201
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Milazzotto MP, de Lima CB, da Fonseca AM, dos Santos EC, Ispada J. Erasing gametes to write blastocysts: metabolism as the new player in epigenetic reprogramming. Anim Reprod 2020; 17:e20200015. [PMID: 33029209 PMCID: PMC7534565 DOI: 10.1590/1984-3143-ar2020-0015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding preimplantation embryonic development is crucial for the improvement of assisted reproductive technologies and animal production. To achieve this goal, it is important to consider that gametes and embryos are highly susceptible to environmental changes. Beyond the metabolic adaptation, the dynamic status imposed during follicular growth and early embryogenesis may create marks that will guide the molecular regulation during prenatal development, and consequently impact the offspring phenotype. In this context, metaboloepigenetics has gained attention, as it investigates the crosstalk between metabolism and molecular control, i.e., how substrates generated by metabolic pathways may also act as players of epigenetic modifications. In this review, we present the main metabolic and epigenetic events of pre-implantation development, and how these systems connect to open possibilities for targeted manipulation of reproductive technologies and animal production systems.
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Affiliation(s)
- Marcella Pecora Milazzotto
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Camila Bruna de Lima
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Département des Sciences Animales, Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Quebec, Canada
| | - Aldcejam Martins da Fonseca
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Erika Cristina dos Santos
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Jessica Ispada
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
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202
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Wang J, Lin H, Zhou M, Xiang Q, Deng Y, Luo L, Liu Y, Zhu Z, Zhao Z. The m6A methylation regulator-based signature for predicting the prognosis of prostate cancer. Future Oncol 2020; 16:2421-2432. [PMID: 32687727 DOI: 10.2217/fon-2020-0330] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To construct a survival prediction signature for prostate cancer (PC) based on the RNA N6-methyladenosine (m6A) methylation regulator. Materials & methods: This paper explores the interaction network of differentially expressed m6A RNA methylation regulators in PC by Pearson correlation analysis. Univariate Cox risk regression and LASSO regression analysis were used to construct a predictive signature of PC. Kaplan-Meier survival analysis compared the overall survival of the high- and low-risk groups. Results & Conclusion: We first constructed a prognostic two gene signature for PC based on the m6A RNA methylation regulators MRTTL14 and YTHDF2. The interaction network of m6A RNA methylation regulators in PC was also established.
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Affiliation(s)
- Jiamin Wang
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Han Lin
- Department of Gynecology of Traditional Chinese Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Mingda Zhou
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Qian Xiang
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Yihan Deng
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Lianmin Luo
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Yangzhou Liu
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Zhiguo Zhu
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
| | - Zhigang Zhao
- Department of Urology & Andrology, Minimally Invasive Surgery Center, Guangdong Provincial Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, PR China
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203
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Abstract
As a unique subpopulation of cancer cells, cancer stem cells (CSCs) acquire the resistance to conventional therapies and appear to be the prime cause of cancer recurrence. Like their normal counterparts, CSCs can renew themselves and generate differentiated progenies. Cancer stem cells are distinguished among heterogenous cancer cells by molecular markers and their capacity of efficiently forming new tumors composed of diverse and heterogenous cancer cells. Tumor heterogeneity can be inter- or intra-tumor, molecularly resulting from the accumulation of genetic and non-genetic alterations. Non-genetic alterations are mainly changes on epigenetic modifications of DNA and histone, and chromatin remodeling. As tumor-initiating cells and contributing to the tumor heterogeneity in the brain, glioblastoma stem cells (GSCs) attract extensive research interests. Epigenetic modifications confer on tumor cells including CSCs reversible and inheritable genomic changes and affect gene expression without alteration in DNA sequence. Here, we will review recent advances in histone demethylation, DNA methylation, RNA methylation and ubiquitination in glioblastomas and their impacts on tumorigenesis with a focus on CSCs.
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Affiliation(s)
- Kezhou Zhu
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Victoria Xie
- M.D. Program, Baylor College of Medicine, Houston, TX, United States
| | - Suyun Huang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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204
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Wang J, Wang WA, Zhang A, Liu HB. Molecular mechanism of methyltransferase-like protein family: Relationship with gastric cancer. Shijie Huaren Xiaohua Zazhi 2020; 28:428-434. [DOI: 10.11569/wcjd.v28.i11.428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methyltransferase-like proteins (METTL) are part of a large protein family, which is characterized by the presence of an S-adenosylmethionine (SAM; a common substrate for methylation reactions) binding domain. Although members of this protein family have been shown or predicted as methyltransferases of RNA, DNA, or proteins, most methyltransferases are still poorly characterized. Identifying the complexes where these potential enzymes work can help to understand their function and substrate specificity. The METTL protein family is closely related to the occurrence and development of gastric cancer (GC), and its relationship with GC is of great importance in the diagnosis, treatment, and prognosis of GC. Here we give a systematic and comprehensive review of the mechanism of METTL protein family and its relationship with GC, with an aim to provide important resources for further research on these potential new methyltransferases and the diagnosis and treatment of GC.
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Affiliation(s)
- Jing Wang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - Wen-An Wang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - An Zhang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - Hong-Bin Liu
- People's Liberation Army Joint Logistics Support Unit 940 Hospital, Lanzhou 730000, Gansu Province, China
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205
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Chen Y, Lin Y, Shu Y, He J, Gao W. Interaction between N 6-methyladenosine (m 6A) modification and noncoding RNAs in cancer. Mol Cancer 2020; 19:94. [PMID: 32443966 PMCID: PMC7243333 DOI: 10.1186/s12943-020-01207-4] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
As a critical internal RNA modification in higher eukaryotes, N6-methyladenosine (m6A) has become the hotspot of epigenetics research in recent years. Extensive studies on messenger RNAs have revealed that m6A affects RNA fate and cell functions in various bioprocesses, such as RNA splicing, export, translation, and stability, some of which seem to be directly or indirectly regulated by noncoding RNAs. Intriguingly, abundant noncoding RNAs such as microRNAs, long noncoding RNAs, circular RNAs, small nuclear RNAs, and ribosomal RNAs are also highly modified with m6A and require m6A modification for their biogenesis and functions. Here, we discuss the interaction between m6A modification and noncoding RNAs by focusing on the functional relevance of m6A in cancer progression, metastasis, drug resistance, and immune response. Furthermore, the investigation of m6A regulatory proteins and its inhibitors provides new opportunities for early diagnosis and effective treatment of cancer, especially in combination with immunotherapy.
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Affiliation(s)
- Yi Chen
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yu Lin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Jing He
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Wen Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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206
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Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL, Roignant JY. The 18S ribosomal RNA m 6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep 2020; 21:e49443. [PMID: 32350990 DOI: 10.15252/embr.201949443] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently emerged as an important layer of gene regulation. N6-methyladenosine (m6 A) is the most prominent modification on eukaryotic messenger RNA and has also been found on noncoding RNA, including ribosomal and small nuclear RNA. Recently, several m6 A methyltransferases were identified, uncovering the specificity of m6 A deposition by structurally distinct enzymes. In order to discover additional m6 A enzymes, we performed an RNAi screen to deplete annotated orthologs of human methyltransferase-like proteins (METTLs) in Drosophila cells and identified CG9666, the ortholog of human METTL5. We show that CG9666 is required for specific deposition of m6 A on 18S ribosomal RNA via direct interaction with the Drosophila ortholog of human TRMT112, CG12975. Depletion of CG9666 yields a subsequent loss of the 18S rRNA m6 A modification, which lies in the vicinity of the ribosome decoding center; however, this does not compromise rRNA maturation. Instead, a loss of CG9666-mediated m6 A impacts fly behavior, providing an underlying molecular mechanism for the reported human phenotype in intellectual disability. Thus, our work expands the repertoire of m6 A methyltransferases, demonstrates the specialization of these enzymes, and further addresses the significance of ribosomal RNA modifications in gene expression and animal behavior.
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Affiliation(s)
| | | | | | - Ludivine Wacheul
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Minh Anh Vu
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Pablo Mier
- Faculty of Biology, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | | | - Marc Graille
- BIOC, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Denis Lj Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Mainz, Germany.,Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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207
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The rRNA m 6A methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev 2020; 34:715-729. [PMID: 32217665 PMCID: PMC7197354 DOI: 10.1101/gad.333369.119] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Abstract
Covalent chemical modifications of cellular RNAs directly impact all biological processes. However, our mechanistic understanding of the enzymes catalyzing these modifications, their substrates and biological functions, remains vague. Amongst RNA modifications N6-methyladenosine (m6A) is widespread and found in messenger (mRNA), ribosomal (rRNA), and noncoding RNAs. Here, we undertook a systematic screen to uncover new RNA methyltransferases. We demonstrate that the methyltransferase-like 5 (METTL5) protein catalyzes m6A in 18S rRNA at position A1832 We report that absence of Mettl5 in mouse embryonic stem cells (mESCs) results in a decrease in global translation rate, spontaneous loss of pluripotency, and compromised differentiation potential. METTL5-deficient mice are born at non-Mendelian rates and develop morphological and behavioral abnormalities. Importantly, mice lacking METTL5 recapitulate symptoms of patients with DNA variants in METTL5, thereby providing a new mouse disease model. Overall, our biochemical, molecular, and in vivo characterization highlights the importance of m6A in rRNA in stemness, differentiation, development, and diseases.
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208
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O-GlcNAcylation regulates the methionine cycle to promote pluripotency of stem cells. Proc Natl Acad Sci U S A 2020; 117:7755-7763. [PMID: 32193337 DOI: 10.1073/pnas.1915582117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Methionine metabolism is critical for the maintenance of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) pluripotency. However, little is known about the regulation of the methionine cycle to sustain ESC pluripotency. Here, we show that adenosylhomocysteinase (AHCY), an important enzyme in the methionine cycle, is critical for the maintenance and differentiation of mouse embryonic stem cells (mESCs). We show that mESCs exhibit high levels of methionine metabolism, whereas decreasing methionine metabolism via depletion of AHCY promotes mESCs to differentiate into the three germ layers. AHCY is posttranslationally modified with an O-linked β-N-acetylglucosamine sugar (O-GlcNAcylation), which is rapidly removed upon differentiation. O-GlcNAcylation of threonine 136 on AHCY increases its activity and is important for the maintenance of trimethylation of histone H3 lysine 4 (H3K4me3) to sustain mESC pluripotency. Blocking glycosylation of AHCY decreases the ratio of S-adenosylmethionine versus S-adenosylhomocysteine (SAM/SAH), reduces the level of H3K4me3, and poises mESC for differentiation. In addition, blocking glycosylation of AHCY reduces somatic cell reprogramming. Thus, our findings reveal a critical role of AHCY and a mechanistic understanding of O-glycosylation in regulating ESC pluripotency and differentiation.
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209
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He RZ, Jiang J, Luo DX. The functions of N6-methyladenosine modification in lncRNAs. Genes Dis 2020; 7:598-605. [PMID: 33335959 PMCID: PMC7729116 DOI: 10.1016/j.gendis.2020.03.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/05/2020] [Accepted: 03/08/2020] [Indexed: 01/08/2023] Open
Abstract
Increasing evidence indicates that mRNAs are often subject to posttranscriptional modifications. Among them, N6-methyladenosine (m6A), which has been shown to play key roles in RNA splicing, stability, nuclear export, and translation, is the most abundant modification of RNA. Extensive studies of m6A modification of mRNAs have been carried out, while little is known about m6A modification of long non-coding RNAs (lncRNAs). Recently, several studies reported m6A modification of lncRNAs. In this review, we focus on these m6A-modified lncRNAs and discuss possible functions of m6A modification.
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Affiliation(s)
- Rong-Zhang He
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China.,Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China
| | - Jing Jiang
- Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China.,Center for Clinical Pathology, The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, People's Republic of China
| | - Di-Xian Luo
- Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China.,Center for Clinical Pathology, The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, People's Republic of China
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210
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Huang H, Weng H, Chen J. m 6A Modification in Coding and Non-coding RNAs: Roles and Therapeutic Implications in Cancer. Cancer Cell 2020; 37:270-288. [PMID: 32183948 PMCID: PMC7141420 DOI: 10.1016/j.ccell.2020.02.004] [Citation(s) in RCA: 723] [Impact Index Per Article: 180.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Abstract
N6-Methyladenosine (m6A) RNA modification has emerged in recent years as a new layer of regulatory mechanism controlling gene expression in eukaryotes. As a reversible epigenetic modification found not only in messenger RNAs but also in non-coding RNAs, m6A affects the fate of the modified RNA molecules and plays important roles in almost all vital bioprocesses, including cancer development. Here we review the up-to-date knowledge of the pathological roles and underlying molecular mechanism of m6A modifications (in both coding and non-coding RNAs) in cancer pathogenesis and drug response/resistance, and discuss the therapeutic potential of targeting m6A regulators for cancer therapy.
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Affiliation(s)
- Huilin Huang
- Department of Systems Biology & the Gehr Family Center for Leukemia Research, the Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Hengyou Weng
- Department of Systems Biology & the Gehr Family Center for Leukemia Research, the Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Jianjun Chen
- Department of Systems Biology & the Gehr Family Center for Leukemia Research, the Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA.
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211
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Boo SH, Kim YK. The emerging role of RNA modifications in the regulation of mRNA stability. Exp Mol Med 2020; 52:400-408. [PMID: 32210357 PMCID: PMC7156397 DOI: 10.1038/s12276-020-0407-z] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 01/02/2023] Open
Abstract
Many studies have highlighted the importance of the tight regulation of mRNA stability in the control of gene expression. mRNA stability largely depends on the mRNA nucleotide sequence, which affects the secondary and tertiary structures of the mRNAs, and the accessibility of various RNA-binding proteins to the mRNAs. Recent advances in high-throughput RNA-sequencing techniques have resulted in the elucidation of the important roles played by mRNA modifications and mRNA nucleotide sequences in regulating mRNA stability. To date, hundreds of different RNA modifications have been characterized. Among them, several RNA modifications, including N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am), 8-oxo-7,8-dihydroguanosine (8-oxoG), pseudouridine (Ψ), 5-methylcytidine (m5C), and N4-acetylcytidine (ac4C), have been shown to regulate mRNA stability, consequently affecting diverse cellular and biological processes. In this review, we discuss our current understanding of the molecular mechanisms underlying the regulation of mammalian mRNA stability by various RNA modifications.
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Affiliation(s)
- Sung Ho Boo
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, 02841, Republic of Korea
- Division of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, 02841, Republic of Korea.
- Division of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
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212
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Nance DJ, Satterwhite ER, Bhaskar B, Misra S, Carraway KR, Mansfield KD. Characterization of METTL16 as a cytoplasmic RNA binding protein. PLoS One 2020; 15:e0227647. [PMID: 31940410 PMCID: PMC6961929 DOI: 10.1371/journal.pone.0227647] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022] Open
Abstract
mRNA modification by N6-methyladenosine (m6A) is involved in many post-transcriptional regulation processes including mRNA stability, splicing and promotion of translation. Accordingly, the recently identified mRNA methylation complex containing METTL3, METTL14, and WTAP has been the subject of intense study. However, METTL16 (METT10D) has also been identified as an RNA m6A methyltransferase that can methylate both coding and noncoding RNAs, but its biological role remains unclear. While global studies have identified many potential RNA targets of METTL16, only a handful, including the long noncoding RNA MALAT1, the snRNA U6, as well as the mRNA MAT2A have been verified and/or studied to any great extent. In this study we identified/verified METTL16 targets by immunoprecipitation of both endogenous as well as exogenous FLAG-tagged protein. Interestingly, exogenously overexpressed METTL16 differed from the endogenous protein in its relative affinity for RNA targets which prompted us to investigate METTL16's localization within the cell. Surprisingly, biochemical fractionation revealed that a majority of METTL16 protein resides in the cytoplasm of a number of cells. Furthermore, siRNA knockdown of METTL16 resulted in expression changes of a few mRNA targets suggesting that METTL16 may play a role in regulating gene expression. Thus, while METTL16 has been reported to be a nuclear protein, our findings suggest that METTL16 is also a cytoplasmic methyltransferase that may alter its RNA binding preferences depending on its cellular localization. Future studies will seek to confirm differences between cytoplasmic and nuclear RNA targets in addition to exploring the physiological role of METTL16 through long-term knockdown.
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Affiliation(s)
- Daniel J. Nance
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Emily R. Satterwhite
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Brinda Bhaskar
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Sway Misra
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Kristen R. Carraway
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Kyle D. Mansfield
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
- * E-mail:
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213
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Luo JH, Wang Y, Wang M, Zhang LY, Peng HR, Zhou YY, Jia GF, He Y. Natural Variation in RNA m 6A Methylation and Its Relationship with Translational Status. PLANT PHYSIOLOGY 2020; 182:332-344. [PMID: 31591151 PMCID: PMC6945879 DOI: 10.1104/pp.19.00987] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/23/2019] [Indexed: 05/04/2023]
Abstract
N 6 -methyladenosine (m6A) is the most abundant modification of eukaryotic mRNA. Although m6A has been demonstrated to affect almost all aspects of RNA metabolism, its global contribution to the post-transcriptional balancing of translational efficiency remains elusive in plants. In this study, we performed a parallel analysis of the transcriptome-wide mRNA m6A distribution and polysome profiling in two maize (Zea mays) inbred lines to assess the global correlation of m6A modification with translational status. m6A sites are widely distributed in thousands of protein-coding genes, confined to a consensus motif and primarily enriched in the 3' untranslated regions, and highly coordinated with alternative polyadenylation usage, suggesting a role of m6A modification in regulating alternative polyadenylation site choice. More importantly, we identified that the m6A modification shows multifaceted correlations with the translational status depending on its strength and genic location. Moreover, we observed a substantial intraspecies variation in m6A modification, and this natural variation was shown to be partly driven by gene-specific expression and alternative splicing. Together, these findings provide an invaluable resource for ascertaining transcripts that are subject to m6A modification in maize and pave the way to a better understanding of natural m6A variation in mediating gene expression regulation.
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Affiliation(s)
- Jin-Hong Luo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100094, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, National Maize Improvement Center, China Agricultural University, Beijing 100094, China
| | - Ye Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Min Wang
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, National Maize Improvement Center, China Agricultural University, Beijing 100094, China
| | - Li-Yuan Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Hui-Ru Peng
- Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Yu-Yi Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Gui-Fang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yan He
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, National Maize Improvement Center, China Agricultural University, Beijing 100094, China
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214
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Arribas-Hernández L, Brodersen P. Occurrence and Functions of m 6A and Other Covalent Modifications in Plant mRNA. PLANT PHYSIOLOGY 2020; 182:79-96. [PMID: 31748418 PMCID: PMC6945878 DOI: 10.1104/pp.19.01156] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/13/2019] [Indexed: 05/07/2023]
Abstract
Posttranscriptional control of gene expression is indispensable for the execution of developmental programs and environmental adaptation. Among the many cellular mechanisms that regulate mRNA fate, covalent nucleotide modification has emerged as a major way of controlling the processing, localization, stability, and translatability of mRNAs. This powerful mechanism is conserved across eukaryotes and controls the cellular events that lead to development and growth. As in other eukaryotes, N 6-methylation of adenosine is the most abundant and best studied mRNA modification in flowering plants. It is essential for embryonic and postembryonic plant development and it affects growth rate and stress responses, including susceptibility to plant RNA viruses. Although the mRNA modification field is young, the intense interest triggered by its involvement in stem cell differentiation and cancer has led to rapid advances in understanding how mRNA modifications control gene expression in mammalian systems. An equivalent effort from plant molecular biologists has been lagging behind, but recent work in Arabidopsis (Arabidopsis thaliana) and other plant species is starting to give insights into how this essential layer of posttranscriptional regulation works in plants, and both similarities and differences with other eukaryotes are emerging. In this Update, we summarize, connect, and evaluate the experimental work that supports our current knowledge of the biochemistry, molecular mechanisms, and biological functions of mRNA modifications in plants. We devote particular attention to N 6-methylation of adenosine and attempt to place the knowledge gained from plant studies within the context of a more general framework derived from studies in other eukaryotes.
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Affiliation(s)
| | - Peter Brodersen
- University of Copenhagen, Department of Biology, DK-2200 Copenhagen N, Denmark
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215
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Yu S, Li X, Liu S, Yang R, Liu X, Wu S. N 6-Methyladenosine: A Novel RNA Imprint in Human Cancer. Front Oncol 2019; 9:1407. [PMID: 31921664 PMCID: PMC6930912 DOI: 10.3389/fonc.2019.01407] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022] Open
Abstract
N6-Methyladenosine (m6A), a pervasive posttranscriptional modification which is reversible, has been among hotspot issues in the past several years. The balance of intracellular m6A levels is dynamically maintained by methyltransferase complex and demethylases. Meanwhile, m6A reader proteins specifically recognize modified residues and convey messages so as to set up an efficient and orderly network of m6A regulation. The m6A mark has proved to affect every step of RNA life cycle, from processing in nucleus to translation or degradation in cytoplasm. Subsequently, disorders in m6A methylation are directly related to aberrant RNA metabolism, which results in tumorigenesis and altered drug response. Therefore, uncovering the underlying mechanism of m6A in oncogenic transformation and tumor progression seeks opportunities for novel targets in cancer therapy. In this review, we conclude the extensive impact of m6A on RNA metabolism and highlight its relevance with human cancer, implicating the far-reaching value in clinical application.
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Affiliation(s)
- Sihui Yu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi Li
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyun Liu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Yang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangnan Liu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sufang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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216
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Functions of N6-methyladenosine and its role in cancer. Mol Cancer 2019; 18:176. [PMID: 31801551 PMCID: PMC6892141 DOI: 10.1186/s12943-019-1109-9] [Citation(s) in RCA: 762] [Impact Index Per Article: 152.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023] Open
Abstract
N6-methyladenosine (m6A) is methylation that occurs in the N6-position of adenosine, which is the most prevalent internal modification on eukaryotic mRNA. Accumulating evidence suggests that m6A modulates gene expression, thereby regulating cellular processes ranging from cell self-renewal, differentiation, invasion and apoptosis. M6A is installed by m6A methyltransferases, removed by m6A demethylases and recognized by reader proteins, which regulate of RNA metabolism including translation, splicing, export, degradation and microRNA processing. Alteration of m6A levels participates in cancer pathogenesis and development via regulating expression of tumor-related genes like BRD4, MYC, SOCS2 and EGFR. In this review, we elaborate on recent advances in research of m6A enzymes. We also highlight the underlying mechanism of m6A in cancer pathogenesis and progression. Finally, we review corresponding potential targets in cancer therapy.
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217
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Huang H, Weng H, Chen J. The Biogenesis and Precise Control of RNA m 6A Methylation. Trends Genet 2019; 36:44-52. [PMID: 31810533 DOI: 10.1016/j.tig.2019.10.011] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/18/2019] [Accepted: 10/28/2019] [Indexed: 12/27/2022]
Abstract
N6-Methyladenosine (m6A) is the most prevalent internal RNA modification in mRNA, and has been found to be highly conserved and hard-coded in mammals and other eukaryotic species. The importance of m6A for gene expression regulation and cell fate decisions has been well acknowledged in the past few years. However, it was only until recently that the mechanisms underlying the biogenesis and specificity of m6A modification in cells were uncovered. We review up-to-date knowledge on the biogenesis of the RNA m6A modification, including the cis-regulatory elements and trans-acting factors that determine general de novo m6A deposition and modulate cell type-specific m6A patterns, and we discuss the biological significance of such regulation.
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Affiliation(s)
- Huilin Huang
- Department of Systems Biology and Gehr Family Center for Leukemia Research, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Hengyou Weng
- Department of Systems Biology and Gehr Family Center for Leukemia Research, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Jianjun Chen
- Department of Systems Biology and Gehr Family Center for Leukemia Research, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA.
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218
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Structure and regulation of ZCCHC4 in m 6A-methylation of 28S rRNA. Nat Commun 2019; 10:5042. [PMID: 31695039 PMCID: PMC6834594 DOI: 10.1038/s41467-019-12923-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/09/2019] [Indexed: 02/07/2023] Open
Abstract
N6-methyladenosine (m6A) modification provides an important epitranscriptomic mechanism that critically regulates RNA metabolism and function. However, how m6A writers attain substrate specificities remains unclear. We report the 3.1 Å-resolution crystal structure of human CCHC zinc finger-containing protein ZCCHC4, a 28S rRNA-specific m6A methyltransferase, bound to S-adenosyl-L-homocysteine. The methyltransferase (MTase) domain of ZCCHC4 is packed against N-terminal GRF-type and C2H2 zinc finger domains and a C-terminal CCHC domain, creating an integrated RNA-binding surface. Strikingly, the MTase domain adopts an autoinhibitory conformation, with a self-occluded catalytic site and a fully-closed cofactor pocket. Mutational and enzymatic analyses further substantiate the molecular basis for ZCCHC4-RNA recognition and a role of the stem-loop structure within substrate in governing the substrate specificity. Overall, this study unveils unique structural and enzymatic characteristics of ZCCHC4, distinctive from what was seen with the METTL family of m6A writers, providing the mechanistic basis for ZCCHC4 modulation of m6A RNA methylation. The N6-methyladenosine (m6A) RNA modification is an evolutionarily conserved epitranscriptomic mechanism that impacts several cellular processes. Here the authors present a structure-function analysis of the ZCCHC4, 28S RNA-specific m6A methyltransferase, shedding light on its regulation and mechanisms that ensure substrate specificity.
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219
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Baquero-Perez B, Antanaviciute A, Yonchev ID, Carr IM, Wilson SA, Whitehouse A. The Tudor SND1 protein is an m 6A RNA reader essential for replication of Kaposi's sarcoma-associated herpesvirus. eLife 2019; 8:e47261. [PMID: 31647415 PMCID: PMC6812964 DOI: 10.7554/elife.47261] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal RNA modification of cellular mRNAs. m6A is recognised by YTH domain-containing proteins, which selectively bind to m6A-decorated RNAs regulating their turnover and translation. Using an m6A-modified hairpin present in the Kaposi's sarcoma associated herpesvirus (KSHV) ORF50 RNA, we identified seven members from the 'Royal family' as putative m6A readers, including SND1. RIP-seq and eCLIP analysis characterised the SND1 binding profile transcriptome-wide, revealing SND1 as an m6A reader. We further demonstrate that the m6A modification of the ORF50 RNA is critical for SND1 binding, which in turn stabilises the ORF50 transcript. Importantly, SND1 depletion leads to inhibition of KSHV early gene expression showing that SND1 is essential for KSHV lytic replication. This work demonstrates that members of the 'Royal family' have m6A-reading ability, greatly increasing their epigenetic functions beyond protein methylation.
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Affiliation(s)
- Belinda Baquero-Perez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
- Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
| | - Agne Antanaviciute
- Leeds Institute of Medical Research, School of MedicineUniversity of Leeds, St James's University HospitalLeedsUnited Kingdom
| | - Ivaylo D Yonchev
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUnited Kingdom
- Sheffield Institute For Nucleic AcidsUniversity of SheffieldSheffieldUnited Kingdom
| | - Ian M Carr
- Leeds Institute of Medical Research, School of MedicineUniversity of Leeds, St James's University HospitalLeedsUnited Kingdom
| | - Stuart A Wilson
- Department of Molecular Biology and BiotechnologyUniversity of SheffieldSheffieldUnited Kingdom
- Sheffield Institute For Nucleic AcidsUniversity of SheffieldSheffieldUnited Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
- Astbury Centre of Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
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220
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Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance. Sci Rep 2019; 9:14607. [PMID: 31601908 PMCID: PMC6787224 DOI: 10.1038/s41598-019-51174-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022] Open
Abstract
Pathogens often receive antibiotic resistance genes through horizontal gene transfer from bacteria that produce natural antibiotics. ErmE is a methyltransferase (MTase) from Saccharopolyspora erythraea that dimethylates A2058 in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor, protecting the ribosomes from macrolide binding. To gain insights into the mechanism of macrolide resistance, the crystal structure of ErmE was determined to 1.75 Å resolution. ErmE consists of an N-terminal Rossmann-like α/ß catalytic domain and a C-terminal helical domain. Comparison with ErmC’ that despite only 24% sequence identity has the same function, reveals highly similar catalytic domains. Accordingly, superposition with the catalytic domain of ErmC’ in complex with SAM suggests that the cofactor binding site is conserved. The two structures mainly differ in the C-terminal domain, which in ErmE contains a longer loop harboring an additional 310 helix that interacts with the catalytic domain to stabilize the tertiary structure. Notably, ErmE also differs from ErmC’ by having long disordered extensions at its N- and C-termini. A C-terminal disordered region rich in arginine and glycine is also a present in two other MTases, PikR1 and PikR2, which share about 30% sequence identity with ErmE and methylate the same nucleotide in 23S rRNA.
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221
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Zhao X, Cui L. Development and validation of a m 6A RNA methylation regulators-based signature for predicting the prognosis of head and neck squamous cell carcinoma. Am J Cancer Res 2019; 9:2156-2169. [PMID: 31720080 PMCID: PMC6834477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is among the most common types of cancers that threat the public health worldwide. A growing body of evidence has demonstrated that m6A RNA methylation plays a critical role in tumorigenesis. However, the association between m6A RNA methylation regulators and prognosis of HNSCC remains poorly known. This study aimed to construct a m6A RNA methylation regulators-based biomarker signature that efficiently predicted the prognosis of HNSCC. The gene expression profile of m6A RNA methylation regulators and the corresponding clinical information were downloaded from The Cancer Genome Atlas (TCGA) HNSCC dataset. The differentially expressed m6A RNA methylation regulators between tumor samples and normal control samples, as well as the interaction and correlation of m6A RNA methylation regulators were evaluated. Consensus clustering analysis was performed to identify the clusters of HNSCC with different clinical outcome. Then a prognostic signature was built on TCGA HNSCC cohort and further validated in an external independent cohort. The expression levels of METTL3, YTHDF1, KIAA1429, ALKBH5, YTHDF2, METTL14, FTO, WTAP, RBM15 and HNRNPC were significantly upregulated in tumor samples, while YTHDC2 was remarkably downregulated in the cancer specimens. WTAP and METTL14 might be the hub genes of the interaction network among m6A RNA methylation regulators. Two clusters of HNSCC cases were identified and significant differences were found with respect to overall survival (OS) and tumor grade between the two subgroups of patients. A two-gene prognostic signature including YTHDC2 and HNRNPC was constructed and could predict OS in HNSCC patients from TCGA dataset. In addition, the prognostic signature-based risk score was identified as an independent prognostic indicator for HNSCC. More importantly, these findings were successfully validated in an external independent HNSCC cohort. In conclusion, our study has built up a robust m6A RNA methylation regulators-based molecular signature that predicts the prognosis of patients with HNSCC with high accuracy, which might provide important guidance for therapeutic strategies.
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Affiliation(s)
- Xinyuan Zhao
- Stomatological Hospital, Southern Medical UniversityGuangzhou 510280, China
| | - Li Cui
- UCLA School of DentistryLos Angeles, CA 90095, USA
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222
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van Tran N, Ernst FG, Hawley BR, Zorbas C, Ulryck N, Hackert P, Bohnsack KE, Bohnsack MT, Jaffrey SR, Graille M, Lafontaine DL. The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res 2019; 47:7719-7733. [PMID: 31328227 PMCID: PMC6735865 DOI: 10.1093/nar/gkz619] [Citation(s) in RCA: 288] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/14/2019] [Accepted: 07/12/2019] [Indexed: 12/29/2022] Open
Abstract
N6-methyladenosine (m6A) has recently been found abundantly on messenger RNA and shown to regulate most steps of mRNA metabolism. Several important m6A methyltransferases have been described functionally and structurally, but the enzymes responsible for installing one m6A residue on each subunit of human ribosomes at functionally important sites have eluded identification for over 30 years. Here, we identify METTL5 as the enzyme responsible for 18S rRNA m6A modification and confirm ZCCHC4 as the 28S rRNA modification enzyme. We show that METTL5 must form a heterodimeric complex with TRMT112, a known methyltransferase activator, to gain metabolic stability in cells. We provide the first atomic resolution structure of METTL5-TRMT112, supporting that its RNA-binding mode differs distinctly from that of other m6A RNA methyltransferases. On the basis of similarities with a DNA methyltransferase, we propose that METTL5-TRMT112 acts by extruding the adenosine to be modified from a double-stranded nucleic acid.
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MESH Headings
- Adenosine/chemistry
- Adenosine/genetics
- Adenosine/metabolism
- Base Sequence
- Binding Sites
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Cell Line, Tumor
- Crystallography, X-Ray
- Gene Deletion
- Gene Expression Regulation, Neoplastic
- HCT116 Cells
- Humans
- Methyltransferases/chemistry
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Stability
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- Signal Transduction
- Substrate Specificity
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Nhan van Tran
- BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Felix G M Ernst
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Ben R Hawley
- Department of Pharmacology, Weill Medical College, Cornell University, NY 10065, New York, USA
| | - Christiane Zorbas
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Nathalie Ulryck
- BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, NY 10065, New York, USA
| | - Marc Graille
- BIOC, CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Denis L J Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
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223
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Heck AM, Wilusz CJ. Small changes, big implications: The impact of m 6A RNA methylation on gene expression in pluripotency and development. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194402. [PMID: 31325527 PMCID: PMC6742438 DOI: 10.1016/j.bbagrm.2019.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/21/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022]
Abstract
In order to maintain a state of self-renewal, yet retain the ability to rapidly differentiate in response to external signals, pluripotent cells exert tight control over gene expression at many levels. Recent studies have suggested that N6-methyladenosine (m6A) RNA methylation, one of the most abundant post-transcriptional modifications, is important for both pluripotency and differentiation. In this review, we summarize the current state of the m6A field, with emphasis on the impact of writers, erasers and readers of m6A on RNA metabolism and stem cell biology.
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Affiliation(s)
- Adam M Heck
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America
| | - Carol J Wilusz
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America.
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224
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Wang H, Xu B, Shi J. N6-methyladenosine METTL3 promotes the breast cancer progression via targeting Bcl-2. Gene 2019; 722:144076. [PMID: 31454538 DOI: 10.1016/j.gene.2019.144076] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/07/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification in mammalian mRNAs and methyltransferase-like 3 (METTL3) is a vital methyltransferase in m6A modification. Here, this study tries to discover the regulatory role of METTL3 and its mechanism in the breast cancer tumorigenesis. Results found that METTL3 was up-regulated in the breast cancer tissue and cells. In vivo and vitro, METTL3 knockdown could decrease the methylation level, reduce the proliferation, accelerate the apoptosis and inhibited the tumor growth. Moreover, we found that Bcl-2 acted as the target of METTL3, thereby regulating the proliferation and apoptosis of breast cancer. This study could reveal the potential mechanism of m6A modification in the breast cancer tumorigenesis, providing potential drug targets in the treatment.
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Affiliation(s)
- Hong Wang
- Breast Surgery Medicine, Zhong-Shan Hospital Affiliated with Fudan University, Shanghai 200032, China
| | - Bei Xu
- Internal Medicine-Oncology, Zhong-Shan Hospital Affiliated with Fudan University, Shanghai 200032, China
| | - Jun Shi
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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225
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Fazi F, Fatica A. Interplay Between N 6-Methyladenosine (m 6A) and Non-coding RNAs in Cell Development and Cancer. Front Cell Dev Biol 2019; 7:116. [PMID: 31316981 PMCID: PMC6611489 DOI: 10.3389/fcell.2019.00116] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
RNA chemical modifications in coding and non-coding RNAs have been known for decades. They are generally installed by specific enzymes and, in some cases, can be read and erased by other specific proteins. The impact of RNA chemical modifications on gene expression regulation and the reversible nature of some of these modifications led to the birth of the word epitranscriptomics, in analogy with the changes that occur on DNA and histones. Among more than 100 different modifications identified so far, most of the epitranscriptomics studies focused on the N6-methyladenosine (m6A), which is the more abundant internal modification in protein coding RNAs. m6A can control several pathways of gene expression, including spicing, export, stability, and translation. In this review, we describe the interplay between m6A and non-coding RNAs, in particular microRNAs and lncRNAs, with examples of its role in gene expression regulation. Finally, we discuss its relevance in cell development and disease.
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Affiliation(s)
- Francesco Fazi
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
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226
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Liu J, Harada BT, He C. Regulation of Gene Expression by N 6-methyladenosine in Cancer. Trends Cell Biol 2019; 29:487-499. [PMID: 30940398 PMCID: PMC6527461 DOI: 10.1016/j.tcb.2019.02.008] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/23/2022]
Abstract
As the most abundant mRNA modification in eukaryotic cells, N6-methyladenosine (m6A) has recently emerged as an important regulator of gene expression. m6A modification can be deposited by m6A methyltransferases, removed by m6A demethylases, and recognized by different reader proteins. Numerous lines of evidence have shown that m6A methylation plays critical roles regulating gene expression in development and disease. In this review, we summarize the molecular and cellular function of m6A and highlight some key results which demonstrate the role of m6A in various cancers. Finally, we discuss future directions for research into m6A and its effects in cancer and the potential for targeting RNA modification in cancer treatment.
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Affiliation(s)
- Jun Liu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, Chicago, IL 60637, USA
| | - Bryan T Harada
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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227
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Shi H, Wei J, He C. Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers. Mol Cell 2019; 74:640-650. [PMID: 31100245 PMCID: PMC6527355 DOI: 10.1016/j.molcel.2019.04.025] [Citation(s) in RCA: 1084] [Impact Index Per Article: 216.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 12/18/2022]
Abstract
Cellular RNAs are naturally decorated with a variety of chemical modifications. The structural diversity of the modified nucleosides provides regulatory potential to sort groups of RNAs for organized metabolism and functions, thus affecting gene expression. Recent years have witnessed a burst of interest in and understanding of RNA modification biology, thanks to the emerging transcriptome-wide sequencing methods for mapping modified sites, highly sensitive mass spectrometry for precise modification detection and quantification, and extensive characterization of the modification "effectors," including enzymes ("writers" and "erasers") that alter the modification level and binding proteins ("readers") that recognize the chemical marks. However, challenges remain due to the vast heterogeneity in expression abundance of different RNA species, further complicated by divergent cell-type-specific and tissue-specific expression and localization of the effectors as well as modifications. In this review, we highlight recent progress in understanding the function of N6-methyladenosine (m6A), the most abundant internal mark on eukaryotic mRNA, in light of the specific biological contexts of m6A effectors. We emphasize the importance of context for RNA modification regulation and function.
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Affiliation(s)
- Hailing Shi
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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228
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Zhou Y, Yin Z, Hou B, Yu M, Chen R, Jin H, Jian Z. Expression profiles and prognostic significance of RNA N6-methyladenosine-related genes in patients with hepatocellular carcinoma: evidence from independent datasets. Cancer Manag Res 2019; 11:3921-3931. [PMID: 31118805 PMCID: PMC6503205 DOI: 10.2147/cmar.s191565] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/01/2019] [Indexed: 01/13/2023] Open
Abstract
Background: N6-methyladenosine (m6A) is the most prevalent modification of mammalian RNA. Emerging evidence suggest that m6A has critical roles in multiple biological activities, but little is known about its roles in cancer pathogenesis. Herein, we report the expression profiles and prognostic relevance of twelve m6A-related genes in hepatocellular carcinoma (HCC) by analyzing four independent datasets. Materials and methods: RNA levels of twelve m6A-related genes were detected in samples of 162 HCC patients who underwent curative resection (the Guangdong General Hospital dataset). We additionally analyzed the expression profiles of m6A-related genes in The Cancer Genome Atlas liver HCC dataset and two Gene Expression Omnibus datasets (GSE14520, GSE63898). Prognostic value of genes was evaluated by Kaplan–Meier curves of overall survival (OS) with the log-rank test and multivariate Cox regression analysis. Gene set enrichment analysis (GSEA) was conducted to identify associated KEGG pathways. Results: Five genes (METTL3, YTHDF1, YTHDF2, YTHDF3, and EIF3) showed consistent upregulation in all four datasets. Abnormal expressions of either METTL3 or YTHDF1 but not the other ten genes were associated with OS. Protein expression of METTL3 and YTHDF1 were confirmed in HCC tissues by immunohistochemical staining. Multivariate Cox regression analysis confirmed the independent predictive value of both METTL3 and YTHDF1 on OS. We further divided patients into three groups based on the median expression values of METTL3 and YTHDF1. In all datasets, the low METTL3/low YTHDF1 group showed a consistent better prognosis than other groups. GSEA revealed that both METTL3 and YTHDF1 regulate HCC cell cycle, RNA splicing, DNA replication, base excision repair, and RNA degradation. Conclusion: Both METTL3 and YTHDF1 were upregulated in HCC, and they were independent poor prognostic factors. Combination of METTL3 and YTHDF1 can be regarded as the biological marker that reflect malignant degree and evaluate prognosis in HCC.
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Affiliation(s)
- Yu Zhou
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Zi Yin
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Baohua Hou
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Min Yu
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Ruiwan Chen
- Department of Radiation Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Haosheng Jin
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
| | - Zhixiang Jian
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, People's Republic of China
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229
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m⁶A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins. Genes (Basel) 2019; 10:genes10010049. [PMID: 30650668 PMCID: PMC6356822 DOI: 10.3390/genes10010049] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/04/2023] Open
Abstract
The control of gene expression is a multi-layered process occurring at the level of DNA, RNA, and proteins. With the emergence of highly sensitive techniques, new aspects of RNA regulation have been uncovered leading to the emerging field of epitranscriptomics dealing with RNA modifications. Among those post-transcriptional modifications, N6-methyladenosine (m6A) is the most prevalent in messenger RNAs (mRNAs). This mark can either prevent or stimulate the formation of RNA-protein complexes, thereby influencing mRNA-related mechanisms and cellular processes. This review focuses on proteins containing a YTH domain (for YT521-B Homology), a small building block, that selectively detects the m6A nucleotide embedded within a consensus motif. Thereby, it contributes to the recruitment of various effectors involved in the control of mRNA fates through adjacent regions present in the different YTH-containing proteins.
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230
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Coker H, Wei G, Brockdorff N. m6A modification of non-coding RNA and the control of mammalian gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:310-318. [PMID: 30550772 DOI: 10.1016/j.bbagrm.2018.12.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 12/27/2022]
Abstract
The biology of non-coding RNA (ncRNA) and the regulation of mammalian gene expression is a rapidly expanding field. In this review, we consider how recent advances in technology, enabling the precise mapping of modifications to RNA transcripts, has provided new opportunities to dissect post-transcriptional gene regulation. With this has come the realisation that in the absence of translation, the modification of ncRNAs may play a fundamental role in their regulation, protein interactome and subsequent downstream effector functions. We focus upon modification of RNA by N6-methyladenosine (m6A); its readers, writers and erasers, before considering the differing role of m6A modified lncRNAs MALAT1 and Xist. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Heather Coker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Guifeng Wei
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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231
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Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. N 6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol 2018; 15:88-94. [PMID: 30531910 DOI: 10.1038/s41589-018-0184-3] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/30/2018] [Indexed: 01/09/2023]
Abstract
N6-Methyladenosine (m6A) RNA modification is present in messenger RNAs (mRNA), ribosomal RNAs (rRNA), and spliceosomal RNAs (snRNA) in humans. Although mRNA m6A modifications have been extensively studied and shown to play critical roles in many cellular processes, the identity of m6A methyltransferases for rRNAs and the function of rRNA m6A modifications are unknown. Here we report a new m6A methyltransferase, ZCCHC4, which primarily methylates human 28S rRNA and also interacts with a subset of mRNAs. ZCCHC4 knockout eliminates m6A4220 modification in 28S rRNA, reduces global translation, and inhibits cell proliferation. We also find that ZCCHC4 protein is overexpressed in hepatocellular carcinoma tumors, and ZCCHC4 knockout significantly reduces tumor size in a xenograft mouse model. Our results highlight the functional significance of an rRNA m6A modification in translation and in tumor biology.
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Affiliation(s)
- Honghui Ma
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jiabin Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Ruitu Lv
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Kai Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhike Lu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Hao Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yujiang Geno Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
| | - Yang Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China. .,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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