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Li T, Shu X, Gao M, Huang C, Li T, Cao J, Ying X, Liu D, Liu J. N4-Allylcytidine: a new nucleoside analogue for RNA labelling and chemical sequencing. RSC Chem Biol 2024; 5:225-235. [PMID: 38456037 PMCID: PMC10915972 DOI: 10.1039/d3cb00189j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/15/2023] [Indexed: 03/09/2024] Open
Abstract
RNA labelling has become indispensable in studying RNA biology. Nucleoside analogues with a chemical sequencing power represent desirable RNA labelling molecules because precise labelling information at base resolution can be obtained. Here, we report a new nucleoside analogue, N4-allylcytidine (a4C), which is able to tag RNA through both in vitro and in vivo pathways and further specifically reacts with iodine to form 3, N4-cyclized cytidine (cyc-C) in a catalyst-free, fast and complete manner. Full spectroscopic characterization concluded that cyc-C consisted of paired diastereoisomers with opposite chiral carbon centers in the fused 3, N4-five-membered ring. During RNA reverse transcription into complementary DNA, cyc-C induces base misincorporation due to the disruption of canonical hydrogen bonding by the cyclized structure and thus can be accurately identified by sequencing at single base resolution. With the chemical sequencing rationale of a4C, successful applications have been performed including pinpointing N4-methylcytidine methyltransferases' substrate modification sites, metabolically labelling mammalian cellular RNAs, and mapping active cellular RNA polymerase locations with the chromatin run-on RNA sequencing technique. Collectively, our work demonstrates that a4C is a promising molecule for RNA labelling and chemical sequencing and expands the toolkit for studying sophisticated RNA biology.
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Affiliation(s)
- Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Chenyang Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Ting Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
- Life Sciences Institute, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Xiner Ying
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Donghong Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
- Life Sciences Institute, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
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Ying X, Huang C, Li T, Li T, Gao M, Wang F, Cao J, Liu J. An RNA Methylation-Sensitive AIEgen-Aptamer Reporting System for Quantitatively Evaluating m 6A Methylase and Demethylase Activities. ACS Chem Biol 2024; 19:162-172. [PMID: 38105499 DOI: 10.1021/acschembio.3c00613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
N6-Methyladenosine (m6A) chemical modification determines the fate of the mammalian cellular mRNA to modulate crucial physiological and pathological processes. Dysregulations of m6A methylase and demethylase have been linked to cancer diseases. Therefore, evaluations of enzyme mutants' activities and related inhibitors for discovery of targeted therapeutic strategies are very necessary. Here, we report an RNA methylation-sensitive fluorescent aptamer reporting assay to measure the catalytic activities of m6A enzymes under various conditions. The rationale is that when an RNA aptamer, named A-Pepper, is methylated at a specific adenosine position to generate m6A-Pepper, the latter displays stronger fluorescence than the former upon binding the ligand, which is an aggregation-induced emission-active luminogen. The fluorescence signal enhancement is linearly proportional to the RNA methylation extent, which is equivalent to the methylase activity. On the contrary, the m6A demethylase activity is measured through calculating the fluorescence signal decrease caused by the switching from m6A-Pepper to A-Pepper. The assay has been successfully applied to quantitatively evaluate the mutation and inhibitor effects on the activities of m6A methylases METTL3/METTL14 and demethylase FTO, and the obtained results are well-consistent with those quantified by the expensive and time-consuming golden standard LC-MS/MS. Our work provides a simple tool capable of detecting m6A enzymes' activities and screening their inhibitors in a rapid, quantitative, cost-effective, and high-throughput manner.
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Affiliation(s)
- Xiner Ying
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Chenyang Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Ting Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Fengqin Wang
- College of Animal Sciences, Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Center for RNA Medicine, International Institutes of Medicine, Zhejiang University, Yiwu 322000, China
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