652-8.
Eulalio A, Huntzinger E, Nishihara T, Rehwinkel J, Fauser M, Izaurralde E. 2009. Deadenylation is a widespread effect of miRNA regulation. RNA 15, 21-32.
Felippes FF, Schneeberger K, Dezulian T, Huson DH, Weigel D. 2008. Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA 14, 2455-9.
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. Nature Biotechnology 26, 941-6.
Guo C, Li L, Wang X, Liang C. 2015. Alterations in siRNA and miRNA expression profiles detected by deep sequencing of transgenic rice with siRNA-mediated viral resistance. PLoS One 10, e0116175.
Guo HS, Xie Q, Fei JF, Chua NH. 2005. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to down regulate auxin signals for Arabidopsis lateral root development. The Plant Cell 17, 1376-86.
Guo S, Xu Y, Liu H, Mao Z, Zhang C, Ma Y, Zhang Q, Meng Z, Chong K. 2013. The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14. Nature Communications 4, 1566.
Guo X, Gui Y, Wang Y, Zhu QH, Helliwell C, Fan L. 2008. Selection and mutation on microRNA target sequences during rice evolution. BMC Genomics 9, 454.
Han MH, Goud S, Song L, Fedoroff N. 2004. The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. Proceedings of the National Academy of Sciences 101, 1093-8.
Harvey J, Lewsey, M, Patel, K, Westwood, J, Heimstadt S. 2011. An Antiviral Defense Role of AGO2 in Plants. PLoS One 6, e14639.
He H, Li J. 2008. Proteomic analysis of phosphoproteins regulated by abscisic acid in rice leaves. Biochemicaland Biophysical Research Communications 371, 883-8.
He L, Hannon GJ. 2004. MicroRNAs: small RNAs with a big role in gene regulation. Nature Reviews Genetics 5, 522-531.
Iki T, Yoshikawa M, Nishikiori M, Jaudal MC, Matsumoto-Yokoyama E, Mitsuhara I, Meshi T, Ishikawa M. 2010. In vitro assembly of plant RNA-induced silencing complexes facilitated by molecular chaperone HSP90. Molecular Cell 39, 282-91.
Jia-Fu Wang Hui Zhou, Yue-Qin Chen, Qing-Jun Luo, Liang-Hu QU. 2004. Identification of 20 microRNAs from Oryza Sativa. Nucleic Acids Research 32,1688-1695.
Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J. 2010. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nature Genetics 42, 541-4.
Jones-Rhoades MW, Bartel DP. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular Cell 14, 787-99.
Jones-Rhoades M. 2006. MicroRNAs and Their Regulatory Roles in Plants. Annual Review of Plant Biology 57, 19-53.
Kamanu TK, Radovanovic A, Archer JA, Bajic VB. 2013. Exploration of miRNA families for hypotheses generation. Scientific Reports 3, 2940.
Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH. Kim VN. 2004. MicroRNA genes are transcribed by RNA polymerase II. The EMBO Journal 23, 4051-406.
Li A, Mao L. 2007. Evolution of plant microRNA gene families. Cell Research 17, 212-8.
Li J, Yang Z, Yu B, Liu J, Chen X. 2005. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Current Biology 15, 1501-7.
Li Y, Lu Y G, Shi Y, Wu L, Xu YJ, Huang F, Guo XY, Zhang Y, Fan J, Zhao J. Q, Zhang HY, Xu PZ, Zhou JM, Wu XJ, Wang PR, Wang WM. 2014. Multiple rice microRNAs are involved in immunity against the blast fungus Magnaportheoryzae. Plant Physiology 164, 1077-92.
Li Y, Zhang Q, Zhang J, Wu L, Qi Y, Zhou JM. 2010. Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity. Plant Physiology 152, 2222-31.
Liu HH, Tian X, Li YJ, Wu CA, Zheng CC. 2008. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14, 836-43.
Liu Q, Wang H, Zhu L, Hu H, Sun Y. 2013. Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice. Rice (NY) 6, 10.
Llave C, Xie Z, Kasschau KD, Carrington JC. 2002. Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA. Science (New York, N.Y) 297, 2053-6.
Luo Y, Guo Z, Li L. 2013. Evolutionary conservation of microRNA regulatory programs in plant flower development. Developmental Biology 380, 133-44.
Martinez de Alba AE, Elvira-Matelot E, Vaucheret H. 2013. Gene silencing in plants: a diversity of pathways. Biochimicaet Biophysica Acta 1829, 1300-8.
Maunoury N, Vaucheret, H. 2011. AGO1 and AGO2 Act Redundantly in miR408-Mediated Plantacyanin Regulation. PLoS ONE 6, e28729.
Mentlak TA, Kombrink A, Shinya T, Ryder LS, Otomo I, Saitoh H, Terauchi R, Nishizawa Y, Shibuya N, Thomma BP, Talbot NJ. 2012. Effector-mediated suppression of chitin-triggered immunity by magnaportheoryzae is necessary for rice blast disease. Plant Cell 24, 322-35.
Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M. 2010. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nature Genetics 42, 545-9.
Nath U. Crawford BCW, Carpenter R, Coen E. 2003. Genetic Control of Surface Curvature. Science 299,1404-1407.
Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, Carrington JC, Weigel D. 2003. Control of leaf morphogenesis by microRNAs. Nature 425, 257-63.
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. Current Biology 12, 1484-1495.
Qiu S, Adema CM, Lane T. 2005. A computational study of off-target effects of RNA interference. Nucleic Acids Research 33, 1834-47.
Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes & Development 20, 3407-25.
Ramachandran V, Chen X. 2008. Degradation of microRNAs by a family of exoribonucleases in Arabidopsis. Science 321, 1490-2.
Rogers K, Chen X. 2013. Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25, 2383-99.
Schwarz DS. Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD. 2003. Asymmetry in the Assembly of theRNAi Enzyme Complex. Cell 115, 199-208.
Smith MR, Willmann MR, Wu G, Berardini TZ, Moller B, Weijers D, Poethig RS. 2009. Cyclophilin 40 is required for microRNA activity in Arabidopsis. Proceedings of the National Academy of Sciences 106, 5424-9.
Sun G, Yan J, Noltner K, Feng J, Li H, Sarkis DA, Sommer SS, Rossi JJ. 2009. SNPs in human miRNA genes affect biogenesis and function. RNA 15, 1640-51.
Sun G. 2012. MicroRNAs and their diverse functions in plants. Plant Molecular Biology 80, 17-36.
Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK. 2008. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biology 8, 25.
Takuno S, Innan H. 2008. Evolution of complexity in miRNA-mediated gene regulation systems. Trends in Genetics 24, 56-9.
Wang L, Song X, Gu L, Li X, Cao S, Chu C, Cui X, Chen, X, Cao X. 2013. NOT2 proteins promote polymerase II-dependent transcription and interact with multiple MicroRNA biogenesis factors in Arabidopsis. The Plant Cell 25, 715-27.
Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nature Genetics 44, 950-4.
Wen-wen K, Hong-bo W, Jing L. 2014. Biogenesis of Plant MicroRNAs. Journal of Northeast Agricultural University 21, 84-96.
Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y. 2009. Rice MicroRNA effector complexes and targets. The Plant Cell 21, 3421-35.
Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y. 2010. DNA methylation mediated by a microRNA pathway. Molecular Cell 38, 465-75.
Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y. 2010. DNA Methylation Mediated by a MicroRNA Pathway. Molecular Cell 38, 465-475.
Xie K, Wu C, Xiong L. 2006. Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice. Plant Physiology 142, 280-93.
Xie ZR, Yang HT, Liu WC, Hwang MJ. 2007. The role of microRNA in the delayed negative feedback regulation of gene expression. Biochemical and Biophysical Research Communications 358, 722-6.
Xiu-Jie Wang, José L, Reyes Nam-Hai Chua and Terry Gaasterland. 2004. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biology 5, R65.
Ye X, Al-Babili S, Klöti A, Zhang J, Lucca P, Beyer P, Potrykus I. 2000. Engineering the provitaminA beta-carotene biosynthetic pathway into carotenoid-free Rice endosperm. Science 287, 303-5.
Younis A, Siddique MI, Kim CK, Lim KB. 2014. RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding. International Journal of Biological Sciences 10, 1150-8.
Zeng Y, Yi R, Cullen BR. 2003. MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proceedings of the National Academy of Sciences 100, 9779-84.
Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, Zhang CY. 2012. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Research 22, 107-26.
Zhang YC, Yu Y, Wang CY, Li ZY, Liu Q, Xu J, Liao JY, Wang XJ, Qu LH, Chen F, Xin P, Yan C, Chu J, Li HQ, Chen YQ. 2013. Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching. Nature Biotechnology 31, 848-52.
Zhou H, Liu Q, Li J, Jiang D, Zhou L, Wu P, Lu S, Li F, Zhu L, Liu Z, Chen L, Liu YG, Zhuang C. 2012. Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Research 22, 649-60.
Zhou Y, Honda M, Zhu H, Zhang Z, Guo X, Li T, Li Z, Peng X, Nakajima K, Duan L, Zhang X.2015. Spatiotemporal Sequestration of miR165/166 by Arabidopsis Argonaute10 Promotes Shoot Apical Meristem Maintenance. Cell Reports 10, 1819-1827.
Zhou Z, Wang Z, Li W, Fang C, Shen Y, Li C, Wu Y, Tian Z. 2013. Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome. The Plant Journal 76, 332-44.