Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors
Abstract
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 and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots. Four different amiRNA sequences designed to target specifically endogenous genes and expressed from OsMIR390-based vectors were validated in transgenic Brachypodium distachyon plants. Surprisingly, amiRNAs accumulated to higher levels and were processed more accurately when expressed from chimeric OsMIR390-based precursors that include distal stem-loop sequences from Arabidopsis thaliana MIR390a (AtMIR390a). In all cases, transgenic plants displayed the predicted phenotypes induced by target gene repression, and accumulated high levels of amiRNAs and low levels of the corresponding target transcripts. Genome-wide transcriptome profiling combined with 5-RLM-RACE analysis in transgenic plants confirmed that amiRNAs were highly specific. Finally, significance Statement A series of amiRNA vectors based on Oryza sativa MIR390 (OsMIR390) precursor were developed for simple, cost-effective and large-scale synthesis of amiRNA constructs to silence genes in monocots. Unexpectedly, amiRNAs produced from chimeric OsMIR390-based precursors including Arabidopsis thaliana MIR390a distal stem-loop sequences accumulated elevated levels ofmore »
- Authors:
-
- Donald Danforth Plant Science Center, St. Louis MO 63132 USA
- Publication Date:
- Research Org.:
- Donald Danforth Plant Science Center, St. Louis, MO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)
- OSTI Identifier:
- 1295954
- Alternate Identifier(s):
- OSTI ID: 1295955; OSTI ID: 1457329
- Grant/Contract Number:
- SC0006627; MCB-1231726; MCB-1330562; AI043288
- Resource Type:
- Published Article
- Journal Name:
- The Plant Journal
- Additional Journal Information:
- Journal Name: The Plant Journal Journal Volume: 82 Journal Issue: 6; Journal ID: ISSN 0960-7412
- Publisher:
- Society for Experimental Biology
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; RNA silencing; artificial microRNA; MIRNA precursor; Brachypodium distachyon; monocot; Arabidopsis thaliana; technical advance
Citation Formats
Carbonell, Alberto, Fahlgren, Noah, Mitchell, Skyler, Cox, Jr, Kevin L., Reilly, Kevin C., Mockler, Todd C., and Carrington, James C. Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors. United Kingdom: N. p., 2015.
Web. doi:10.1111/tpj.12835.
Carbonell, Alberto, Fahlgren, Noah, Mitchell, Skyler, Cox, Jr, Kevin L., Reilly, Kevin C., Mockler, Todd C., & Carrington, James C. Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors. United Kingdom. https://doi.org/10.1111/tpj.12835
Carbonell, Alberto, Fahlgren, Noah, Mitchell, Skyler, Cox, Jr, Kevin L., Reilly, Kevin C., Mockler, Todd C., and Carrington, James C. Wed .
"Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors". United Kingdom. https://doi.org/10.1111/tpj.12835.
@article{osti_1295954,
title = {Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors},
author = {Carbonell, Alberto and Fahlgren, Noah and Mitchell, Skyler and Cox, Jr, Kevin L. and Reilly, Kevin C. and Mockler, Todd C. and Carrington, James C.},
abstractNote = {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 and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots. Four different amiRNA sequences designed to target specifically endogenous genes and expressed from OsMIR390-based vectors were validated in transgenic Brachypodium distachyon plants. Surprisingly, amiRNAs accumulated to higher levels and were processed more accurately when expressed from chimeric OsMIR390-based precursors that include distal stem-loop sequences from Arabidopsis thaliana MIR390a (AtMIR390a). In all cases, transgenic plants displayed the predicted phenotypes induced by target gene repression, and accumulated high levels of amiRNAs and low levels of the corresponding target transcripts. Genome-wide transcriptome profiling combined with 5-RLM-RACE analysis in transgenic plants confirmed that amiRNAs were highly specific. Finally, significance Statement A series of amiRNA vectors based on Oryza sativa MIR390 (OsMIR390) precursor were developed for simple, cost-effective and large-scale synthesis of amiRNA constructs to silence genes in monocots. Unexpectedly, amiRNAs produced from chimeric OsMIR390-based precursors including Arabidopsis thaliana MIR390a distal stem-loop sequences accumulated elevated levels of highly effective and specific amiRNAs in transgenic Brachypodium distachyon plants.},
doi = {10.1111/tpj.12835},
journal = {The Plant Journal},
number = 6,
volume = 82,
place = {United Kingdom},
year = {Wed May 20 00:00:00 EDT 2015},
month = {Wed May 20 00:00:00 EDT 2015}
}
https://doi.org/10.1111/tpj.12835
Web of Science
Works referenced in this record:
Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome
journal, May 2008
- Addo-Quaye, Charles; Eshoo, Tifani W.; Bartel, David P.
- Current Biology, Vol. 18, Issue 10
A Two-Hit Trigger for siRNA Biogenesis in Plants
journal, November 2006
- Axtell, Michael J.; Jan, Calvin; Rajagopalan, Ramya
- Cell, Vol. 127, Issue 3
T-DNA mutagenesis in Brachypodium distachyon
journal, November 2011
- Thole, Vera; Peraldi, Antoine; Worland, Barbara
- Journal of Experimental Botany, Vol. 63, Issue 2
Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173
journal, January 2009
- Felippes, Felipe F.; Weigel, Detlef
- EMBO reports, Vol. 10, Issue 3
Disrupting the cinnamyl alcohol dehydrogenase 1 gene ( BdCAD1 ) leads to altered lignification and improved saccharification in Brachypodium distachyon
journal, December 2012
- Bouvier d'Yvoire, Madeleine; Bouchabke-Coussa, Oumaya; Voorend, Wannes
- The Plant Journal, Vol. 73, Issue 3
Undesired Small RNAs Originate from an Artificial microRNA Precursor in Transgenic Petunia (Petunia hybrida)
journal, June 2014
- Guo, Yulong; Han, Yao; Ma, Jing
- PLoS ONE, Vol. 9, Issue 6
Fragrance of the rice grain achieved via artificial microRNA-induced down-regulation of OsBADH2 : Fragrance of the rice grain achieved via artificial microRNA
journal, July 2012
- Chen, Mingliang; Wei, Xiangjin; Shao, Gaoneng
- Plant Breeding, Vol. 131, Issue 5
ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis
journal, November 2014
- Zhang, Xiaoming; Niu, DongDong; Carbonell, Alberto
- Nature Communications, Vol. 5, Issue 1
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
journal, January 2013
- Rapaport, Franck; Khanin, Raya; Liang, Yupu
- Genome Biology, Vol. 14, Issue 9
miRNA Target Prediction in Plants
book, January 2009
- Fahlgren, Noah; Carrington, James C.
- Methods in Molecular Biology
Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay
journal, February 2014
- Liu, Qikun; Wang, Feng; Axtell, Michael J.
- The Plant Cell, Vol. 26, Issue 2
GATEWAY™ vectors for Agrobacterium-mediated plant transformation
journal, May 2002
- Karimi, Mansour; Inzé, Dirk; Depicker, Ann
- Trends in Plant Science, Vol. 7, Issue 5, p. 193-195
Impact of down-regulation of starch branching enzyme IIb in rice by artificial microRNA- and hairpin RNA-mediated RNA silencing
journal, July 2011
- Butardo, Vito M.; Fitzgerald, Melissa A.; Bird, Anthony R.
- Journal of Experimental Botany, Vol. 62, Issue 14
Classification and Comparison of Small RNAs from Plants
journal, April 2013
- Axtell, Michael J.
- Annual Review of Plant Biology, Vol. 64, Issue 1
Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly
journal, June 2013
- Endo, Yayoi; Iwakawa, Hiro-oki; Tomari, Yukihide
- EMBO reports, Vol. 14, Issue 7
New Generation of Artificial MicroRNA and Synthetic Trans-Acting Small Interfering RNA Vectors for Efficient Gene Silencing in Arabidopsis
journal, March 2014
- Carbonell, Alberto; Takeda, Atsushi; Fahlgren, Noah
- Plant Physiology, Vol. 165, Issue 1
Clusters and superclusters of phased small RNAs in the developing inflorescence of rice
journal, July 2009
- Johnson, C.; Kasprzewska, A.; Tennessen, K.
- Genome Research, Vol. 19, Issue 8
Artificial microRNA mediated gene silencing in plants: progress and perspectives
journal, July 2014
- Tiwari, Manish; Sharma, Deepika; Trivedi, Prabodh Kumar
- Plant Molecular Biology, Vol. 86, Issue 1-2
The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs in Arabidopsis
journal, April 2014
- Bologna, Nicolas G.; Voinnet, Olivier
- Annual Review of Plant Biology, Vol. 65, Issue 1
Evolution and Functional Diversification of MIRNA Genes
journal, February 2011
- Cuperus, Josh T.; Fahlgren, Noah; Carrington, James C.
- The Plant Cell, Vol. 23, Issue 2
Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis
journal, March 2006
- Schwab, Rebecca; Ossowski, Stephan; Riester, Markus
- The Plant Cell, Vol. 18, Issue 5
Gene silencing in plants using artificial microRNAs and other small RNAs: Engineering small RNA-mediated gene silencing
journal, February 2008
- Ossowski, Stephan; Schwab, Rebecca; Weigel, Detlef
- The Plant Journal, Vol. 53, Issue 4
Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon
journal, January 2013
- Trabucco, Gina M.; Matos, Dominick A.; Lee, Scott J.
- BMC Biotechnology, Vol. 13, Issue 1
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa
journal, October 2008
- Zhou, X.; Sunkar, R.; Jin, H.
- Genome Research, Vol. 19, Issue 1
Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants
journal, September 2012
- Carbonell, Alberto; Fahlgren, Noah; Garcia-Ruiz, Hernan
- The Plant Cell, Vol. 24, Issue 9
Brassinosteroid signalling
journal, March 2013
- Zhu, J. -Y.; Sae-Seaw, J.; Wang, Z. -Y.
- Development, Vol. 140, Issue 8
Preparation of Multiplexed Small RNA Libraries from Plants
journal, January 2014
- Gilbert, Kerrigan; Fahlgren, Noah; Kasschau, Kristin
- BIO-PROTOCOL, Vol. 4, Issue 21
Biogenesis and function of rice small RNAs from non-coding RNA precursors
journal, May 2013
- Arikit, Siwaret; Zhai, Jixian; Meyers, Blake C.
- Current Opinion in Plant Biology, Vol. 16, Issue 2
Chloroplast biogenesis: The use of mutants to study the etioplast-chloroplast transition
journal, January 2007
- Philippar, K.; Geis, T.; Ilkavets, I.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 2
Spotted leaf11 , a Negative Regulator of Plant Cell Death and Defense, Encodes a U-Box/Armadillo Repeat Protein Endowed with E3 Ubiquitin Ligase Activity
journal, September 2004
- Zeng, Li-Rong; Qu, Shaohong; Bordeos, Alicia
- The Plant Cell, Vol. 16, Issue 10
Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes
journal, August 1992
- Bernard, Philippe; Couturier, Martine
- Journal of Molecular Biology, Vol. 226, Issue 3
Improving panicle exsertion of rice cytoplasmic male sterile line by combination of artificial microRNA and artificial target mimic
journal, November 2012
- Chen, Hao; Jiang, Shan; Zheng, Jie
- Plant Biotechnology Journal, Vol. 11, Issue 3
The Mechanism Selecting the Guide Strand from Small RNA Duplexes is Different Among Argonaute Proteins
journal, April 2008
- Takeda, Atsushi; Iwasaki, Shintaro; Watanabe, Toshiaki
- Plant and Cell Physiology, Vol. 49, Issue 4
Cloning and functional expression of the gene encoding the key enzyme for chlorophyll b biosynthesis (CAO) from Arabidopsis thaliana
journal, February 2000
- Oster, Ulrike; Tanaka, Ryouichi; Tanaka, Ayumi
- The Plant Journal, Vol. 21, Issue 3
Endogenous and Synthetic MicroRNAs Stimulate Simultaneous, Efficient, and Localized Regulation of Multiple Targets in Diverse Species
journal, April 2006
- Alvarez, John Paul; Pekker, Irena; Goldshmidt, Alexander
- The Plant Cell, Vol. 18, Issue 5
Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids
journal, January 2010
- He, Guangming; Zhu, Xiaopeng; Elling, Axel A.
- The Plant Cell, Vol. 22, Issue 1
Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide
journal, April 2008
- Mi, Shijun; Cai, Tao; Hu, Yugang
- Cell, Vol. 133, Issue 1
Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation
journal, April 2008
- Montgomery, Taiowa A.; Howell, Miya D.; Cuperus, Josh T.
- Cell, Vol. 133, Issue 1
Highly Specific Gene Silencing by Artificial miRNAs in Rice
journal, March 2008
- Warthmann, Norman; Chen, Hao; Ossowski, Stephan
- PLoS ONE, Vol. 3, Issue 3
Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis
journal, June 2010
- Cuperus, Josh T.; Carbonell, Alberto; Fahlgren, Noah
- Nature Structural & Molecular Biology, Vol. 17, Issue 8
A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq
journal, October 2011
- Wang, Lin; Si, Yaqing; Dedow, Lauren K.
- PLoS ONE, Vol. 6, Issue 10
A new strategy for construction of artificial miRNA vectors in Arabidopsis
journal, February 2012
- Liang, Gang; He, Hua; Li, Yang
- Planta, Vol. 235, Issue 6
Arabidopsis Argonaute10 Specifically Sequesters miR166/165 to Regulate Shoot Apical Meristem Development
journal, April 2011
- Zhu, Hongliang; Hu, Fuqu; Wang, Ronghui
- Cell, Vol. 145, Issue 2
Chlorophyll a oxygenase (CAO) is involved in chlorophyll b formation from chlorophyll a
journal, October 1998
- Tanaka, A.; Ito, H.; Tanaka, R.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 21
High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3
journal, November 2007
- Vogel, John; Hill, Theresa
- Plant Cell Reports, Vol. 27, Issue 3
miRBase: annotating high confidence microRNAs using deep sequencing data
journal, November 2013
- Kozomara, Ana; Griffiths-Jones, Sam
- Nucleic Acids Research, Vol. 42, Issue D1
A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
journal, July 2008
- Zhu, Q. -H.; Spriggs, A.; Matthew, L.
- Genome Research, Vol. 18, Issue 9
Characterization of Unique Small RNA Populations from Rice Grain
journal, August 2008
- Heisel, Sara E.; Zhang, Yuanji; Allen, Edwards
- PLoS ONE, Vol. 3, Issue 8