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Mol Plant. 2018 Sep 19. pii: S1674-2052(18)30275-2. doi: 10.1016/j.molp.2018.09.003. [Epub ahead of print]

A Resource for Inactivation of microRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants.

Author information

1
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA.
2
Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA.
3
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA.
4
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China.
5
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
6
School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA.
7
Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA.
8
Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China; Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
9
Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China.
10
College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China.
11
Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Department of Kinesiology and Integrative Physiology, Life Science and Technology Instituted, Michigan Technological University, Houghton, MI 49931, USA.
12
School of Technology, Michigan Technological University, Houghton, MI 49931, USA.
13
School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, P.R. China.
14
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China.
15
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China.

Abstract

microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to the target mRNAs for cleavage and/or translational repression, leading to gene silencing. We previously developed Short Tandem Target Mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created a resource of hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice and maize for functional interrogation of miRNAs. We not only showed the overall functions of miRNAs in plant development, but also demonstrated that tissue-specific inactivation of certain miRNAs led to an increase in rice grain size without adversely affecting overall plant growth and development. Inducible expression of STTM was fulfilled for dissecting functions of miRNAs spatio-temporally. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, ion channel activity-associated electrophysiology, demonstrating an effective approach to studying miRNA functions by using the STTM resource. To facilitate the study and application of STTM transgenic plants, an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) has been established to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants, forming a useful platform for storing and sharing of information of miRNA-regulated gene networks.

KEYWORDS:

Arabidopsis; RNA-seq; Rice; Short Tandem Target Mimic (STTM); Tomato; and Maize; miRNA

PMID:
30243763
DOI:
10.1016/j.molp.2018.09.003

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