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Zhong C, Smith NA, Zhang D, Gou X, Greaves IK, Millar AA, Walsh TK, Shan W, Wang MB. G-U base-paired hpRNA confers potent inhibition of small RNA function in plants. Plant J 2024; 117:1206-1222. [PMID: 38038953 DOI: 10.1111/tpj.16555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
MicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G-U base-paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem-loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460-bp G-U base-paired double-stranded stem and a 312-576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) effectively inhibited Y-Sat siRNA-directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G-U base-paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA-mediated diseases.
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Affiliation(s)
- Chengcheng Zhong
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Neil A Smith
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Daai Zhang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Xiuhong Gou
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ian K Greaves
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Tom K Walsh
- CSIRO Environment, Canberra, 2601, ACT, Australia
| | - Weixing Shan
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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Othman SMIS, Mustaffa AF, Che-Othman MH, Samad AFA, Goh HH, Zainal Z, Ismail I. Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology. Plants (Basel) 2023; 12:669. [PMID: 36771753 PMCID: PMC9918958 DOI: 10.3390/plants12030669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial-temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.
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Affiliation(s)
- Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - M. Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Abdul Fatah A. Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor Bahru 81310, Johor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Zamri Zainal
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
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Shu Y, Wu K, Zeng Z, Huang S, Ji X, Yuan C, Zhang L, Liu W, Huang B, Feng Y, Zhang B, Dai Z, Shen Y, Luo W, Wang X, Liu B, Lei Y, Ye Z, Zhao L, Cao D, Yang L, Chen X, Luu HH, Reid RR, Wolf JM, Lee MJ, He TC. A Simplified System to Express Circularized Inhibitors of miRNA for Stable and Potent Suppression of miRNA Functions. Mol Ther Nucleic Acids 2018; 13:556-567. [PMID: 30414569 PMCID: PMC6226557 DOI: 10.1016/j.omtn.2018.09.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 08/27/2018] [Accepted: 09/26/2018] [Indexed: 12/09/2022]
Abstract
MicroRNAs (miRNAs) are an evolutionarily conserved class of small regulatory noncoding RNAs, binding to complementary target mRNAs and resulting in mRNA translational inhibition or degradation, and they play an important role in regulating many aspects of physiologic and pathologic processes in mammalian cells. Thus, efficient manipulations of miRNA functions may be exploited as promising therapeutics for human diseases. Two commonly used strategies to inhibit miRNA functions include direct transfection of chemically synthesized miRNA inhibitors and delivery of a gene vector that instructs intracellular transcription of miRNA inhibitors. While most miRNA inhibitors are based on antisense molecules to bind and sequester miRNAs from their natural targets, it is challenging to achieve effective and stable miRNA inhibition. Here we develop a user-friendly system to express circular inhibitors of miRNA (CimiRs) by exploiting the noncanonical head-to-tail backsplicing mechanism for generating endogenous circular RNA sponges. In our proof-of-principle experiments, we demonstrate that the circular forms of the hsa-miR223-binding site of human β-arrestin1 (ARRB1) 3′ UTR sponge RNA (BUTR), the bulged anti-miR223 (cirBulg223) and bulged anti-miR21 (cirBulg21), exhibit more potent suppression of miRNA functions than their linear counterparts. Therefore, the engineered CimiR expression system should be a valuable tool to target miRNAs for basic and translational research.
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Affiliation(s)
- Yi Shu
- Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Chongqing 400014, China; Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Ke Wu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China.
| | - Zongyue Zeng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Shifeng Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Xiaojuan Ji
- Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Chongqing 400014, China; Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Chengfu Yuan
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, China Three Gorges University School of Medicine, Yichang 443002, China
| | - Linghuan Zhang
- Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Chongqing 400014, China; Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Wei Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Bo Huang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China; Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yixiao Feng
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Bo Zhang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Key Laboratory of Orthopaedic Surgery of Gansu Province, First and Second Hospitals of Lanzhou University, Lanzhou 730030, China; Departments of Orthopaedic Surgery and Obstetrics and Gynecology, First and Second Hospitals of Lanzhou University, Lanzhou 730030, China
| | - Zhengyu Dai
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Department of Orthopaedic Surgery, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, China
| | - Yi Shen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Department of Orthopaedic Surgery, Xiangya Second Hospital of Central South University, Changsha 410011, China
| | - Wenping Luo
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Xi Wang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Bo Liu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Yan Lei
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Zhenyu Ye
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Department of General Surgery, the Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Ling Zhao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Daigui Cao
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Ministry of Education Key Laboratory of Diagnostic Medicine, School of Laboratory Medicine, The Affiliated Hospitals of Chongqing Medical University, Chongqing 400016, China; Department of Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing 400046, China
| | - Lijuan Yang
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Key Laboratory of Orthopaedic Surgery of Gansu Province, First and Second Hospitals of Lanzhou University, Lanzhou 730030, China; Departments of Orthopaedic Surgery and Obstetrics and Gynecology, First and Second Hospitals of Lanzhou University, Lanzhou 730030, China
| | - Xian Chen
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Department of Clinical Laboratory Medicine, Affiliated Hospital of Qingdao University, Qingdao 266061, China
| | - Hue H Luu
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Russell R Reid
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA; Department of Surgery, Section of Plastic Surgery, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Jennifer Moriatis Wolf
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Michael J Lee
- Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Tong-Chuan He
- Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Chongqing 400014, China; Molecular Oncology Laboratory, Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medical Center, Chicago, IL 60637, USA.
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