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Yan F, Xiao X, Long C, Tang L, Wang C, Zhang M, Zhang J, Lin H, Huang H, Zhang Y, Li S. Molecular Characterization of U6 Promoters from Orange-Spotted Grouper (Epinephelus coioides) and Its Application in DNA Vector-Based RNAi Technology. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023:10.1007/s10126-023-10212-9. [PMID: 37154998 DOI: 10.1007/s10126-023-10212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
The U6 promoter, a typical RNA polymerase III promoter, is widely used to transcribe small RNAs in vector-based siRNA systems. The RNAi efficiency is mainly dependent on the transcriptional activity of the U6 promoter. However, studies have found that U6 promoters isolated from some fishes do not work well in distantly related species. To isolate a U6 promoter with high transcriptional efficiency from fish, in this study, we cloned five U6 promoters in orange-spotted grouper, of which only the grouper U6-1 (GU6-1) promoter contains the OCT element in the distant region. Functional studies revealed that the GU6-1 promoter has high transcriptional ability, which could efficiently transcribe shRNA and result in target gene knockdown in vitro and in vivo. Subsequently, the deletion or mutation of the OCT motif resulted in a significant decrease in promoter transcriptional activity, demonstrating that the OCT element plays an important role in enhancing the grouper U6 promoter transcription. Moreover, the transcriptional activity of the GU6-1 promoter showed little species specificity. It not only works in the grouper but also possesses high transcriptional activity in the zebrafish. Knockdown of the mstn gene in zebrafish and grouper through shRNA driven by the GU6-1 promoter could promote fish growth, suggesting that the GU6-1 promoter can be used as a potential molecular tool in aquaculture practice.
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Affiliation(s)
- Fengying Yan
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Xinxun Xiao
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Chen Long
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Lin Tang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Chongwei Wang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Mingqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Jin Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
| | - Haoran Lin
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266373, Qingdao, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, 572022, Sanya, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266373, Qingdao, China.
| | - Shuisheng Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Sun Yat-Sen University, Xin Gang Xi Road, Haizhu District, 510275, Guangzhou, Guangdong Province, China.
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Tu CF, Peng SH, Chuang CK, Wong CH, Yang TS. - Invited Review - Reproductive technologies needed for the generation of precise gene-edited pigs in the pathways from laboratory to farm. Anim Biosci 2023; 36:339-349. [PMID: 36397683 PMCID: PMC9899582 DOI: 10.5713/ab.22.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 11/15/2022] Open
Abstract
Gene editing (GE) offers a new breeding technique (NBT) of sustainable value to animal agriculture. There are 3 GE working sites covering 5 feasible pathways to generate GE pigs along with the crucial intervals of GE/genotyping, microinjection/electroporation, induced pluripotent stem cells, somatic cell nuclear transfer, cryopreservation, and nonsurgical embryo transfer. The extension of NBT in the new era of pig breeding depends on the synergistic effect of GE and reproductive biotechnologies; the outcome relies not only on scientific due diligence and operational excellence but also on the feasibility of application on farms to improve sustainability.
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Affiliation(s)
- Ching-Fu Tu
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan,Corresponding Author: Ching-Fu Tu, Tel: +886-37-585815, E-mail:
| | - Shu-Hui Peng
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan
| | - Chin-kai Chuang
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan
| | - Chi-Hong Wong
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan
| | - Tien-Shuh Yang
- Division of Animal Technology, Animal Technology Research Center, Agricultural Technology Research Institute, Hsinchu 30093,
Taiwan,Department of Biotechnology and Animal Science, National Ilan University, Yilan 260007,
Taiwan
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Yin HC, Chen XY, Wang W, Meng QW. Identification and comparison of the porcine H1, U6, and 7SK RNA polymerase III promoters for short hairpin RNA expression. Mamm Genome 2020; 31:110-116. [PMID: 32318815 DOI: 10.1007/s00335-020-09838-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/11/2020] [Indexed: 10/24/2022]
Abstract
RNA polymerase III is an essential enzyme in eukaryotes for synthesis of tRNA, 5S rRNA, and other small nuclear and cytoplasmic RNAs. Thus, RNA polymerase III promoters are often used in small hairpin RNA (shRNA) expression. In this study, the porcine H1, U6, and 7SK RNA polymerase III type promoters were cloned into a pcDNA3.1( +) expression vector containing a shRNA sequence targeting enhanced green fluorescent protein (EGFP). PK and DF-1 cells were cotransfected with the construction of recombinant interference expression vector and the EGFP expression vector, pEGFP-N1. The average fluorescence intensity of EGFP in transfected cells was measured by fluorescence microscopy and flow cytometry. Real-time PCR was used to detect expressed shRNAs and the relative expression of EGFP, to confirm the activity of the promoters. The results showed that the activity of porcine 7SK promoter is stronger than the U6 promoter, which is in turn stronger than porcine H1. While the high levels of expression of the U6 and 7SK promoters saturate the shRNAs level in the host cell, which can cause cytotoxicity and tissue damage. Therefore, porcine H1 promoter is effective for expression of shRNA, and may be an excellent tool to knockdown gene expression in pigs for functional genomics studies. The results also lay a foundation for the development of porcine RNAi technology and genetically modified porcine research.
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Affiliation(s)
- Hai-Chang Yin
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, 161006, Heilongjiang, People's Republic of China.,Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, 161006, Heilongjiang, People's Republic of China
| | - Xin-Yu Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Qing-Wen Meng
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China.
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Chuang CK, Tu CF, Chen CH. Generation of Mutant Pigs by Direct Pronuclear Microinjection of CRISPR/Cas9 Plasmid Vectors. Bio Protoc 2017; 7:e2321. [PMID: 34541083 DOI: 10.21769/bioprotoc.2321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/05/2017] [Accepted: 05/15/2017] [Indexed: 11/02/2022] Open
Abstract
A set of Cas9 and single guide CRISPR RNA expression vectors was constructed. Only a very simple procedure was needed to prepare specific single-guide RNA expression vectors with high target accuracy. Since the de novo zygotic transcription had been detected in mouse embryo at the 1-cell stage, the plasmid DNA vectors encoding Cas9 and GGTA1 gene specific single-guide RNAs were micro-injected into zygotic pronuclei to confirm such phenomenon in 1-cell pig embryo. Our results demonstrated that mutations caused by these CRISPR/Cas9 plasmids occurred before and at the 2-cell stage of pig embryos, indicating that besides the cytoplasmic microinjection of in vitro transcribed RNA, the pronuclear microinjection of CRISPR/Cas9 DNA vectors provided an efficient solution to generate gene-knockout pig.
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Affiliation(s)
- Chin-Kai Chuang
- Division of Animal Technology, Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu City, Taiwan
| | - Ching-Fu Tu
- Division of Animal Technology, Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu City, Taiwan
| | - Chien-Hong Chen
- Division of Animal Technology, Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu City, Taiwan.,Currenrtly: Lee Women's Hospital, Reproductive Medicine Center, Taichung City, Taiwan
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Chuang CK, Chen CH, Huang CL, Su YH, Peng SH, Lin TY, Tai HC, Yang TS, Tu CF. Generation of GGTA1 Mutant Pigs by Direct Pronuclear Microinjection of CRISPR/Cas9 Plasmid Vectors. Anim Biotechnol 2016; 28:174-181. [PMID: 27834588 DOI: 10.1080/10495398.2016.1246453] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study was conducted to confirm that 1-site and 4-site ppU6-GGTA1-gRNA CRISPR vectors together with the pCX-Flag2-NLS1-Cas9-NLS2 plasmid can both generate KO pigs by direct pronuclear microinjection. In total, 41 and 53 fertilized eggs were microinjected on 1-site and 4-site strategies, respectively. The 1-site construction generated a litter of 8 piglets, and 2 were mono-allelic mutant (mMt). The injection of 4-site constructions resulted in one biallelic mutant (bMt) and one mMt piglet in a litter of 7. Those 3 mMt pigs had a 4 bp deletion, 5 bp insertion, or 7 bp insertion at site I, and the bMt pig had 5 types of mutations at cleavage sites I and III. The expression of alpha-Gal on the bMt peripheral blood mononuclear cells (PBMCs) was reduced, and survival rate of bMt PBMCs was maintained as indicated by results of cultivation with sera of humans or Formosan Macaques. We concluded that mutant pigs could be generated by direct pronuclear microinjection of ppU6-GGTA1-gRNA CRISPR vectors with the pCX-Flag2-NLS1-Cas9-NLS2 plasmid and that the 4-site strategy has a better mutant efficiency. Porcine U6 promoter was firstly used to express KO vectors and effectively generate mutant pigs, worthily to adopt for future KO studies.
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Affiliation(s)
- Chin-Kai Chuang
- a Division of Animal Technology, Animal Technology Laboratories , Agricultural Technology Research Institute , Taiwan , Republic of China
| | - Chien-Hong Chen
- a Division of Animal Technology, Animal Technology Laboratories , Agricultural Technology Research Institute , Taiwan , Republic of China
| | - Chung-Ling Huang
- a Division of Animal Technology, Animal Technology Laboratories , Agricultural Technology Research Institute , Taiwan , Republic of China
| | - Yu-Hsiu Su
- a Division of Animal Technology, Animal Technology Laboratories , Agricultural Technology Research Institute , Taiwan , Republic of China
| | - Shu-Hui Peng
- a Division of Animal Technology, Animal Technology Laboratories , Agricultural Technology Research Institute , Taiwan , Republic of China
| | - Tai-Yun Lin
- a Division of Animal Technology, Animal Technology Laboratories , Agricultural Technology Research Institute , Taiwan , Republic of China
| | - Hao-Chih Tai
- b Department of Surgery , National Taiwan University Hospital , Taipei, Taiwan , Republic of China
| | - Tien-Shuh Yang
- c Department of Biotechnology and Animal Science , National Ilan University , Taiwan , Republic of China
| | - Ching-Fu Tu
- a Division of Animal Technology, Animal Technology Laboratories , Agricultural Technology Research Institute , Taiwan , Republic of China
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Su YH, Lin TY, Huang CL, Tu CF, Chuang CK. Construction of a CRISPR-Cas9 System for Pig Genome Targeting. Anim Biotechnol 2015; 26:279-88. [PMID: 26158460 DOI: 10.1080/10495398.2015.1027774] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A Cas9/sgRNA RNA-guided endonuclease expression system including a codon-optimized Streptococcus pyogenes A20 Cas9 recombinant protein expression vector and a spacer-guide chimeric RNA expression vector using the porcine U6 promoter was constructed for application in pigs. Only the Flag2-NLS1-Cas9-NLS2 recombinant protein in complex with sgRNA was translocated into the nucleus; the Flag2-NLS1-Cas9-NLS2 protein alone was excluded from the nucleus. Up to 13% of porcine PK1 cells targeted in vitro were observed, regardless of transfection efficiency.
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Affiliation(s)
- Yu-Hsiu Su
- a Division of Animal Technology, Laboratories of Animal Technology, Agricultural Technology Research Institute, Xiangshan District , Hsinchu City , Taiwan
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Abstract
Since the first application of RNA interference (RNAi) in mammalian cells, the expression of short hairpin RNAs (shRNAs) for targeted gene silencing has become a benchmark technology. Using plasmid and viral vectoring systems, the transcription of shRNA precursors that are effectively processed by the RNAi pathway can lead to potent gene knockdown. The past decade has seen continual advancement and improvement to the various strategies that can be used for shRNA delivery, and the use of shRNAs for clinical applications is well underway. Driving these developments has been the many benefits afforded by shRNA technologies, including the stable integration of expression constructs for long-term expression, infection of difficult-to-target cell lines and tissues using viral vectors, and the temporal control of shRNA transcription by inducible promoters. The use of different effector molecule formats, promoters, and vector types, has meant that experiments can be tailored to target specific cell types and minimize cellular toxicities. Through the application of combinatorial RNAi (co-RNAi), multiple shRNA delivery strategies can improve gene knockdown, permit multiple transcripts to be targeted simultaneously, and curtail the emergence of viral escape mutants. This chapter reviews the history, cellular processing, and various applications of shRNAs in mammalian systems, including options for effector molecule design, vector and promoter types, and methods for multiple shRNA delivery.
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Affiliation(s)
- Luke S Lambeth
- Murdoch Childrens Research Institute, Royal Childrens Hospital, Melbourne, VIC, Australia.
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Cloning and functional verification of U6 and 7SK promoter of small RNA from Bama mini-pig in Guangxi. YI CHUAN = HEREDITAS 2012; 34:445-53. [DOI: 10.3724/sp.j.1005.2012.00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hu S, Ni W, Hazi W, Zhang H, Zhang N, Meng R, Chen C. Cloning and Functional Analysis of Sheep U6 Promoters. Anim Biotechnol 2011; 22:170-4. [DOI: 10.1080/10495398.2011.580669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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