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Liu H, Rauch S, Dickinson BC. Programmable technologies to manipulate gene expression at the RNA level. Curr Opin Chem Biol 2021; 64:27-37. [PMID: 33930627 DOI: 10.1016/j.cbpa.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
RNA has long been an enticing therapeutic target, but is now garnering increased attention, largely driven by clinical successes of RNA interference-based drugs. While gene knockdown by well-established RNA interference- and other oligonucleotide-based strategies continues to advance in the clinic, the repertoire of targetable effectors capable of altering gene expression at the RNA level is also rapidly expanding. In this review, we focus on several recently developed bifunctional molecular technologies that both interact with and act upon a target RNA. These new approaches for programmable RNA knockdown, editing, splicing, translation, and chemical modifications stand to provide impactful new modalities for therapeutic development in the coming decades.
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Affiliation(s)
- Huachun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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Huang X, Zhao Y, Pu Q, Liu G, Peng Y, Wang F, Chen G, Sun M, Du F, Dong J, Cui X, Tang Z, Mo X. Intracellular selection of trans-cleaving hammerhead ribozymes. Nucleic Acids Res 2019; 47:2514-2522. [PMID: 30649474 PMCID: PMC6412130 DOI: 10.1093/nar/gkz018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 02/05/2023] Open
Abstract
Hammerhead ribozyme is the smallest and best characterized catalytic RNA-cleaving ribozyme. It has been reported as potential therapeutic tools to manipulate the expression of target genes. However, most of naturally occurring hammerhead ribozymes process self-cleavage rather than cleave substrate RNA in trans, and its high intracellular activity relies on the tertiary interaction of Loop II and steam I bulge, resulting in decreased performance as applied in gene silencing. We described a direct intracellular selection method to evolve hammerhead variants based on trans-cleavage mode via using a toxin gene as the reporter. And a dual fluorescence proteins system has also been established to quantitatively evaluate the efficiency of selected ribozymes in the cell. Based on this selection strategy, we obtained three mutants with enhanced intracellular cleaving activity compared to wide type hammerhead ribozyme. The best one, TX-2 was revealed to possess better and consistent gene knockdown ability at different positions on diverse targeted mRNA either in prokaryotic or eukaryotic cells than wild-type hammerhead ribozyme. These observations imply the efficiency of the intracellular selection method of the trans-acting ribozyme and the potentials of improved ribozyme variants for research and therapeutic purposes.
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Affiliation(s)
- Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yongyun Zhao
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Getong Liu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yan Peng
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Fei Wang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Meiling Sun
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
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Fukuda M, Umeno H, Nose K, Nishitarumizu A, Noguchi R, Nakagawa H. Construction of a guide-RNA for site-directed RNA mutagenesis utilising intracellular A-to-I RNA editing. Sci Rep 2017; 7:41478. [PMID: 28148949 PMCID: PMC5288656 DOI: 10.1038/srep41478] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 12/20/2016] [Indexed: 01/24/2023] Open
Abstract
As an alternative to DNA mutagenesis, RNA mutagenesis can potentially become a powerful gene-regulation method for fundamental research and applied life sciences. Adenosine-to-inosine (A-to-I) RNA editing alters genetic information at the transcript level and is an important biological process that is commonly conserved in metazoans. Therefore, a versatile RNA-mutagenesis method can be achieved by utilising the intracellular RNA-editing mechanism. Here, we report novel guide RNAs capable of inducing A-to-I mutations by guiding the editing enzyme, human adenosine deaminase acting on RNA (ADAR). These guide RNAs successfully introduced A-to-I mutations into the target-site, which was determined by the reprogrammable antisense region. In ADAR2-over expressing cells, site-directed RNA editing could also be performed by simply introducing the guide RNA. Our guide RNA framework provides basic insights into establishing a generally applicable RNA-mutagenesis method.
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Affiliation(s)
- Masatora Fukuda
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0180, Japan
| | - Hiromitsu Umeno
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0180, Japan
| | - Kanako Nose
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0180, Japan
| | - Azusa Nishitarumizu
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0180, Japan
| | - Ryoma Noguchi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, Fukuoka 814-0180, Japan
| | - Hiroyuki Nakagawa
- Department of Earth System Science, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, Fukuoka, 814-0180, Japan
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