Abstract
Artificial microRNAs (amiRNAs) have been shown to facilitate efficient gene silencing with high specificity to the intended target gene(s). For the plant breeder, gene silencing by artificial miRNAs will certainly accelerate gene discovery, because it allows targeting of all genes in a mapping interval, independent of the genetic background. In addition, beneficial knockout phenotypes can easily be transferred between varieties and across incompatibility barriers. This chapter describes the generation and application of amiRNAs as a gene silencing tool in rice.
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References
Krishnan A, Guiderdoni E, An G et al (2009) Mutant resources in rice for functional genomics of the grasses. Plant Physiol 149:165–170
Chapman EJ, Carrington JC (2007) Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8:884–896
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
Palatnik JF, Allen E, Wu X et al (2003) Control of leaf morphogenesis by microRNAs. Nature 425:257–263
Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121–1133
Warthmann N, Chen H, Ossowski S, Weigel D, Herve P (2008) Highly specific gene silencing by artificial miRNAs in rice. PLoS One 3:e1829
Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221
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
Ossowski O, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53:674–690
Vaucheret H (2005) MicroRNA-dependent trans-acting siRNA production. Sci STKE 2005:pe43
Alvarez JP, Pekker I, Goldshmidt A, Blum E, Amsellem Z, Eshed Y (2006) Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 18:1134–1151
Niu QW, Lin SS, Reyes JL et al (2006) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 24:1420–1428
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 a plant miRNA. Genes Dev 18:2237–2242
Qu J, Ye J, Fang R (2007) Artificial miRNA-mediated virus resistance in plants. J Virol 81:6690–6699
Khraiwesh B, Ossowski S, Weigel D, Reski R, Frank W (2008) Specific gene silencing by artificial MicroRNAs in Physcomitrella patens: an alternative to targeted gene knockouts. Plant Physiol 148:684–693
Chen S, Songkumarn P, Liu J, Wang G (2009) A versatile zero background T-vector system for gene cloning and functional genomics. Plant Physiol 150:1111–1121
Michniewicz M, Zago MK, Abas L et al (2007) Antagonistic regulation of PIN phosphorylation by PP2A and PINOID directs auxin flux. Cell 130:1044–1056
Abouelhoda MI, Kurtz S, Ohlebusch E (2004) Replacing suffix trees with enhanced suffix arrays. J Discrete Algorithm 2:53–86
Schneeberger K, Hagmann J, Ossowski S et al (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biol 10:R98
Molnar A, Bassett A, Thuenemann E et al (2009) Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. Plant J 58:165–174
Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32:D109–D111
Ameres SL, Martinez J, Schroeder R (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130:101–112
Muckstein U, Tafer H, Hackermuller J, Bernhart SH, Stadler PF, Hofacker IL (2006) Thermodynamics of RNA-RNA binding. Bioinformatics 22:1177–1182
Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ (2006) RNA-directed DNA methylation and pol IVb in Arabidopsis. Cold Spring Harb Symp Quant Biol 71:449–459
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
Chen X (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303:2022–2025
Gandikota M, Birkenbihl RP, Hohmann S, Cardon GH, Saedler H, Huijser P (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 49:683–693
Acknowledgements
We thank Hao Chen and Philippe Hervé, who generated and evaluated the first transgenic rice plants (Nipponbare and IR64) carrying aMIRNA transgenes at the International Rice Research Institute in the Philippines (IRRI). Markus Riester contributed to earlier versions of WMD and Joffrey Fitz codeveloped AmiRNA/WMD3; we are further thankful to everybody who contributed by sharing technical expertise and discussion, namely, Alexis Maizel, Javier Palatnik, Heike Wollmann, and Wolfgang Busch. Work on small RNAs in the Weigel laboratory is supported by European Community FP6 IP SIROCCO (contract LSHG-CT-2006-037900) and by the Max Planck Society.
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Warthmann, N., Ossowski, S., Schwab, R., Weigel, D. (2013). Artificial MicroRNAs for Specific Gene Silencing in Rice. In: Yang, Y. (eds) Rice Protocols. Methods in Molecular Biology, vol 956. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-194-3_11
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DOI: https://doi.org/10.1007/978-1-62703-194-3_11
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