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Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors

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Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors

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Carbonell, A.; Fahlgren, N.; Mitchell, S.; Cox, KLJ.; Reilly, KC.; Mockler, TC.; Carrington, JC. (2015). Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors. The Plant Journal. 82(6):1061-1075. https://doi.org/10.1111/tpj.12835

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Título: Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric MIRNA precursors
Autor: CARBONELL, ALBERTO Fahlgren, Noah Mitchell, Skyler Cox, Kevin L., Jr. Reilly, Kevin C. Mockler, Todd C. Carrington, James C.
Entidad UPV: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Fecha difusión:
Resumen:
[EN] Artificial microRNAs (amiRNAs) are used for selective gene silencing in plants. However, current methods to produce amiRNA constructs for silencing transcripts in monocot species are not suitable for simple, cost-effective ...[+]
Palabras clave: RNA silencing , Artificial microRNA , MIRNA precursor , Brachypodium distachyon , Monocot , Arabidopsis thaliana , Technical advance
Derechos de uso: Reconocimiento (by)
Fuente:
The Plant Journal. (issn: 0960-7412 )
DOI: 10.1111/tpj.12835
Editorial:
Blackwell Publishing
Versión del editor: https://doi.org/10.1111/tpj.12835
Código del Proyecto:
info:eu-repo/grantAgreement/NSF//1231726/US/Function of Arabidopsis Small RNA-ARGONAUTE Complexes/
info:eu-repo/grantAgreement/NIH//AI043288/
info:eu-repo/grantAgreement/NSF//1330562/US/Integration of developmental signals by plant ARGONAUTES/
info:eu-repo/grantAgreement/NIFA//MOW-2012-01361/
info:eu-repo/grantAgreement/DOE//DE-SC0006627/
Agradecimientos:
We thank Goretti Nguyen, Robyn Stevens, Jacob Mreen, Fangfang Ma and Madison Schniers for invaluable technical assistance, and Zacchery R. Smith for his initial contribution to develop the pH7WG2B-OsMIR390-B/c vector. Noah ...[+]
Tipo: Artículo

References

Addo-Quaye, C., Eshoo, T. W., Bartel, D. P., & Axtell, M. J. (2008). Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome. Current Biology, 18(10), 758-762. doi:10.1016/j.cub.2008.04.042

Alvarez, J. P., 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. The Plant Cell, 18(5), 1134-1151. doi:10.1105/tpc.105.040725

Arikit, S., Zhai, J., & Meyers, B. C. (2013). Biogenesis and function of rice small RNAs from non-coding RNA precursors. Current Opinion in Plant Biology, 16(2), 170-179. doi:10.1016/j.pbi.2013.01.006 [+]
Addo-Quaye, C., Eshoo, T. W., Bartel, D. P., & Axtell, M. J. (2008). Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome. Current Biology, 18(10), 758-762. doi:10.1016/j.cub.2008.04.042

Alvarez, J. P., 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. The Plant Cell, 18(5), 1134-1151. doi:10.1105/tpc.105.040725

Arikit, S., Zhai, J., & Meyers, B. C. (2013). Biogenesis and function of rice small RNAs from non-coding RNA precursors. Current Opinion in Plant Biology, 16(2), 170-179. doi:10.1016/j.pbi.2013.01.006

Axtell, M. J. (2013). Classification and Comparison of Small RNAs from Plants. Annual Review of Plant Biology, 64(1), 137-159. doi:10.1146/annurev-arplant-050312-120043

Axtell, M. J., Jan, C., Rajagopalan, R., & Bartel, D. P. (2006). A Two-Hit Trigger for siRNA Biogenesis in Plants. Cell, 127(3), 565-577. doi:10.1016/j.cell.2006.09.032

Bartel, D. P. (2004). MicroRNAs. Cell, 116(2), 281-297. doi:10.1016/s0092-8674(04)00045-5

Bernard, P., & Couturier, M. (1992). Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. Journal of Molecular Biology, 226(3), 735-745. doi:10.1016/0022-2836(92)90629-x

Bologna, N. G., & Voinnet, O. (2014). The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs in Arabidopsis. Annual Review of Plant Biology, 65(1), 473-503. doi:10.1146/annurev-arplant-050213-035728

Bouvier d’Yvoire, M., Bouchabke-Coussa, O., Voorend, W., Antelme, S., Cézard, L., Legée, F., … Sibout, R. (2012). Disrupting thecinnamyl alcohol dehydrogenase 1gene (BdCAD1) leads to altered lignification and improved saccharification inBrachypodium distachyon. The Plant Journal, 73(3), 496-508. doi:10.1111/tpj.12053

Butardo, V. M., Fitzgerald, M. A., Bird, A. R., Gidley, M. J., Flanagan, B. M., Larroque, O., … Rahman, S. (2011). Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing. Journal of Experimental Botany, 62(14), 4927-4941. doi:10.1093/jxb/err188

Carbonell, A., Fahlgren, N., Garcia-Ruiz, H., Gilbert, K. B., Montgomery, T. A., Nguyen, T., … Carrington, J. C. (2012). Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants  . The Plant Cell, 24(9), 3613-3629. doi:10.1105/tpc.112.099945

Carbonell, A., Takeda, A., Fahlgren, N., Johnson, S. C., Cuperus, J. T., & Carrington, J. C. (2014). New Generation of Artificial MicroRNA and Synthetic Trans-Acting Small Interfering RNA Vectors for Efficient Gene Silencing in Arabidopsis. Plant Physiology, 165(1), 15-29. doi:10.1104/pp.113.234989

Chen, H., Jiang, S., Zheng, J., & Lin, Y. (2012). Improving panicle exsertion of rice cytoplasmic male sterile line by combination of artificial microRNA and artificial target mimic. Plant Biotechnology Journal, 11(3), 336-343. doi:10.1111/pbi.12019

Chen, M., Wei, X., Shao, G., Tang, S., Luo, J., & Hu, P. (2012). Fragrance of the rice grain achieved via artificial microRNA-induced down-regulation ofOsBADH2. Plant Breeding, 131(5), 584-590. doi:10.1111/j.1439-0523.2012.01989.x

Cuperus, J. T., Carbonell, A., Fahlgren, N., Garcia-Ruiz, H., Burke, R. T., Takeda, A., … Carrington, J. C. (2010). Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nature Structural & Molecular Biology, 17(8), 997-1003. doi:10.1038/nsmb.1866

Cuperus, J. T., Fahlgren, N., & Carrington, J. C. (2011). Evolution and Functional Diversification of MIRNA Genes. The Plant Cell, 23(2), 431-442. doi:10.1105/tpc.110.082784

Endo, Y., Iwakawa, H., & Tomari, Y. (2013). Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly. EMBO reports, 14(7), 652-658. doi:10.1038/embor.2013.73

Fahlgren, N., & Carrington, J. C. (2009). miRNA Target Prediction in Plants. Plant MicroRNAs, 51-57. doi:10.1007/978-1-60327-005-2_4

Felippes, F. F., & Weigel, D. (2009). Triggering the formation of tasiRNAs in Arabidopsis thaliana  : the role of microRNA miR173. EMBO reports, 10(3), 264-270. doi:10.1038/embor.2008.247

Gilbert, K., Fahlgren, N., Kasschau, K., Chapman, E., Carrington, J., & Carbonell, A. (2014). Preparation of Multiplexed Small RNA Libraries from Plants. BIO-PROTOCOL, 4(21). doi:10.21769/bioprotoc.1275

Guo, Y., Han, Y., Ma, J., Wang, H., Sang, X., & Li, M. (2014). Undesired Small RNAs Originate from an Artificial microRNA Precursor in Transgenic Petunia (Petunia hybrida). PLoS ONE, 9(6), e98783. doi:10.1371/journal.pone.0098783

He, G., Zhu, X., Elling, A. A., Chen, L., Wang, X., Guo, L., … Deng, X.-W. (2010). Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids. The Plant Cell, 22(1), 17-33. doi:10.1105/tpc.109.072041

Heisel, S. E., Zhang, Y., Allen, E., Guo, L., Reynolds, T. L., Yang, X., … Roberts, J. K. (2008). Characterization of Unique Small RNA Populations from Rice Grain. PLoS ONE, 3(8), e2871. doi:10.1371/journal.pone.0002871

Johnson, C., Kasprzewska, A., Tennessen, K., Fernandes, J., Nan, G.-L., Walbot, V., … Bowman, L. H. (2009). Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Research, 19(8), 1429-1440. doi:10.1101/gr.089854.108

Karimi, M., Inzé, D., & Depicker, A. (2002). GATEWAY™ vectors for Agrobacterium-mediated plant transformation. Trends in Plant Science, 7(5), 193-195. doi:10.1016/s1360-1385(02)02251-3

Kozomara, A., & Griffiths-Jones, S. (2013). miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research, 42(D1), D68-D73. doi:10.1093/nar/gkt1181

Liang, G., He, H., Li, Y., & Yu, D. (2012). A new strategy for construction of artificial miRNA vectors in Arabidopsis. Planta, 235(6), 1421-1429. doi:10.1007/s00425-012-1610-5

Liu, Q., Wang, F., & Axtell, M. J. (2014). Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay  . The Plant Cell, 26(2), 741-753. doi:10.1105/tpc.113.120972

Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., … Qi, Y. (2008). Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide. Cell, 133(1), 116-127. doi:10.1016/j.cell.2008.02.034

Montgomery, T. A., Howell, M. D., Cuperus, J. T., Li, D., Hansen, J. E., Alexander, A. L., … Carrington, J. C. (2008). Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation. Cell, 133(1), 128-141. doi:10.1016/j.cell.2008.02.033

Ossowski, S., Schwab, R., & Weigel, D. (2008). Gene silencing in plants using artificial microRNAs and other small RNAs. The Plant Journal, 53(4), 674-690. doi:10.1111/j.1365-313x.2007.03328.x

Oster, U., Tanaka, R., Tanaka, A., & Rüdiger, W. (2000). Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana. The Plant Journal, 21(3), 305-310. doi:10.1046/j.1365-313x.2000.00672.x

Philippar, K., Geis, T., Ilkavets, I., Oster, U., Schwenkert, S., Meurer, J., & Soll, J. (2007). Chloroplast biogenesis: The use of mutants to study the etioplast-chloroplast transition. Proceedings of the National Academy of Sciences, 104(2), 678-683. doi:10.1073/pnas.0610062104

Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., … Betel, D. (2013). Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biology, 14(9), R95. doi:10.1186/gb-2013-14-9-r95

Schwab, R., Ossowski, S., Riester, M., Warthmann, N., & Weigel, D. (2006). Highly Specific Gene Silencing by Artificial MicroRNAs inArabidopsis. The Plant Cell, 18(5), 1121-1133. doi:10.1105/tpc.105.039834

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 and Cell Physiology, 49(4), 493-500. doi:10.1093/pcp/pcn043

Tanaka, A., Ito, H., Tanaka, R., Tanaka, N. K., Yoshida, K., & Okada, K. (1998). Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a. Proceedings of the National Academy of Sciences, 95(21), 12719-12723. doi:10.1073/pnas.95.21.12719

Thole, V., Peraldi, A., Worland, B., Nicholson, P., Doonan, J. H., & Vain, P. (2011). T-DNA mutagenesis in Brachypodium distachyon. Journal of Experimental Botany, 63(2), 567-576. doi:10.1093/jxb/err333

Tiwari, M., Sharma, D., & Trivedi, P. K. (2014). Artificial microRNA mediated gene silencing in plants: progress and perspectives. Plant Molecular Biology, 86(1-2), 1-18. doi:10.1007/s11103-014-0224-7

Trabucco, G. M., Matos, D. A., Lee, S. J., Saathoff, A. J., Priest, H. D., Mockler, T. C., … Hazen, S. P. (2013). Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon. BMC Biotechnology, 13(1). doi:10.1186/1472-6750-13-61

Vogel, J., & Hill, T. (2007). High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Reports, 27(3), 471-478. doi:10.1007/s00299-007-0472-y

Wang, L., Si, Y., Dedow, L. K., Shao, Y., Liu, P., & Brutnell, T. P. (2011). A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq. PLoS ONE, 6(10), e26426. doi:10.1371/journal.pone.0026426

Warthmann, N., Chen, H., Ossowski, S., Weigel, D., & Hervé, P. (2008). Highly Specific Gene Silencing by Artificial miRNAs in Rice. PLoS ONE, 3(3), e1829. doi:10.1371/journal.pone.0001829

Zeng, L.-R., Qu, S., Bordeos, A., Yang, C., Baraoidan, M., Yan, H., … Wang, G.-L. (2004). Spotted leaf11, a Negative Regulator of Plant Cell Death and Defense, Encodes a U-Box/Armadillo Repeat Protein Endowed with E3 Ubiquitin Ligase Activityw⃞. The Plant Cell, 16(10), 2795-2808. doi:10.1105/tpc.104.025171

Zhang, X., Niu, D., Carbonell, A., Wang, A., Lee, A., Tun, V., … Jin, H. (2014). ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis. Nature Communications, 5(1). doi:10.1038/ncomms6468

Zhou, X., Sunkar, R., Jin, H., Zhu, J.-K., & Zhang, W. (2008). Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. Genome Research, 19(1), 70-78. doi:10.1101/gr.084806.108

Zhu, Q.-H., Spriggs, A., Matthew, L., Fan, L., Kennedy, G., Gubler, F., & Helliwell, C. (2008). A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Research, 18(9), 1456-1465. doi:10.1101/gr.075572.107

Zhu, H., Hu, F., Wang, R., Zhou, X., Sze, S.-H., Liou, L. W., … Zhang, X. (2011). Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development. Cell, 145(2), 242-256. doi:10.1016/j.cell.2011.03.024

Zhu, J.-Y., Sae-Seaw, J., & Wang, Z.-Y. (2013). Brassinosteroid signalling. Development, 140(8), 1615-1620. doi:10.1242/dev.060590

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