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Han X, Zhu Y, Ke J, Zhai Y, Huang M, Zhang X, He H, Zhang X, Zhao X, Guo K, Li X, Han Z, Zhang Y. Progression of m 6A in the tumor microenvironment: hypoxia, immune and metabolic reprogramming. Cell Death Discov 2024; 10:331. [PMID: 39033180 PMCID: PMC11271487 DOI: 10.1038/s41420-024-02092-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Recently, N6-methyladenosine (m6A) has aroused widespread discussion in the scientific community as a mode of RNA modification. m6A comprises writers, erasers, and readers, which regulates RNA production, nuclear export, and translation and is very important for human health. A large number of studies have found that the regulation of m6A is closely related to the occurrence and invasion of tumors, while the homeostasis and function of the tumor microenvironment (TME) determine the occurrence and development of tumors to some extent. TME is composed of a variety of immune cells (T cells, B cells, etc.) and nonimmune cells (tumor-associated mesenchymal stem cells (TA-MSCs), cancer-associated fibroblasts (CAFs), etc.). Current studies suggest that m6A is involved in regulating the function of various cells in the TME, thereby affecting tumor progression. In this manuscript, we present the composition of m6A and TME, the relationship between m6A methylation and characteristic changes in TME, the role of m6A methylation in TME, and potential therapeutic strategies to provide new perspectives for better treatment of tumors in clinical work.
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Affiliation(s)
- Xuan Han
- First Clinical College of Changzhi Medical College, Changzhi, China
| | - Yu Zhu
- Linfen Central Hospital, Linfen, China
| | - Juan Ke
- Linfen Central Hospital, Linfen, China
| | | | - Min Huang
- Linfen Central Hospital, Linfen, China
| | - Xin Zhang
- Linfen Central Hospital, Linfen, China
| | | | | | | | | | | | - Zhongyu Han
- School of Medicine and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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2
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Sighel D, Destefanis E, Quattrone A. Therapeutic strategies to target the epitranscriptomic machinery. Curr Opin Genet Dev 2024; 87:102230. [PMID: 39024774 DOI: 10.1016/j.gde.2024.102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Altered RNA modification patterns and dysregulated expression of epitranscriptomic machinery proteins (EMPs) have been causatively correlated with several diseases. Modulation of EMP gene expression has shown promise in reversing disease-associated phenotypes, making EMPs attractive therapeutic targets. Various therapeutic strategies, including small-molecule modulators, proteolysis-targeting chimeras, and molecular tools for site-specific engineering of RNA modifications, have been introduced to modulate EMPs and RNA modifications themselves and are currently being investigated to enrich the physician's armamentarium. At the forefront of research are small-molecule inhibitors of the key players involved in the N6-methyladenosine RNA modification, with an inhibitor of methyltransferase 3 in clinical trials. Preclinical studies have also demonstrated proof-of-concept for the other approaches, raising expectations for this exciting new frontier of therapy.
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Affiliation(s)
- Denise Sighel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy. https://twitter.com/@DSighel
| | - Eliana Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy. https://twitter.com/@Destefanis_E
| | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy.
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3
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Yang H, Patel DJ. Structures, mechanisms and applications of RNA-centric CRISPR-Cas13. Nat Chem Biol 2024; 20:673-688. [PMID: 38702571 DOI: 10.1038/s41589-024-01593-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/27/2024] [Indexed: 05/06/2024]
Abstract
Prokaryotes are equipped with a variety of resistance strategies to survive frequent viral attacks or invading mobile genetic elements. Among these, CRISPR-Cas surveillance systems are abundant and have been studied extensively. This Review focuses on CRISPR-Cas type VI Cas13 systems that use single-subunit RNA-guided Cas endonucleases for targeting and subsequent degradation of foreign RNA, thereby providing adaptive immunity. Notably, distinct from single-subunit DNA-cleaving Cas9 and Cas12 systems, Cas13 exhibits target RNA-activated substrate RNase activity. This Review outlines structural, biochemical and cell biological studies toward elucidation of the unique structural and mechanistic principles underlying surveillance effector complex formation, precursor CRISPR RNA (pre-crRNA) processing, self-discrimination and RNA degradation in Cas13 systems as well as insights into suppression by bacteriophage-encoded anti-CRISPR proteins and regulation by endogenous accessory proteins. Owing to its programmable ability for RNA recognition and cleavage, Cas13 provides powerful RNA targeting, editing, detection and imaging platforms with emerging biotechnological and therapeutic applications.
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Affiliation(s)
- Hui Yang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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4
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Cerneckis J, Ming GL, Song H, He C, Shi Y. The rise of epitranscriptomics: recent developments and future directions. Trends Pharmacol Sci 2024; 45:24-38. [PMID: 38103979 PMCID: PMC10843569 DOI: 10.1016/j.tips.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023]
Abstract
The epitranscriptomics field has undergone tremendous growth since the discovery that the RNA N6-methyladenosine (m6A) modification is reversible and is distributed throughout the transcriptome. Efforts to map RNA modifications transcriptome-wide and reshape the epitranscriptome in disease settings have facilitated mechanistic understanding and drug discovery in the field. In this review we discuss recent advancements in RNA modification detection methods and consider how these developments can be applied to gain novel insights into the epitranscriptome. We also highlight drug discovery efforts aimed at developing epitranscriptomic therapeutics for cancer and other diseases. Finally, we consider engineering of the epitranscriptome as an emerging direction to investigate RNA modifications and their causal effects on RNA processing at high specificity.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Department of Cell and Developmental Biology, Department of Psychiatry, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Department of Cell and Developmental Biology, the Epigenetics Institute, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, the University of Chicago, Chicago, IL 60637, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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5
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Wang B, Yang H. Progress of CRISPR-based programmable RNA manipulation and detection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1804. [PMID: 37282821 DOI: 10.1002/wrna.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Prokaryotic clustered regularly interspaced short palindromic repeats and CRISPR associated (CRISPR-Cas) systems provide adaptive immunity by using RNA-guided endonucleases to recognize and eliminate invading foreign nucleic acids. Type II Cas9, type V Cas12, type VI Cas13, and type III Csm/Cmr complexes have been well characterized and developed as programmable platforms for selectively targeting and manipulating RNA molecules of interest in prokaryotic and eukaryotic cells. These Cas effectors exhibit remarkable diversity of ribonucleoprotein (RNP) composition, target recognition and cleavage mechanisms, and self discrimination mechanisms, which are leveraged for various RNA targeting applications. Here, we summarize the current understanding of mechanistic and functional characteristics of these Cas effectors, give an overview on RNA detection and manipulation toolbox established so far including knockdown, editing, imaging, modification, and mapping RNA-protein interactions, and discuss the future directions for CRISPR-based RNA targeting tools. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Beibei Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Hui Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
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6
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Huang L, Wang Q, Gu S, Cao N. Integrated metabolic and epigenetic mechanisms in cardiomyocyte proliferation. J Mol Cell Cardiol 2023; 181:79-88. [PMID: 37331466 DOI: 10.1016/j.yjmcc.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023]
Abstract
Heart disease continues to be the leading cause of mortality worldwide, primarily attributed to the restricted regenerative potential of the adult human heart following injury. In contrast to their adult counterparts, many neonatal mammals can spontaneously regenerate their myocardium in the first few days of life via extensive proliferation of the pre-existing cardiomyocytes. Reasons for the decline in regenerative capacity during postnatal development, and how to control it, remain largely unexplored. Accumulated evidence suggests that the preservation of regenerative potential depends on a conducive metabolic state in the embryonic and neonatal heart. Along with the postnatal increase in oxygenation and workload, the mammalian heart undergoes a metabolic transition, shifting its primary metabolic substrate from glucose to fatty acids shortly after birth for energy advantage. This metabolic switch causes cardiomyocyte cell-cycle arrest, which is widely regarded as a key mechanism for the loss of regenerative capacity. Beyond energy provision, emerging studies have suggested a link between this intracellular metabolism dynamics and postnatal epigenetic remodeling of the mammalian heart that reshapes the expression of many genes important for cardiomyocyte proliferation and cardiac regeneration, since many epigenetic enzymes utilize kinds of metabolites as obligate cofactors or substrates. This review summarizes the current state of knowledge of metabolism and metabolite-mediated epigenetic modifications in cardiomyocyte proliferation, with a particular focus on highlighting the potential therapeutic targets that hold promise to treat human heart failure via metabolic and epigenetic regulations.
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Affiliation(s)
- Liying Huang
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China
| | - Qiyuan Wang
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China
| | - Shanshan Gu
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China
| | - Nan Cao
- Zhongshan School of Medicine and the Seventh Affiliated Hospital, Sun Yat-Sen University, Guangdong 510080, China; Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China.
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7
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Deacon S, Walker L, Radhi M, Smith S. The Regulation of m6A Modification in Glioblastoma: Functional Mechanisms and Therapeutic Approaches. Cancers (Basel) 2023; 15:3307. [PMID: 37444417 DOI: 10.3390/cancers15133307] [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: 05/30/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Glioblastoma is the most prevalent primary brain tumour and invariably confers a poor prognosis. The immense intra-tumoral heterogeneity of glioblastoma and its ability to rapidly develop treatment resistance are key barriers to successful therapy. As such, there is an urgent need for the greater understanding of the tumour biology in order to guide the development of novel therapeutics in this field. N6-methyladenosine (m6A) is the most abundant of the RNA modifications in eukaryotes. Studies have demonstrated that the regulation of this RNA modification is altered in glioblastoma and may serve to regulate diverse mechanisms including glioma stem-cell self-renewal, tumorigenesis, invasion and treatment evasion. However, the precise mechanisms by which m6A modifications exert their functional effects are poorly understood. This review summarises the evidence for the disordered regulation of m6A in glioblastoma and discusses the downstream functional effects of m6A modification on RNA fate. The wide-ranging biological consequences of m6A modification raises the hope that novel cancer therapies can be targeted against this mechanism.
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Affiliation(s)
- Simon Deacon
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | - Lauryn Walker
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Masar Radhi
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stuart Smith
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
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8
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Chen ZB, He M, Li JYS, Shyy JYJ, Chien S. Epitranscriptional Regulation: From the Perspectives of Cardiovascular Bioengineering. Annu Rev Biomed Eng 2023; 25:157-184. [PMID: 36913673 DOI: 10.1146/annurev-bioeng-081922-021233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The central dogma of gene expression involves DNA transcription to RNA and RNA translation into protein. As key intermediaries and modifiers, RNAs undergo various forms of modifications such as methylation, pseudouridylation, deamination, and hydroxylation. These modifications, termed epitranscriptional regulations, lead to functional changes in RNAs. Recent studies have demonstrated crucial roles for RNA modifications in gene translation, DNA damage response, and cell fate regulation. Epitranscriptional modifications play an essential role in development, mechanosensing, atherogenesis, and regeneration in the cardiovascular (CV) system, and their elucidation is critically important to understanding the molecular mechanisms underlying CV physiology and pathophysiology. This review aims at providing biomedical engineers with an overview of the epitranscriptome landscape, related key concepts, recent findings in epitranscriptional regulations, and tools for epitranscriptome analysis. The potential applications of this important field in biomedical engineering research are discussed.
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Affiliation(s)
- Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Ming He
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Julie Yi-Shuan Li
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
| | - John Y-J Shyy
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Shu Chien
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
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9
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Liu S, Chen S, Tang C, Zhao Y, Cui W, Jia L, Wang L. The emerging therapeutic target of dynamic and reversible N6-methyladenosine modification during cancer development. Front Oncol 2022; 12:970833. [PMID: 36226062 PMCID: PMC9548694 DOI: 10.3389/fonc.2022.970833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
As a reversible and dynamic epigenetic modification, N6-methyladenosine (m6A) modification is ubiquitous in eukaryotic cells. m6A methylation is prevalent in almost all RNA metabolism processes that affect the fate of cells, including cancer development. As indicated by the available evidence, targeting m6A regulators may play a crucial role in tumor therapy and multidrug resistance. Currently, many questions remain uncovered. Here, we review recent studies on m6A modification in various aspects of tumor progression, tumor immunity, multidrug resistance, and therapeutic targets to provide new insight into the m6A methylation process.
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Affiliation(s)
- Shougeng Liu
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, China
| | - Sihong Chen
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, China
| | - Chengfang Tang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, China
| | - Yingxi Zhao
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, China
| | - Wei Cui
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
| | - Lina Jia
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, China
- *Correspondence: Lihui Wang, ; Lina Jia,
| | - Lihui Wang
- Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, China
- Benxi Institute of Pharmaceutical Research, Shenyang Pharmaceutical University, Shenyang, China
- *Correspondence: Lihui Wang, ; Lina Jia,
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10
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Zhang F, Liu H, Duan M, Wang G, Zhang Z, Wang Y, Qian Y, Yang Z, Jiang X. Crosstalk among m6A RNA methylation, hypoxia and metabolic reprogramming in TME: from immunosuppressive microenvironment to clinical application. J Hematol Oncol 2022; 15:84. [PMID: 35794625 PMCID: PMC9258089 DOI: 10.1186/s13045-022-01304-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 12/13/2022] Open
Abstract
The tumor microenvironment (TME), which is regulated by intrinsic oncogenic mechanisms and epigenetic modifications, has become a research hotspot in recent years. Characteristic features of TME include hypoxia, metabolic dysregulation, and immunosuppression. One of the most common RNA modifications, N6-methyladenosine (m6A) methylation, is widely involved in the regulation of physiological and pathological processes, including tumor development. Compelling evidence indicates that m6A methylation regulates transcription and protein expression through shearing, export, translation, and processing, thereby participating in the dynamic evolution of TME. Specifically, m6A methylation-mediated adaptation to hypoxia, metabolic dysregulation, and phenotypic shift of immune cells synergistically promote the formation of an immunosuppressive TME that supports tumor proliferation and metastasis. In this review, we have focused on the involvement of m6A methylation in the dynamic evolution of tumor-adaptive TME and described the detailed mechanisms linking m6A methylation to change in tumor cell biological functions. In view of the collective data, we advocate treating TME as a complete ecosystem in which components crosstalk with each other to synergistically achieve tumor adaptive changes. Finally, we describe the potential utility of m6A methylation-targeted therapies and tumor immunotherapy in clinical applications and the challenges faced, with the aim of advancing m6A methylation research.
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11
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Tatekawa S, Tamari K, Chijimatsu R, Konno M, Motooka D, Mitsufuji S, Akita H, Kobayashi S, Murakumo Y, Doki Y, Eguchi H, Ishii H, Ogawa K. N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. Sci Rep 2022; 12:11074. [PMID: 35773310 PMCID: PMC9246847 DOI: 10.1038/s41598-022-15196-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/20/2022] [Indexed: 12/20/2022] Open
Abstract
In pancreatic cancer, methyltransferase-like 3 (METTL3), a N(6)-methyladenosine (m6A) methyltransferase, has a favorable effect on tumors and is a risk factor for patients' prognosis. However, the details of what genes are regulated by METTL3 remain unknown. Several RNAs are methylated, and what genes are favored in pancreatic cancer remains unclear. By epitranscriptomic analysis, we report that polo-like kinase 1 (PLK1) is an important hub gene defining patient prognosis in pancreatic cancer and that RNA methylation is involved in regulating its cell cycle-specific expression. We found that insulin like growth factor 2 mRNA binding protein 2 (IGF2BP2) binds to m6A of PLK1 3' untranslated region and is involved in upregulating PLK1 expression and that demethylation of this site activates the ataxia telangiectasia and Rad3-related protein pathway by replicating stress and increasing mitotic catastrophe, resulting in increased radiosensitivity. This suggests that PLK1 methylation is essential for cell cycle maintenance in pancreatic cancer and is a new therapeutic target.
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Affiliation(s)
- Shotaro Tatekawa
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Keisuke Tamari
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Ryota Chijimatsu
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
| | - Masamitsu Konno
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan
- Division of Tumor Biology, Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, Noda, Chiba, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Suguru Mitsufuji
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hirofumi Akita
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shogo Kobayashi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yoshiki Murakumo
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Center of Medical Innovation and Translational Research, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan.
| | - Kazuhiko Ogawa
- Department of Radiation Oncology, Osaka University Graduate School of Medicine, Yamadaoka 2-2, Suita, Osaka, 565-0871, Japan.
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12
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Li L, Xu N, Liu J, Chen Z, Liu X, Wang J. m6A Methylation in Cardiovascular Diseases: From Mechanisms to Therapeutic Potential. Front Genet 2022; 13:908976. [PMID: 35836571 PMCID: PMC9274458 DOI: 10.3389/fgene.2022.908976] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023] Open
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide. Recent studies have shown that n6-methyladenosine (m6A) plays a major role in cardiovascular homeostasis and pathophysiology. These studies have confirmed that m6A methylation affects the pathophysiology of cardiovascular diseases by regulating cellular processes such as differentiation, proliferation, inflammation, autophagy, and apoptosis. Moreover, plenty of research has confirmed that m6A modification can delay the progression of CVD via the post-transcriptional regulation of RNA. However, there are few available summaries of m6A modification regarding CVD. In this review, we highlight advances in CVD-specific research concerning m6A modification, summarize the mechanisms underlying the involvement of m6A modification during the development of CVD, and discuss the potential of m6A modification as a therapeutic target of CVD.
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Affiliation(s)
| | | | | | | | | | - Junnan Wang
- Department of Cardiology, Second Hospital of Jilin University, Changchun, China
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13
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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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14
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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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15
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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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16
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Zhang Q, Xu K. The role of regulators of RNA m6A methylation in lung cancer. Genes Dis 2022; 10:495-504. [DOI: 10.1016/j.gendis.2021.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
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17
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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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18
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Tang T, Han Y, Wang Y, Huang H, Qian P. Programmable System of Cas13-Mediated RNA Modification and Its Biological and Biomedical Applications. Front Cell Dev Biol 2021; 9:677587. [PMID: 34386490 PMCID: PMC8353156 DOI: 10.3389/fcell.2021.677587] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13 has drawn broad interest to control gene expression and cell fate at the RNA level in general. Apart from RNA interference mediated by its endonuclease activity, the nuclease-deactivated form of Cas13 further provides a versatile RNA-guided RNA-targeting platform for manipulating kinds of RNA modifications post-transcriptionally. Chemical modifications modulate various aspects of RNA fate, including translation efficiency, alternative splicing, RNA–protein affinity, RNA–RNA interaction, RNA stability and RNA translocation, which ultimately orchestrate cellular biologic activities. This review summarizes the history of the CRISPR-Cas13 system, fundamental components of RNA modifications and the related physiological and pathological functions. We focus on the development of epi-transcriptional editing toolkits based on catalytically inactive Cas13, including RNA Editing for Programmable A to I Replacement (REPAIR) and xABE (adenosine base editor) for adenosine deamination, RNA Editing for Specific C-to-U Exchange (RESCUE) and xCBE (cytidine base editor) for cytidine deamination and dm6ACRISPR, as well as the targeted RNA methylation (TRM) and photoactivatable RNA m6A editing system using CRISPR-dCas13 (PAMEC) for m6A editing. We further highlight the emerging applications of these useful toolkits in cell biology, disease and imaging. Finally, we discuss the potential limitations, such as off-target editing, low editing efficiency and limitation for AAV delivery, and provide possible optimization strategies.
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Affiliation(s)
- Tian Tang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
| | - Yingli Han
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
| | - Yuran Wang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
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19
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Stroppel AS, Lappalainen R, Stafforst T. Controlling Site-Directed RNA Editing by Chemically Induced Dimerization. Chemistry 2021; 27:12300-12304. [PMID: 34169589 PMCID: PMC8456898 DOI: 10.1002/chem.202101985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Various RNA‐targeting approaches have been engineered to modify specific sites on endogenous transcripts, breaking new ground for a variety of basic research tools and promising clinical applications in the future. Here, we combine site‐directed adenosine‐to‐inosine RNA editing with chemically induced dimerization. Specifically, we achieve tight and dose‐dependent control of the editing reaction with gibberellic acid, and obtain editing yields up to 20 % and 44 % in the endogenous STAT1 and GAPDH transcript in cell culture. Furthermore, the disease‐relevant MECP2 R106Q mutation was repaired with editing yields up to 42 %. The introduced principle will enable new applications where temporal or spatiotemporal control of an RNA‐targeting mechanism is desired.
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Affiliation(s)
- Anna S Stroppel
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Ruth Lappalainen
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
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20
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Stroppel AS, Latifi N, Hanswillemenke A, Tasakis RN, Papavasiliou FN, Stafforst T. Harnessing self-labeling enzymes for selective and concurrent A-to-I and C-to-U RNA base editing. Nucleic Acids Res 2021; 49:e95. [PMID: 34197596 PMCID: PMC8450088 DOI: 10.1093/nar/gkab541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/05/2021] [Accepted: 06/18/2021] [Indexed: 12/26/2022] Open
Abstract
The SNAP-ADAR tool enables precise and efficient A-to-I RNA editing in a guideRNA-dependent manner by applying the self-labeling SNAP-tag enzyme to generate RNA-guided editases in cell culture. Here, we extend this platform by combining the SNAP-tagged tool with further effectors steered by the orthogonal HALO-tag. Due to their small size (ca. 2 kb), both effectors are readily integrated into one genomic locus. We demonstrate selective and concurrent recruitment of ADAR1 and ADAR2 deaminase activity for optimal editing with extended substrate scope and moderate global off-target effects. Furthermore, we combine the recruitment of ADAR1 and APOBEC1 deaminase activity to achieve selective and concurrent A-to-I and C-to-U RNA base editing of endogenous transcripts inside living cells, again with moderate global off-target effects. The platform should be readily transferable to further epitranscriptomic writers and erasers to manipulate epitranscriptomic marks in a programmable way with high molecular precision.
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Affiliation(s)
- Anna S Stroppel
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Ngadhnjim Latifi
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Alfred Hanswillemenke
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Rafail Nikolaos Tasakis
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - F Nina Papavasiliou
- Division of Immune Diversity (D150), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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21
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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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22
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Chen X, Zhao Q, Zhao Y, Chai G, Cheng W, Zhao Z, Wang J, Luo G, Cao N. Targeted RNA N 6 -Methyladenosine Demethylation Controls Cell Fate Transition in Human Pluripotent Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2003902. [PMID: 34105279 PMCID: PMC8188216 DOI: 10.1002/advs.202003902] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/14/2021] [Indexed: 05/17/2023]
Abstract
Deficiency of the N6 -methyladenosine (m6 A) methyltransferase complex results in global reduction of m6 A abundance and defective cell development in embryonic stem cells (ESCs). However, it's unclear whether regional m6 A methylation affects cell fate decisions due to the inability to modulate individual m6 A modification in ESCs with precise temporal control. Here, a targeted RNA m6 A erasure (TRME) system is developed to achieve site-specific demethylation of RNAs in human ESCs (hESCs). TRME, in which a stably transfected, doxycycline-inducible dCas13a is fused to the catalytic domain of ALKBH5, can precisely and reversibly demethylate the targeted m6 A site of mRNA and increase mRNA stability with limited off-target effects. It is further demonstrated that temporal m6 A erasure on a single site of SOX2 is sufficient to control the differentiation of hESCs. This study provides a versatile toolbox to reveal the function of individual m6 A modification in hESCs, enabling cell fate control studies at the epitranscriptional level.
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Affiliation(s)
- Xuena Chen
- The Seventh Affiliated HospitalZhongshan School of MedicineSun Yat‐sen UniversityGuangdong510080P.R. China
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat‐sen University)Ministry of EducationGuangdong510080P.R. China
| | - Qingquan Zhao
- The Seventh Affiliated HospitalZhongshan School of MedicineSun Yat‐sen UniversityGuangdong510080P.R. China
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat‐sen University)Ministry of EducationGuangdong510080P.R. China
| | - Yu‐Li Zhao
- MOE Key Laboratory of Gene Function and RegulationState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐sen UniversityGuangzhou510275P.R. China
| | - Guo‐Shi Chai
- MOE Key Laboratory of Gene Function and RegulationState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐sen UniversityGuangzhou510275P.R. China
| | - Weisheng Cheng
- The Seventh Affiliated HospitalZhongshan School of MedicineSun Yat‐sen UniversityGuangdong510080P.R. China
| | - Zhiju Zhao
- The Seventh Affiliated HospitalZhongshan School of MedicineSun Yat‐sen UniversityGuangdong510080P.R. China
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat‐sen University)Ministry of EducationGuangdong510080P.R. China
| | - Jia Wang
- The Seventh Affiliated HospitalZhongshan School of MedicineSun Yat‐sen UniversityGuangdong510080P.R. China
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat‐sen University)Ministry of EducationGuangdong510080P.R. China
| | - Guan‐Zheng Luo
- MOE Key Laboratory of Gene Function and RegulationState Key Laboratory of BiocontrolSchool of Life SciencesSun Yat‐sen UniversityGuangzhou510275P.R. China
| | - Nan Cao
- The Seventh Affiliated HospitalZhongshan School of MedicineSun Yat‐sen UniversityGuangdong510080P.R. China
- Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat‐sen University)Ministry of EducationGuangdong510080P.R. China
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23
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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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24
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Levi O, Arava YS. RNA modifications as a common denominator between tRNA and mRNA. Curr Genet 2021; 67:545-551. [PMID: 33683402 DOI: 10.1007/s00294-021-01168-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022]
Abstract
Recent studies underscore RNA modifications as a novel mechanism to coordinate expression and function of different genes. While modifications on the sugar or base moieties of tRNA are well known, their roles in mRNA regulation are only starting to emerge. Interestingly, some modifications are present in both tRNA and mRNA, and here we discuss the functional significance of these common features. We describe key modifications that are present in both RNA types, elaborate on proteins that interact with them, and indicate recent works that identify roles in communicating tRNA processes and mRNA regulation. We propose that as tools are developed, the shortlist of features that are common between types of RNA will greatly expand and proteins that interact with them will be identified. In conclusion, the presence of the same modification in both RNA types provides an intersect between tRNA processes and mRNA regulation and implies a novel mechanism for connecting diverse cellular processes.
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Affiliation(s)
- Ofri Levi
- Faculty of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Yoav S Arava
- Faculty of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
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25
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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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26
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Rauch S, Jones KA, Dickinson BC. Small Molecule-Inducible RNA-Targeting Systems for Temporal Control of RNA Regulation. ACS CENTRAL SCIENCE 2020; 6:1987-1996. [PMID: 33274276 PMCID: PMC7706094 DOI: 10.1021/acscentsci.0c00537] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Indexed: 06/12/2023]
Abstract
All aspects of mRNA lifetime and function, including its stability, translation into protein, and trafficking through the cell, are tightly regulated through coordinated post-transcriptional modifications and interactions with a multitude of RNA effector proteins. Despite the increasing recognition of RNA regulation as a critical layer of mammalian gene expression control and its increasing excitement as a therapeutic target, tools to study and control RNA regulatory mechanisms with temporal precision in their endogenous environment are lacking. Here, we present small molecule-inducible RNA-targeting effectors based on our previously developed CRISPR/Cas-inspired RNA targeting system (CIRTS). The CIRTS biosensor platform is based on guide RNA (gRNA)-dependent RNA binding domains that interact with a target transcript using Watson-Crick-Franklin base pair interactions. Addition of a small molecule recruits an RNA effector to the target transcript, thereby eliciting a local effect on the transcript. In this work, we showcase that these CIRTS biosensors can trigger inducible RNA editing, degradation, or translation on target transcripts in a small molecule-dependent manner. We further go on to show that the CIRTS RNA base editor biosensor can induce RNA base editing in a small molecule-controllable manner in vivo. Collectively this work provides a new set of tools to probe the dynamics of RNA regulatory systems and control gene expression at the RNA level.
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Affiliation(s)
- Simone Rauch
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Krysten A. Jones
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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27
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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: 26] [Impact Index Per Article: 6.5] [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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28
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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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29
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Zheng HX, Sun X, Zhang XS, Sui N. m 6A Editing: New Tool to Improve Crop Quality? TRENDS IN PLANT SCIENCE 2020; 25:859-867. [PMID: 32376086 DOI: 10.1016/j.tplants.2020.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
N6-methyladenosine (m6A) is the most common type of eukaryotic mRNA modification. It plays an important role in regulating plant growth and development and stress resistance. m6A modification influences nearly all aspects of RNA metabolism and functionality and has great potential for improving crop quality. However, changing m6A modification levels as a whole may have unpredictable effects, making it impossible to accurately predict the effect of specific m6A modifications on RNA. In this opinion article, the main challenges and possible solutions for exploring m6A modification functions in plant systems are discussed. An m6A editing platform that uses new high-throughput methods to identify m6A modification at single-base resolution, and genome editing for selective editing of specific m6A sites for crop improvement is proposed.
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Affiliation(s)
- Hong-Xiang Zheng
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xi Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xian-Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, Shandong 250014, China.
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30
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Zhu ZM, Huo FC, Pei DS. Function and evolution of RNA N6-methyladenosine modification. Int J Biol Sci 2020; 16:1929-1940. [PMID: 32398960 PMCID: PMC7211178 DOI: 10.7150/ijbs.45231] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is identified as the most prevalent and abundant internal RNA modification, especially within eukaryotic mRNAs, which has attracted much attention in recent years since its importance for regulating gene expression and deciding cell fate. m6A modification is installed by RNA methyltransferases METTL3, METTL14 and WTAP (Writers), removed by the demethylases FTO and ALKBH5 (Erasers) and recognized by m6A binding proteins, such as YT521-B homology YTH domain-containing proteins (Readers). Accumulating evidence shows that m6A RNA methylation participates in almost all aspects of RNA processing, implying an association with important bioprocesses. In this review, we mainly summarize and discuss the functional relevance and importance of m6A modification in cellular processes.
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Affiliation(s)
- Zhi-Man Zhu
- Department of Pathology, Xuzhou Medical University, Xuzhou 221004, China
| | - Fu-Chun Huo
- Department of Pathology, Xuzhou Medical University, Xuzhou 221004, China
| | - Dong-Sheng Pei
- Department of Pathology, Xuzhou Medical University, Xuzhou 221004, China
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31
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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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32
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Liu L, Wang Y, Wu J, Liu J, Qin Z, Fan H. N 6-Methyladenosine: A Potential Breakthrough for Human Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:804-813. [PMID: 31958696 PMCID: PMC7005339 DOI: 10.1016/j.omtn.2019.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Among more than 100 types of identified RNA modification, N6-methyladenosine (m6A) modification is the predominant mRNA modification, which regulates RNA splicing, translocation, stability, and translation. m6A modification plays critical roles in the growth, differentiation, and metabolism of cells. As a dynamic and reversible modification, m6A is catalyzed by "writers" (RNA methyltransferases), removed by "erasers" (demethylases), and interacts with "readers" (m6A-binding proteins). With more advanced technology applied to research, the molecular mechanisms of RNA methyltransferase, demethylase, and m6A-binding protein have been revealed. An increasing number of studies have implicated the correlation between m6A modification and human cancers. In this review, we summarize that the occurrence and development of various human cancers are associated with aberrant m6A modification. We also discuss the progress in research related to m6A modification, providing novel therapeutic insight and potential breakthrough in anticancer therapy.
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Affiliation(s)
- Lina Liu
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China
| | - Yuwei Wang
- School of Stomatology, Qingdao University, Qingdao 266071, P.R. China
| | - Jie Wu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Jingwen Liu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China.
| | - Zongchang Qin
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
| | - Hong Fan
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
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33
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Chen M, Wong CM. The emerging roles of N6-methyladenosine (m6A) deregulation in liver carcinogenesis. Mol Cancer 2020; 19:44. [PMID: 32111216 PMCID: PMC7047367 DOI: 10.1186/s12943-020-01172-y] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is a common cancer worldwide. Although the etiological factors of liver carcinogenesis are well defined, the underlying molecular mechanisms remain largely elusive. Epigenetic deregulations, such as aberrant DNA methylation and histone modifications, play a critical role in liver carcinogenesis. Analogous to DNA and core histone proteins, reversible chemical modifications on mRNA have recently been recognized as important regulatory mechanisms to control gene expression. N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in mammalian cells. m6A modification is important for controlling many cellular and biological processes. Deregulation of m6A modification has been recently implicated in human carcinogenesis, including liver cancer. In this review, we summarize the recent findings on m6A regulation and its biological impacts in normal and cancer cells. We will focus on the deregulation of m6A modification and m6A regulators in liver diseases and liver cancers. We will highlight the clinical relevance of m6A deregulation in liver cancer. We will also discuss the potential of exploiting m6A modification for cancer diagnosis and therapeutics.
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Affiliation(s)
- Mengnuo Chen
- State Key Laboratory of Liver Research, the University of Hong Kong, Hong Kong, China
| | - Chun-Ming Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China.
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34
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Shinoda K, Suda A, Otonari K, Futaki S, Imanishi M. Programmable RNA methylation and demethylation using PUF RNA binding proteins. Chem Commun (Camb) 2020; 56:1365-1368. [DOI: 10.1039/c9cc09298f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new method manipulating local RNA methylation was developed by fusing the programmable RNA binding protein and the m6A demethylase or methyltransferase.
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Affiliation(s)
- Kouki Shinoda
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Akiyo Suda
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Kenko Otonari
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Shiroh Futaki
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Miki Imanishi
- Institute for Chemical Research
- Kyoto University
- Kyoto 611-0011
- Japan
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