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Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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2
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Tanaka K, Suda A, Uesugi M, Futaki S, Imanishi M. Xanthine derivatives inhibit FTO in an L-ascorbic acid-dependent manner. Chem Commun (Camb) 2023; 59:10809-10812. [PMID: 37599611 DOI: 10.1039/d3cc02484a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Xanthine derivatives were identified as inhibitors of the N6-methyladenosine (m6A) demethylase activity of fat-mass-and-obesity-associated protein (FTO) by activity-based high-throughput screening using the m6A-sensitive ribonuclease MazF. Pentoxifylline exhibited L-ascorbic acid concentration-dependent inhibitory activity against FTO, an unprecedented mode of inhibition, indicating that L-ascorbic acid is a promising key for designing FTO-specific inhibitors.
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Affiliation(s)
- Kamui Tanaka
- Institute for Chemical Research, Uji, Kyoto 611-0011, Japan.
| | - Akiyo Suda
- Institute for Chemical Research, Uji, Kyoto 611-0011, Japan.
| | - Motonari Uesugi
- Institute for Chemical Research, Uji, Kyoto 611-0011, Japan.
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
- School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Shiroh Futaki
- Institute for Chemical Research, Uji, Kyoto 611-0011, Japan.
| | - Miki Imanishi
- Institute for Chemical Research, Uji, Kyoto 611-0011, Japan.
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3
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Wang L, Chen Z, Chen D, Kan B, He Y, Cai H. Farnesyl diphosphate synthase promotes cell proliferation by regulating gene expression and alternative splicing profiles in HeLa cells. Oncol Lett 2023; 25:145. [PMID: 36936029 PMCID: PMC10018273 DOI: 10.3892/ol.2023.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/10/2023] [Indexed: 03/04/2023] Open
Abstract
Farnesyl diphosphate synthase (FDPS), an essential enzyme involved in the mevalonate pathway, is implicated in various diseases, including multiple types of cancer. As an RNA-binding protein (RBP), FDPS is also involved in transcriptional and post-transcriptional regulation. However, to the best of our knowledge, transcriptome-wide targets of FDPS still remain unknown. In the present study, FDPS expression patterns in pan-cancer were analyzed. In addition, it was investigated how FDPS overexpression (FDPS-OE) regulates the transcriptome in HeLa cells. FDPS-OE increased the proliferation rate in HeLa cells by MTT assay. Using transcriptome-wide high throughput sequencing and bioinformatics analysis, it was found that FDPS upregulated the expression levels of genes enriched in cell proliferation and extracellular matrix organization, including the laminin subunit γ2, interferon-induced proteins with tetratricopeptide repeats 2 and matrix metallopeptidase 19 genes. According to alternative splicing (AS) analysis, FDPS modulated the splicing patterns of the bone morphogenic protein 1, semaphorin 4D, annexin A2 and sirtuin 2 genes, which are enriched in the cell cycle and DNA repair, and are related to cell proliferation. To corroborate the FDPS-regulated transcriptome findings, FDPS was overexpressed in human osteosarcoma cells. Differentially expressed genes and regulated AS genes in the cells were both validated by reverse transcription-quantitative PCR. The results suggested that, as an emerging RBP, FDPS may serve an important role in transcriptome profiles by altering gene expression and regulating AS. FDPS also affected the cell proliferation rate. These findings broaden the understanding of the molecular functions of FDPS, and the potential of FDPS as a target in therapy should be investigated.
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Affiliation(s)
- Lijuan Wang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Zhigang Chen
- ABLife BioBigData Institute, Wuhan, Hubei 430075, P.R. China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, Hubei 430075, P.R. China
| | - Bo Kan
- Department of Clinical Laboratory, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yangfang He
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Hanqing Cai
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
- Correspondence to: Dr Hanqing Cai, Department of Endocrinology, The Second Hospital of Jilin University, 218 Ziqiang Street, Nanguan, Changchun, Jilin 130021, P.R. China, E-mail:
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4
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Han W, Huang W, Wei T, Ye Y, Mao M, Wang Z. Programmable RNA base editing with a single gRNA-free enzyme. Nucleic Acids Res 2022; 50:9580-9595. [PMID: 36029126 PMCID: PMC9458445 DOI: 10.1093/nar/gkac713] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 07/02/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
Programmable RNA editing enables rewriting gene expression without changing genome sequences. Current tools for specific RNA editing dependent on the assembly of guide RNA into an RNA/protein complex, causing delivery barrier and low editing efficiency. We report a new gRNA-free system, RNA editing with individual RNA-binding enzyme (REWIRE), to perform precise base editing with a single engineered protein. This artificial enzyme contains a human-originated programmable PUF domain to specifically recognize RNAs and different deaminase domains to achieve efficient A-to-I or C-to-U editing, which achieved 60-80% editing rate in human cells, with a few non-specific editing sites in the targeted region and a low level off-target effect globally. The RNA-binding domain in REWIREs was further optimized to improve editing efficiency and minimize off-target effects. We applied the REWIREs to correct disease-associated mutations and achieve both types of base editing in mice. As a single-component system originated from human proteins, REWIRE presents a precise and efficient RNA editing platform with broad applicability.
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Affiliation(s)
- Wenjian Han
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wendi Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwen Ye
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miaowei Mao
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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5
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Rösner L, Reichert D, Rau K, Muthmann N, Rentmeister A. Sequence-specific targeting of RNA. Methods 2022; 205:73-82. [PMID: 35764247 DOI: 10.1016/j.ymeth.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/10/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Post-transcriptional modifications play an important role in several processes, including translation, splicing, and RNA degradation in eukaryotic cells. To investigate the function of specific modifications it is of high interest to develop tools for sequence-specific RNA-targeting. This work focuses on two abundant modifications of eukaryotic mRNA, namely methylation of the guanine-N7 position of the 5'-cap and internal N6-methyladenosine (m6A). We describe the sequence-specific targeting of model RNA transcripts via RNA-binding proteins, such as nuclease-deficient RNA-targeting Cas9 (RCas9) and the Pumilio homology domain (PumHD) fused to two different effector enzymes, the dioxygenase FTO and the guanine-N7 methyltransferase Ecm1. With this tool, we were able to install and remove the methylation at the respective positions with high specificity.
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Affiliation(s)
- Lukas Rösner
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Dennis Reichert
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Kristina Rau
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Nils Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany; Cells in Motion Interfaculty Center, University of Münster, 48149 Münster, Germany
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6
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Imanishi M. Mechanisms and Strategies for Determining m 6 A RNA Modification Sites by Natural and Engineered m 6 A Effector Proteins. Chem Asian J 2022; 17:e202200367. [PMID: 35750635 DOI: 10.1002/asia.202200367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/17/2022] [Indexed: 12/13/2022]
Abstract
N6 -Methyladenosine (m6 A) is the most common internal RNA modification in the consensus sequence of 5'-RRACH-3'. The methyl mark is added by writer proteins (METTL3/METTL14 metyltransferase complex) and removed by eraser proteins (m6 A demethylases; FTO and ALKBH5). Recognition of this methyl mark by m6 A reader proteins leads to changes in RNA metabolism. How the writer and eraser proteins determine their targets is not well-understood, despite the importance of this information in understanding the regulatory mechanisms and physiological roles of m6 A. However, approaches for targeted manipulation of the methylation state at specific sites are being developed. In this review, I summarize the recent findings on the mechanisms of target identification of m6 A regulatory proteins, as well as recent approaches for targeted m6 A modifications.
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Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
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7
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Gao M, Su S, Cao J, Xiang S, Huang Y, Shu X, Ma J, Liu J. Targeted Manipulation of Cellular RNA m 6A Methylation at the Single-Base Level. ACS Chem Biol 2022; 17:854-863. [PMID: 35294178 DOI: 10.1021/acschembio.1c00895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of tools for precise manipulation of cellular mRNA m6A methylation at the base level is highly required. Here, we report an RNA-guided RNA modification strategy using a fusion protein containing deactivated nuclease Cas13b and m6A methyltransferase METTL14, namely, dCas13b-M14, which is designedly positioned in the cytoplasm. dCas13b-M14 naturally heterodimerizes with endogenous METTL3 to form a catalytic complex to methylate specific cytoplasmic mRNA under a guide RNA (gRNA). We developed assays to screen and validate the guiding specificity of varied gRNAs at single-base resolution. With an optimum combination of dCas13b-M14 and gRNAs inside cells, we have successfully tuned methylation levels of several selected mRNA m6A sites. The off-target effect was evaluated by whole transcriptome m6A sequencing, and a very minor perturbation on the methylome was revealed. Finally, we successfully utilized the editing tool to achieve de novo methylations on five selected mRNA sites. Together, this study paves the way for studying position-dependent roles of m6A methylation in a particular transcript.
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Affiliation(s)
- Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Siying Xiang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Ye Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
- Life Sciences Institute, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
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8
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Su Y, Maimaitiyiming Y, Wang L, Cheng X, Hsu CH. Modulation of Phase Separation by RNA: A Glimpse on N 6-Methyladenosine Modification. Front Cell Dev Biol 2021; 9:786454. [PMID: 34957114 PMCID: PMC8703171 DOI: 10.3389/fcell.2021.786454] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022] Open
Abstract
Phase separation is the driving force behind formation of various biomolecular condensates (BioMCs), which sub-compartmentalize certain cellular components in a membraneless manner to orchestrate numerous biological processes. Many BioMCs are composed of proteins and RNAs. While the features and functions of proteins are well studied, less attention was paid to the other essential component RNAs. Here, we describe how RNA contributes to the biogenesis, dissolution, and properties of BioMCs as a multivalence providing scaffold for proteins/RNA to undergo phase separation. Specifically, we focus on N6-methyladenosine (m6A), the most widely distributed dynamic post-transcriptional modification, which would change the charge, conformation, and RNA-binding protein (RBP) anchoring of modified RNA. m6A RNA-modulated phase separation is a new perspective to illustrate m6A-mediated various biological processes. We summarize m6A main functions as “beacon” to recruit reader proteins and “structural switcher” to alter RNA–protein and RNA–RNA interactions to modulate phase separation and regulate the related biological processes.
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Affiliation(s)
- Yingfeng Su
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yasen Maimaitiyiming
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hematology of First Affiliated Hospital, Department of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingfang Wang
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaodong Cheng
- Department of Obstetrics and Gynecology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chih-Hung Hsu
- Women's Hospital, Institute of Genetics, Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
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9
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Yoshida A, Oyoshi T, Suda A, Futaki S, Imanishi M. Recognition of G-quadruplex RNA by a crucial RNA methyltransferase component, METTL14. Nucleic Acids Res 2021; 50:449-457. [PMID: 34908152 PMCID: PMC8755082 DOI: 10.1093/nar/gkab1211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/29/2021] [Accepted: 11/26/2021] [Indexed: 01/04/2023] Open
Abstract
N6-methyladenosine (m6A) is an important epitranscriptomic chemical modification that is mainly catalyzed by the METTL3/METTL14 RNA methyltransferase heterodimer. Although m6A is found at the consensus sequence of 5′-DRACH-3′ in various transcripts, the mechanism by which METTL3/METTL14 determines its target is unclear. This study aimed to clarify the RNA binding property of METTL3/METTL14. We found that the methyltransferase heterodimer itself has a binding preference for RNA G-quadruplex (rG4) structures, which are non-canonical four-stranded structures formed by G-rich sequences, via the METTL14 RGG repeats. Additionally, the methyltransferase heterodimer selectively methylated adenosines close to the rG4 sequences. These results suggest a possible process for direct recruitment of METTL3/METTL14 to specific methylation sites, especially near the G4-forming regions. This study is the first to report the RNA binding preference of the m6A writer complex for the rG4 structure and provides insights into the role of rG4 in epitranscriptomic regulation.
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Affiliation(s)
- Atsuhiro Yoshida
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takanori Oyoshi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Akiyo Suda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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10
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Zhou W, Wang X, Chang J, Cheng C, Miao C. The molecular structure and biological functions of RNA methylation, with special emphasis on the roles of RNA methylation in autoimmune diseases. Crit Rev Clin Lab Sci 2021; 59:203-218. [PMID: 34775884 DOI: 10.1080/10408363.2021.2002256] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Autoimmune diseases such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and systemic vasculitis are caused by the body's immune response to autoantigens. The pathogenesis of autoimmune diseases is complex. RNA methylation is known to play a key role in disease progression as it regulates almost all aspects of RNA processing, including RNA nuclear export, translation, splicing, and noncoding RNA processing. This review summarizes the mechanisms, molecular structures of RNA methylations and their roles in biological functions. Similar to the roles of RNA methylation in cancers, RNA methylation in RA and SLE involves "writers" that deposit methyl groups to form N6-methyladenosine (m6A) and 5-methylcytosine (m5C), "erasers" that remove these modifications, and "readers" that further affect mRNA splicing, export, translation, and degradation. Recent advances in detection methods have identified N1-methyladenosine (m1A), N6,2-O-dimethyladenosine (m6Am), and 7-methylguanosine (m7G) RNA modifications, and their roles in RA and SLE need to be further studied. The relationship between RNA methylation and other autoimmune diseases has not been reported, and the roles and mechanisms of RNA modifications in these diseases need to be explored in the future.
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Affiliation(s)
- Wanwan Zhou
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jun Chang
- Department of Orthopaedics, Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Institute of Prevention and Treatment of Rheumatoid Arthritis, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Department of Pharmacy, School of Life and Health Sciences, Anhui University of Science and Technology, Fengyang, Anhui Province, China
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11
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Zhou W, Wang C, Chang J, Huang Y, Xue Q, Miao C, Wu P. RNA Methylations in Cardiovascular Diseases, Molecular Structure, Biological Functions and Regulatory Roles in Cardiovascular Diseases. Front Pharmacol 2021; 12:722728. [PMID: 34489709 PMCID: PMC8417252 DOI: 10.3389/fphar.2021.722728] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 01/05/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality in the world. Despite considerable progress in the diagnosis, treatment and prognosis of CVDs, new diagnostic biomarkers and new therapeutic measures are urgently needed to reduce the mortality of CVDs and improve the therapeutic effect. RNA methylations regulate almost all aspects of RNA processing, such as RNA nuclear export, translation, splicing and non-coding RNA processing. In view of the importance of RNA methylations in the pathogenesis of diseases, this work reviews the molecular structures, biological functions of five kinds of RNA methylations (m6A, m5C, m1a, m6am and m7G) and their effects on CVDs, including pulmonary hypertension, hypertension, vascular calcification, cardiac hypertrophy, heart failure. In CVDs, m6A “writers” catalyze the installation of m6A on RNAs, while “erasers” remove these modifications. Finally, the “readers” of m6A further influence the mRNA splicing, nuclear export, translation and degradation. M5C, m1A, m6Am and m7G are new types of RNA methylations, their roles in CVDs need to be further explored. RNA methylations have become a new research hotspot and the roles in CVDs is gradually emerging, the review of the molecular characteristics, biological functions and effects of RNA methylation on CVDs will contribute to the elucidation of the pathological mechanisms of CVDs and the discovery of new diagnostic markers and therapeutic targets of CVDs.
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Affiliation(s)
- Wanwan Zhou
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Changhui Wang
- Department of Cardiology, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Jun Chang
- Department of Orthopaedics, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Qiuyun Xue
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China.,Anhui Provincial Key Laboratory of Applied Basis and Development of Modern Internal Medicine of Traditional Chinese Medicine, The First Affiliated Hospital, Anhui University of Chinese Medicine, Hefei, China
| | - Peng Wu
- Department of Anatomy, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
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12
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Hu Y, Zhao X. Role of m6A in osteoporosis, arthritis and osteosarcoma (Review). Exp Ther Med 2021; 22:926. [PMID: 34306195 PMCID: PMC8281110 DOI: 10.3892/etm.2021.10358] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/11/2021] [Indexed: 12/18/2022] Open
Abstract
RNA modification is a type of post-transcriptional modification that regulates important cellular pathways, such as the processing and metabolism of RNA. The most abundant form of methylation modification is RNA N6-methyladenine (m6A), which plays various post-transcriptional regulatory roles in cellular biological functions, including cell differentiation, embryonic development and disease occurrence. Bones play a pivotal role in the skeletal system as they support and protect muscles and other organs, facilitate movement and ensure haematopoiesis. The development and remodelling of bones require a delicate and accurate regulation of gene expression by epigenetic mechanisms that involve modifications of histone, DNA and RNA. The present review discusses the enzymes and proteins involved in mRNA m6A methylation modification and summarises current research progress and the mechanisms of mRNA m6A methylation in common orthopaedic diseases, including osteoporosis, arthritis and osteosarcoma.
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Affiliation(s)
- Yibo Hu
- Department of Orthopaedic Trauma, The Affiliated Hospital of Qinghai University, Xining, Qinghai 810000, P.R. China
| | - Xiaohui Zhao
- Department of Orthopaedic Trauma, The Affiliated Hospital of Qinghai University, Xining, Qinghai 810000, P.R. China
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13
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Abstract
N6-methyladenosine (m6A) is a major epitranscriptomic mark exerting crucial diverse roles in RNA metabolisms, including RNA stability, mRNA translation, and RNA structural rearrangement. m6A modifications at different RNA regions may have distinct molecular effects. Here, we describe a CRISPR-Cas9-based approach that enables targeted m6A addition or removal on endogenous RNA molecules without altering the nucleotide sequence. By fusing a catalytically inactive Cas9 with engineered m6A modification enzymes, the programmable m6A editors are capable of achieving RNA methylation and demethylation at desired sites, facilitating dissection of regional effects of m6A and diversifying the toolkits for RNA manipulation.
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14
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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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15
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Schaefer MR. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics? Genes (Basel) 2021; 12:genes12030345. [PMID: 33652758 PMCID: PMC7996938 DOI: 10.3390/genes12030345] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
RNA modifications, long considered to be molecular curiosities embellishing just abundant and non-coding RNAs, have now moved into the focus of both academic and applied research. Dedicated research efforts (epitranscriptomics) aim at deciphering the underlying principles by determining RNA modification landscapes and investigating the molecular mechanisms that establish, interpret and modulate the information potential of RNA beyond the combination of four canonical nucleotides. This has resulted in mapping various epitranscriptomes at high resolution and in cataloguing the effects caused by aberrant RNA modification circuitry. While the scope of the obtained insights has been complex and exciting, most of current epitranscriptomics appears to be stuck in the process of producing data, with very few efforts to disentangle cause from consequence when studying a specific RNA modification system. This article discusses various knowledge gaps in this field with the aim to raise one specific question: how are the enzymes regulated that dynamically install and modify RNA modifications? Furthermore, various technologies will be highlighted whose development and use might allow identifying specific and context-dependent regulators of epitranscriptomic mechanisms. Given the complexity of individual epitranscriptomes, determining their regulatory principles will become crucially important, especially when aiming at modifying specific aspects of an epitranscriptome both for experimental and, potentially, therapeutic purposes.
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Affiliation(s)
- Matthias R Schaefer
- Centre for Anatomy & Cell Biology, Division of Cell-and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Haus C, 1st Floor, 1090 Vienna, Austria
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16
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Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A. Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m6A) Recognition by the Reader Domain of YTHDC1. J Chem Theory Comput 2021; 17:1240-1249. [DOI: 10.1021/acs.jctc.0c01136] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Rajiv Kumar Bedi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lars Wiedmer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Xianqiang Sun
- Regor Pharmaceuticals, Inc., 1206, Zhangjiang Road, Building C, Pudong New District, Shanghai 201210, China
| | - Danzhi Huang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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17
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Mo J, Chen Z, Qin S, Li S, Liu C, Zhang L, Ran R, Kong Y, Wang F, Liu S, Zhou Y, Zhang X, Weng X, Zhou X. TRADES: Targeted RNA Demethylation by SunTag System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001402. [PMID: 33042753 PMCID: PMC7539198 DOI: 10.1002/advs.202001402] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/15/2020] [Indexed: 05/04/2023]
Abstract
N6-methyladenosine (m6A) is rapidly being studied and uncovered to play a significant role in various biological processes as well as in RNA fate and functions, while the effects of defined m6A sites are rarely characterized for the lack of convenient tools. To provide an applicable method to remove m6A modification at specific loci, an m6A editing system called "targeted RNA demethylation by SunTag system (TRADES)" is engineered. In this system, the targeting element dCas13b is fused to ten copies of GCN4 peptides which can recruit multiple scFv-fusion RNA demethylase to demethylate the target m6A site. Owing to this design, TRADES is more flexible to the indistinct m6A sites for its wide editing window. By site-specific demethylation of messenger RNA (mRNA) SON A2699, the lifetime of SON RNA is successfully prolonged in HeLa cells. Meanwhile, TRADES negligibly influences the lifetime of other non-targeted transcripts. TRADES also can regulate the gene expression of target transcript in an m6A-dependent manner. Moreover, the interference occuring for HBV and HIV replications demonstrates that the TRADES system holds potential in viral life cycle regulation and clinical applications.
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Affiliation(s)
- Jing Mo
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
| | - Zonggui Chen
- The Institute for Advanced StudiesCollege of Life SciencesState Key Laboratory of VirologyWuhan UniversityWuhan430072China
- State Key Laboratory of Freshwater Ecology and BiotechnologyInstitute of HydrobiologyInnovation Academy for Seed DesignChinese Academy of SciencesWuhan430072China
| | - Shanshan Qin
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
| | - Shu Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Chuangang Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Lu Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Ruoxi Ran
- Department of Clinical LaboratoryCenter for Gene Diagnosis and Program of Clinical LaboratoryZhongnan HospitalWuhan UniversityWuhan430071China
| | - Ying Kong
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Fang Wang
- School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Songmei Liu
- Department of Clinical LaboratoryCenter for Gene Diagnosis and Program of Clinical LaboratoryZhongnan HospitalWuhan UniversityWuhan430071China
| | - Yu Zhou
- The Institute for Advanced StudiesCollege of Life SciencesState Key Laboratory of VirologyWuhan UniversityWuhan430072China
| | - Xiaolian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of ImmunologySchool of MedicineWuhan UniversityWuhan430071China
| | - Xiaocheng Weng
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072China
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18
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Effective RNA Regulation by Combination of Multiple Programmable RNA-Binding Proteins. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNAs play important roles in gene expression through translation and RNA splicing. Regulation of specific RNAs is useful to understand and manipulate specific transcripts. Pumilio and fem-3 mRNA-binding factor (PUF) proteins, programmable RNA-binding proteins, are promising tools for regulating specific RNAs by fusing them with various functional domains. The key question is: How can PUF-based molecular tools efficiently regulate RNA functions? Here, we show that the combination of multiple PUF proteins, compared to using a single PUF protein, targeting independent RNA sequences at the 3′ untranslated region (UTR) of a target transcript caused cooperative effects to regulate the function of the target RNA by luciferase reporter assays. It is worth noting that a higher efficacy was achieved with smaller amounts of each PUF expression vector introduced into the cells compared to using a single PUF protein. This strategy not only efficiently regulates target RNA functions but would also be effective in reducing off-target effects due to the low doses of each expression vector.
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19
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Chen LQ, Zhao WS, Luo GZ. Mapping and editing of nucleic acid modifications. Comput Struct Biotechnol J 2020; 18:661-667. [PMID: 32257049 PMCID: PMC7113611 DOI: 10.1016/j.csbj.2020.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/29/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
Modification on nucleic acid plays a pivotal role in controlling gene expression. Various kinds of modifications greatly increase the information-encoding capacity of DNA and RNA by introducing extra chemical group to existing bases instead of altering the genetic sequences. As a marker on DNA or RNA, nucleic acid modification can be recognized by specific proteins, leading to versatile regulation of gene expression. However, modified and regular bases are often indistinguishable by most conventional molecular methods, impeding detailed functional studies that require the information of genomic location. Recently, new technologies are emerging to resolve the positions of varied modifications on both DNA and RNA. Intriguingly, by integrating regional targeting tools and effector proteins, researchers begin to actively control the modification status of desired gene in vivo. In this review, we summarize the characteristics of DNA and RNA modifications, the available mapping and editing tools, and the potential application as well as deficiency of these technologies in basic and translational researches.
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Affiliation(s)
| | | | - Guan-Zheng Luo
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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