201
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Lu Z, Liu J, Yuan C, Jin M, Quan K, Chu M, Wei C. m 6A mRNA methylation analysis provides novel insights into heat stress responses in the liver tissue of sheep. Genomics 2020; 113:484-492. [PMID: 32976974 DOI: 10.1016/j.ygeno.2020.09.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/31/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
N6-methyladenosine (m6A) mRNA methylation varies in response to stress. However, no map of m6A mRNA methylation has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Here, we obtained m6A methylation maps of sheep liver tissues with and without heat stress by MeRIP-seq. In total, 8306 m6A peaks associated with 2697 genes were detected in the heat stress group, and 12,958 m6A peaks associated with 5494 genes were detected in the control group. Peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. Methylation levels of heat stress and control sheep were higher near stop codons, although methylation was significantly lower in heat stress sheep. GO and KEGG revealed that differential m6A-containing genes were significantly enriched in the stress response and fat metabolism. Our results showed that m6A mRNA methylation modifications regulate heat stress in sheep.
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Affiliation(s)
- Zengkui Lu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Meilin Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China..
| | - Caihong Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China..
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202
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Aristizabal MJ, Anreiter I, Halldorsdottir T, Odgers CL, McDade TW, Goldenberg A, Mostafavi S, Kobor MS, Binder EB, Sokolowski MB, O'Donnell KJ. Biological embedding of experience: A primer on epigenetics. Proc Natl Acad Sci U S A 2020; 117:23261-23269. [PMID: 31624126 PMCID: PMC7519272 DOI: 10.1073/pnas.1820838116] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biological embedding occurs when life experience alters biological processes to affect later life health and well-being. Although extensive correlative data exist supporting the notion that epigenetic mechanisms such as DNA methylation underlie biological embedding, causal data are lacking. We describe specific epigenetic mechanisms and their potential roles in the biological embedding of experience. We also consider the nuanced relationships between the genome, the epigenome, and gene expression. Our ability to connect biological embedding to the epigenetic landscape in its complexity is challenging and complicated by the influence of multiple factors. These include cell type, age, the timing of experience, sex, and DNA sequence. Recent advances in molecular profiling and epigenome editing, combined with the use of comparative animal and human longitudinal studies, should enable this field to transition from correlative to causal analyses.
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Affiliation(s)
- Maria J Aristizabal
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, and BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V52 4H4, Canada
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Ina Anreiter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Thorhildur Halldorsdottir
- Centre of Public Health Sciences, Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Candice L Odgers
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Psychological Science, University of California, Irvine, CA 92697
- Sanford School of Public Policy, Duke University, Durham, NC 27708
| | - Thomas W McDade
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Anthropology, Northwestern University, Evanston, IL 60208
- Institute for Policy Research, Northwestern University, Evanston, IL 60208
| | - Anna Goldenberg
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Computer Science, Hospital for Sick Children, Vector Institute, University of Toronto, Toronto, ON, M5G OA4, Canada
| | - Sara Mostafavi
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Statistics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, and BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V52 4H4, Canada
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Elisabeth B Binder
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329
| | - Marla B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada;
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada
| | - Kieran J O'Donnell
- Program in Child and Brain Development, CIFAR, MaRS Centre, Toronto, ON, M5G 1M1, Canada;
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, Department of Psychiatry, McGill University, Montreal, QC, H4H 1R3, Canada
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203
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Navarro-Martín L, Martyniuk CJ, Mennigen JA. Comparative epigenetics in animal physiology: An emerging frontier. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100745. [PMID: 33126028 DOI: 10.1016/j.cbd.2020.100745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/19/2022]
Abstract
The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.
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Affiliation(s)
- Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya 08034, Spain.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jan A Mennigen
- Department of Biology, University of Ottawa, Ottawa, ON K1N6N5, Canada
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204
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Zhang Y, Geng X, Li Q, Xu J, Tan Y, Xiao M, Song J, Liu F, Fang C, Wang H. m6A modification in RNA: biogenesis, functions and roles in gliomas. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020. [PMID: 32943100 DOI: 10.1186/s13046-020-01706-8.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The chemical modification of RNA is a newly discovered epigenetic regulation mechanism in cells and plays a crucial role in a variety of biological processes. N6-methyladenine (m6A) mRNA modification is the most abundant form of posttranscriptional RNA modification in eukaryotes. Through the development of m6A RNA sequencing, the relevant molecular mechanism of m6A modification has gradually been revealed. It has been found that the effect of m6A modification on RNA metabolism involves processing, nuclear export, translation and even decay. As the most common malignant tumour of the central nervous system, gliomas (especially glioblastoma) have a very poor prognosis, and treatment efficacy is not ideal even with the application of high-intensity treatment measures of surgery combined with chemoradiotherapy. Exploring the origin and development mechanisms of tumour cells from the perspective of tumour biogenesis has always been a hotspot in the field of glioma research. Emerging evidence suggests that m6A modification can play a key role in gliomas through a variety of mechanisms, providing more possibilities for early diagnosis and targeted therapy of gliomas. The aim of the present review is to focus on the research progress regarding the association between m6A modification and gliomas. And to provide a theoretical basis according to the currently available literature for further exploring this association. This review may provide new insights for the molecular mechanism, early diagnosis, histologic grading, targeted therapy and prognostic evaluation of gliomas.
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Affiliation(s)
- Yuhao Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Xiuchao Geng
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China
| | - Qiang Li
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, 050200, Shijiazhuang, China
| | - Jianglong Xu
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Yanli Tan
- Department of Pathology, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Menglin Xiao
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Jia Song
- School of Basic Medicine, Hebei University, 071000, Baoding, China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Hong Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China. .,Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China. .,Hebei Key Laboratory of Chinese Medicine Research on Cardio-Cerebrovascular Disease, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China.
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205
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Zhang Y, Geng X, Li Q, Xu J, Tan Y, Xiao M, Song J, Liu F, Fang C, Wang H. m6A modification in RNA: biogenesis, functions and roles in gliomas. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:192. [PMID: 32943100 PMCID: PMC7500025 DOI: 10.1186/s13046-020-01706-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/10/2020] [Indexed: 12/30/2022]
Abstract
The chemical modification of RNA is a newly discovered epigenetic regulation mechanism in cells and plays a crucial role in a variety of biological processes. N6-methyladenine (m6A) mRNA modification is the most abundant form of posttranscriptional RNA modification in eukaryotes. Through the development of m6A RNA sequencing, the relevant molecular mechanism of m6A modification has gradually been revealed. It has been found that the effect of m6A modification on RNA metabolism involves processing, nuclear export, translation and even decay. As the most common malignant tumour of the central nervous system, gliomas (especially glioblastoma) have a very poor prognosis, and treatment efficacy is not ideal even with the application of high-intensity treatment measures of surgery combined with chemoradiotherapy. Exploring the origin and development mechanisms of tumour cells from the perspective of tumour biogenesis has always been a hotspot in the field of glioma research. Emerging evidence suggests that m6A modification can play a key role in gliomas through a variety of mechanisms, providing more possibilities for early diagnosis and targeted therapy of gliomas. The aim of the present review is to focus on the research progress regarding the association between m6A modification and gliomas. And to provide a theoretical basis according to the currently available literature for further exploring this association. This review may provide new insights for the molecular mechanism, early diagnosis, histologic grading, targeted therapy and prognostic evaluation of gliomas.
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Affiliation(s)
- Yuhao Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Xiuchao Geng
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China
| | - Qiang Li
- Faculty of Acupuncture-Moxibustion and Tuina, Hebei University of Chinese Medicine, 050200, Shijiazhuang, China
| | - Jianglong Xu
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Yanli Tan
- Department of Pathology, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Menglin Xiao
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China
| | - Jia Song
- School of Basic Medicine, Hebei University, 071000, Baoding, China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China.
| | - Hong Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, 071000, Baoding, China. .,Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China. .,Hebei Key Laboratory of Chinese Medicine Research on Cardio-Cerebrovascular Disease, Hebei University of Chinese Medicine, 050091, Shijiazhuang, China.
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206
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Altered Expression of the m6A Methyltransferase METTL3 in Alzheimer's Disease. eNeuro 2020; 7:ENEURO.0125-20.2020. [PMID: 32847866 PMCID: PMC7540926 DOI: 10.1523/eneuro.0125-20.2020] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/27/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Cognitive impairment in Alzheimer’s disease (AD) is associated with dysregulation of the RNA and protein expression profiles in the brain. Recent studies have highlighted the importance of RNA post-transcriptional regulation (epitranscriptomics) in higher order brain functions. Specifically, N6-methyladenosine (m6A), which controls RNA stability, splicing, translation and trafficking, plays an important role in learning and memory. This raises the question of whether m6A signaling is perturbed in AD. To address this, we investigated the expression profile of known m6A-regulatory genes using a public RNA-seq dataset and identified a subset of genes which were significantly dysregulated in the human AD brain. Among these, genes encoding the m6A methyltransferase, METTL3, and a member of the m6A methyltransferase complex (MACOM), RBM15B, were downregulated and upregulated in the hippocampus, respectively. These findings were validated at the protein level using an independent cohort of postmortem human brain samples. Unexpectedly, we observed an accumulation of methyltransferase-like 3 (METTL3), but not RBM15B, in the insoluble fractions, which positively correlated with the levels of insoluble Tau protein in the postmortem human AD samples. Aberrant expression and distribution of METTL3 in the hippocampus of the AD brain may therefore represent an epitranscriptomic mechanism underlying the altered gene expression patterns associated with disease pathogenesis.
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207
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Xu Q, Jiang M, Gu S, Wang F, Yuan B. Early Life Stress Induced DNA Methylation of Monoamine Oxidases Leads to Depressive-Like Behavior. Front Cell Dev Biol 2020; 8:582247. [PMID: 33015076 PMCID: PMC7505948 DOI: 10.3389/fcell.2020.582247] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022] Open
Abstract
Major depressive disorder (MDD) is coming to be the regarded as one of the leading causes for human disabilities. Due to its complicated pathological process, the etiology is still unclear and the treatment is still targeting at the monoamine neurotransmitters. Early life stress has been known as a major cause for MDD, but how early life stress affects adult monoaminergic activity is not clear either. Recently, DNA methylation is considered to be the key mechanism of epigenetics and might play a role in early life stress induced mental illness. DNA methylation is an enzymatic covalent modification of DNA, has been one of the main epigenetic mechanisms investigated. The metabolic enzyme for the monoamine neurotransmitters, monoamine oxidases A/B (MAO A/MAO B) are the prime candidates for the investigation into the role of DNA methylation in mental disorders. In this review, we will review recent advances about the structure and physiological function of monoamine oxidases (MAO), brief narrative other factors include stress induced changes, early life stress, perinatal depression (PD) relationship with other epigenetic changes, such as DNA methylation, microRNA (miRNA). This review will shed light on the epigenetic changes involved in MDD, which may provide potential targets for future therapeutics in depression pathogenesis.
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Affiliation(s)
- Qiuyue Xu
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mingchen Jiang
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Simeng Gu
- Department of Psychology, Jiangsu University Medical School, Zhenjiang, China
| | - Fushun Wang
- Institute of Brain and Psychological Sciences, Sichuan Normal University, Chengdu, China
| | - Bin Yuan
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Key Laboratory of Pediatric Respiratory Disease, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
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208
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Dermentzaki G, Lotti F. New Insights on the Role of N 6-Methyladenosine RNA Methylation in the Physiology and Pathology of the Nervous System. Front Mol Biosci 2020; 7:555372. [PMID: 32984403 PMCID: PMC7492240 DOI: 10.3389/fmolb.2020.555372] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
RNA modifications termed epitranscriptomics represent an additional layer of gene regulation similar to epigenetic mechanisms operating on DNA. The dynamic nature and the increasing number of RNA modifications offer new opportunities for a rapid fine-tuning of gene expression in response to specific environmental cues. In cooperation with a diverse and versatile set of effector proteins that "recognize" them, these RNA modifications have the ability to mediate and control diverse fundamental cellular functions, such as pre-mRNA splicing, nuclear export, stability, and translation. N 6-methyladenosine (m6A) is the most abundant of these RNA modifications, particularly in the nervous system, where recent studies have highlighted it as an important post-transcriptional regulator of physiological functions from development to synaptic plasticity, learning and memory. Here we review recent findings surrounding the role of m6A modification in regulating physiological responses of the mammalian nervous system and we discuss its emerging role in pathological conditions such as neuropsychiatric and neurodegenerative disorders.
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Affiliation(s)
- Georgia Dermentzaki
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
- Department of Neurology, Columbia University, New York City, NY, United States
| | - Francesco Lotti
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
- Department of Neurology, Columbia University, New York City, NY, United States
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209
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Huang R, Zhang Y, Bai Y, Han B, Ju M, Chen B, Yang L, Wang Y, Zhang H, Zhang H, Xie C, Zhang Z, Yao H. N 6-Methyladenosine Modification of Fatty Acid Amide Hydrolase Messenger RNA in Circular RNA STAG1-Regulated Astrocyte Dysfunction and Depressive-like Behaviors. Biol Psychiatry 2020; 88:392-404. [PMID: 32387133 DOI: 10.1016/j.biopsych.2020.02.018] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most abundant epigenetic modification in eukaryotic messenger RNAs and is essential for multiple RNA processing events in physiological and pathological processes. However, precisely how m6A methylation is involved in major depressive disorder (MDD) is not fully understood. METHODS Circular RNA STAG1 (circSTAG1) was screened from the hippocampus of chronic unpredictable stress-treated mice using high-throughput RNA sequencing. Microinjection of circSTAG1 lentivirus into the mouse hippocampus was used to observe the role of circSTAG1 in depression. Sucrose preference, forced swim, and tail suspension tests were performed to evaluate the depressive-like behaviors of mice. Astrocyte dysfunction was examined by GFAP immunostaining and 3D reconstruction. Methylated RNA immunoprecipitation sequence analysis was used to identify downstream targets of circSTAG1/ALKBH5 (alkB homolog 5) axis. Cell Counting Kit-8 assay was performed to evaluate astrocyte viability in vitro. RESULTS circSTAG1 was significantly decreased in the chronic unpredictable stress-treated mouse hippocampus and in peripheral blood of patients with MDD. Overexpression of circSTAG1 notably attenuated astrocyte dysfunction and depressive-like behaviors induced by chronic unpredictable stress. Further examination indicated that overexpressed circSTAG1 captured ALKBH5 and decreased the translocation of ALKBH5 into the nucleus, leading to increased m6A methylation of fatty acid amide hydrolase (FAAH) messenger RNA and degradation of FAAH in astrocytes with subsequent attenuation of depressive-like behaviors and astrocyte loss induced by corticosterone in vitro. CONCLUSIONS Our findings dissect the functional link between circSTAG1 and m6A methylation in the context of MDD, providing evidence that circSTAG1 may be a novel therapeutic target for MDD.
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Affiliation(s)
- Rongrong Huang
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Yuan Zhang
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Ying Bai
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Bing Han
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Minzi Ju
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Biling Chen
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Li Yang
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Yu Wang
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China
| | - Hongxing Zhang
- Department of Psychology, Xinxiang Medical University, Xinxiang, Henan, China; Second Affiliated Hospital, Xinxiang Medical University, Xinxiang, Henan, China
| | - Haisan Zhang
- Second Affiliated Hospital, Xinxiang Medical University, Xinxiang, Henan, China
| | - Chunming Xie
- Department of Neurology, Affiliated ZhongDa Hospital, Institute of Neuropsychiatry, Southeast University, Nanjing, China
| | - Zhijun Zhang
- Department of Neurology, Affiliated ZhongDa Hospital, Institute of Neuropsychiatry, Southeast University, Nanjing, China; Department of Psychology, Xinxiang Medical University, Xinxiang, Henan, China; Second Affiliated Hospital, Xinxiang Medical University, Xinxiang, Henan, China
| | - Honghong Yao
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, China; Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China.
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210
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Zhang S, Deng W, Liu Q, Wang P, Yang W, Ni W. Altered m 6 A modification is involved in up-regulated expression of FOXO3 in luteinized granulosa cells of non-obese polycystic ovary syndrome patients. J Cell Mol Med 2020; 24:11874-11882. [PMID: 32869942 PMCID: PMC7578862 DOI: 10.1111/jcmm.15807] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/26/2022] Open
Abstract
The pathophysiology of polycystic ovary syndrome (PCOS) is characterized by granulosa cell (GC) dysfunction. m6A modification affects GC function in patients with premature ovarian insufficiency (POI), but the role of m6A modification in PCOS is unknown. The purpose of the prospective comparative study was to analyse the m6A profile of the luteinized GCs from normovulatory women and non‐obese PCOS patients following controlled ovarian hyperstimulation. RNA m6A methylation levels were measured by m6A quantification assay in the luteinized GCs of the controls and PCOS patients. Then, m6A profiles were analysed by methylated RNA immunoprecipitation sequencing (MeRIP‐seq). We reported that the m6A level was increased in the luteinized GCs of PCOS patients. Comparative analysis revealed differences between the m6A profiles from the luteinized GC of the controls and PCOS patients. We identified FOXO3 mRNA with reduced m6A modification in the luteinized GCs of PCOS patients. Selectively knocking down m6A methyltransferases or demethylases altered expression of FOXO3 in the luteinized GCs from the controls, but did not in PCOS patients. These suggested an absence of m6A‐mediated transcription of FOXO3 in the luteinized GCs of PCOS patients. Furthermore, we demonstrated that the involvement of m6A in the stability of the FOXO3 mRNA that is regulated via a putative methylation site in the 3’‐UTR only in the luteinized GCs of the controls. In summary, our findings showed that altered m6A modification was involved in up‐regulated expression of FOXO3 mRNA in the luteinized GCs from non‐obese PCOS patients following controlled ovarian hyperstimulation.
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Affiliation(s)
- Shen Zhang
- Reproductive Medicine Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenli Deng
- Department of Ophthalmology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qiongyou Liu
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi, China
| | - Peiyu Wang
- Reproductive Medicine Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei Yang
- The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wuhua Ni
- Reproductive Medicine Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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211
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Bali V, Mazei-Robison MS. "Circ-it" for Stress: Role of a Novel Circular RNA in Hippocampal Astrocyte Function and Behavior. Biol Psychiatry 2020; 88:362-364. [PMID: 32792050 DOI: 10.1016/j.biopsych.2020.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/15/2020] [Accepted: 05/15/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Vedrana Bali
- Department of Physiology and Neuroscience Program, Michigan State University, East Lansing, Michigan
| | - Michelle S Mazei-Robison
- Department of Physiology and Neuroscience Program, Michigan State University, East Lansing, Michigan.
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212
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Chen S, Li Y, Zhi S, Ding Z, Wang W, Peng Y, Huang Y, Zheng R, Yu H, Wang J, Hu M, Miao J, Li J. WTAP promotes osteosarcoma tumorigenesis by repressing HMBOX1 expression in an m 6A-dependent manner. Cell Death Dis 2020; 11:659. [PMID: 32814762 PMCID: PMC7438489 DOI: 10.1038/s41419-020-02847-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
N6-methyladenosine (m6A) regulators are involved in the progression of various cancers via regulating m6A modification. However, the potential role and mechanism of the m6A modification in osteosarcoma remains obscure. In this study, WTAP was found to be highly expressed in osteosarcoma tissue and it was an independent prognostic factor for overall survival in osteosarcoma. Functionally, WTAP, as an oncogene, was involved in the proliferation and metastasis of osteosarcoma in vitro and vivo. Mechanistically, M6A dot blot, RNA-seq and MeRIP-seq, MeRIP-qRT-PCR and luciferase reporter assays showed that HMBOX1 was identified as the target gene of WTAP, which regulated HMBOX1 stability depending on m6A modification at the 3′UTR of HMBOX1 mRNA. In addition, HMBOX1 expression was downregulated in osteosarcoma and was an independent prognostic factor for overall survival in osteosarcoma patients. Silenced HMBOX1 evidently attenuated shWTAP-mediated suppression on osteosarcoma growth and metastasis in vivo and vitro. Finally, WTAP/HMBOX1 regulated osteosarcoma growth and metastasis via PI3K/AKT pathway. In conclusion, this study demonstrated the critical role of the WTAP-mediated m6A modification in the progression of osteosarcoma, which could provide novel insights into osteosarcoma treatment.
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Affiliation(s)
- Shijie Chen
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.,Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yuezhan Li
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Shuang Zhi
- Four Gynecological Wards, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Zhiyu Ding
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Weiguo Wang
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Yi Peng
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Yan Huang
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ruping Zheng
- School of Basic Medical Science, Central South University, Changsha, China
| | - Haiyang Yu
- School of Basic Medical Science, Central South University, Changsha, China
| | - Jianlong Wang
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Minghua Hu
- Department of Anatomy, Histology and Embryology, Changsha Medical University, Changsha, China
| | - Jinglei Miao
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.
| | - Jinsong Li
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.
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213
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Wang YJ, Yang B, Lai Q, Shi JF, Peng JY, Zhang Y, Hu KS, Li YQ, Peng JW, Yang ZZ, Li YT, Pan Y, Koeffler HP, Liao JY, Yin D. Reprogramming of m 6A epitranscriptome is crucial for shaping of transcriptome and proteome in response to hypoxia. RNA Biol 2020; 18:131-143. [PMID: 32746693 DOI: 10.1080/15476286.2020.1804697] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Hypoxia causes a series of responses supporting cells to survive in harsh environments. Substantial post-transcriptional and translational regulation during hypoxia has been observed. However, detailed regulatory mechanism in response to hypoxia is still far from complete. RNA m6A modification has been proven to govern the life cycle of RNAs. Here, we reported that total m6A level of mRNAs was decreased during hypoxia, which might be mediated by the induction of m6A eraser, ALKBH5. Meanwhile, expression levels of most YTH family members of m6A readers were systematically down-regulated. Transcriptome-wide analysis of m6A revealed a drastic reprogramming of m6A epitranscriptome during cellular hypoxia. Integration of m6A epitranscriptome with either RNA-seq based transcriptome analysis or mass spectrometry (LC-MS/MS) based proteome analysis of cells upon hypoxic stress revealed that reprogramming of m6A epitranscriptome reshaped the transcriptome and proteome, thereby supporting efficient generation of energy for adaption to hypoxia. Moreover, ATP production was blocked when silencing an m6A eraser, ALKBH5, under hypoxic condition, demonstrating that m6A pathway is an important regulator during hypoxic response. Collectively, our studies indicate that crosstalk between m6A and HIF1 pathway is essential for cellular response to hypoxia, providing insights into the underlying molecular mechanisms during hypoxia.
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Affiliation(s)
- Yan-Jie Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Bing Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Qiao Lai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China.,Department of Science and Teaching, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University , Guangzhou, China
| | - Jun-Fang Shi
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University , Guangzhou, China
| | - Jiang-Yun Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Kai-Shun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Ya-Qing Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China.,Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou P.R. China
| | - Jing-Wen Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Zhi-Zhi Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Yao-Ting Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Yue Pan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore , Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California Los Angeles School of Medicine , Los Angeles, CA, USA
| | - Jian-You Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Dong Yin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou, P.R. China
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214
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Zhen D, Wu Y, Zhang Y, Chen K, Song B, Xu H, Tang Y, Wei Z, Meng J. m 6A Reader: Epitranscriptome Target Prediction and Functional Characterization of N 6-Methyladenosine (m 6A) Readers. Front Cell Dev Biol 2020; 8:741. [PMID: 32850851 PMCID: PMC7431669 DOI: 10.3389/fcell.2020.00741] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/16/2020] [Indexed: 12/24/2022] Open
Abstract
N 6-methyladenosine (m6A) is the most abundant post-transcriptional modification in mRNA, and regulates critical biological functions via m6A reader proteins that bind to m6A-containing transcripts. There exist multiple m6A reader proteins in the human genome, but their respective binding specificity and functional relevance under different biological contexts are not yet fully understood due to the limitation of experimental approaches. An in silico study was devised to unveil the target specificity and regulatory functions of different m6A readers. We established a support vector machine-based computational framework to predict the epitranscriptome-wide targets of six m6A reader proteins (YTHDF1-3, YTHDC1-2, and EIF3A) based on 58 genomic features as well as the conventional sequence-derived features. Our model achieved an average AUC of 0.981 and 0.893 under the full-transcript and mature mRNA model, respectively, marking a substantial improvement in accuracy compared to the sequence encoding schemes tested. Additionally, the distinct biological characteristics of each individual m6A reader were explored via the distribution, conservation, Gene Ontology enrichment, cellular components and molecular functions of their target m6A sites. A web server was constructed for predicting the putative binding readers of m6A sites to serve the research community, and is freely accessible at: http://m6areader.rnamd.com.
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Affiliation(s)
- Di Zhen
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Yuxuan Wu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Yuxin Zhang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Kunqi Chen
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Bowen Song
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Haiqi Xu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Yujiao Tang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.,Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.,AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, China
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215
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Yi YC, Chen XY, Zhang J, Zhu JS. Novel insights into the interplay between m 6A modification and noncoding RNAs in cancer. Mol Cancer 2020; 19:121. [PMID: 32767982 PMCID: PMC7412851 DOI: 10.1186/s12943-020-01233-2] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/03/2020] [Indexed: 01/17/2023] Open
Abstract
N6-methyladenosine (m6A) is one of the most common RNA modifications in eukaryotes, mainly in messenger RNA (mRNA). Increasing evidence shows that m6A methylation modification acts an essential role in various physiological and pathological bioprocesses. Noncoding RNAs (ncRNAs), including miRNAs, lncRNAs and circRNAs, are known to participate in regulating cell differentiation, angiogenesis, immune response, inflammatory response and carcinogenesis. m6A regulators, such as METTL3, ALKBH5 and IGF2BP1 have been reported to execute a m6A-dependent modification of ncRNAs involved in carcinogenesis. Meanwhile, ncRNAs can target or modulate m6A regulators to influence cancer development. In this review, we provide an insight into the interplay between m6A modification and ncRNAs in cancer.
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Affiliation(s)
- You-Cai Yi
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Xiao-Yu Chen
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China
| | - Jing Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China.
| | - Jin-Shui Zhu
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600 Yishan Road, Shanghai, 200233, China.
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216
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Keverne J, Binder EB. A Review of epigenetics in psychiatry: focus on environmental risk factors. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Epigenetic modifications play a key role in development and cell type specificity. These modifications seem to be particularly critical for brain development, where mutations in epigenetic enzymes have been associated with neurodevelopmental disorders as well as with the function of post-mitotic neurons. Epigenetic modifications can be influenced by genetic and environmental factors, both known major risk factors for psychiatric disorders. Epigenetic modifications may thus be an important mediator of the effects of genetic and environmental risk factors on cell function.
This review summarizes the different types of epigenetic regulation and then focuses on the mechanisms transducing environmental signals, especially adverse life events that are major risk factors for psychiatric disorders, into lasting epigenetic changes. This is followed by examples of how the environment can induce epigenetic changes that relate to the risk of psychiatric disorders.
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Affiliation(s)
| | - Elisabeth B. Binder
- Dept. of Translational Research in Psychiatry , Max Planck Institute of Psychiatry , Kraepelinstr. 2-10 , Munich , Germany
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217
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Barbon A, Magri C. RNA Editing and Modifications in Mood Disorders. Genes (Basel) 2020; 11:genes11080872. [PMID: 32752036 PMCID: PMC7464464 DOI: 10.3390/genes11080872] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
Major depressive disorder (MDD) is a major health problem with significant limitations in functioning and well-being. The World Health Organization (WHO) evaluates MDD as one of the most disabling disorders in the world and with very high social cost. Great attention has been given to the study of the molecular mechanism underpinning MDD at the genetic, epigenetic and proteomic level. However, the importance of RNA modifications has attracted little attention until now in this field. RNA molecules are extensively and dynamically altered by a variety of mechanisms. Similar to "epigenomic" changes, which modify DNA structure or histones, RNA alterations are now termed "epitranscriptomic" changes and have been predicted to have profound consequences for gene expression and cellular functionality. Two of these modifications, adenosine to inosine (A-to-I) RNA editing and m6A methylations, have fascinated researchers over the last years, showing a new level of complexity in gene expression. In this review, we will summary the studies that focus on the role of RNA editing and m6A methylation in MDD, trying to underline their potential breakthroughs and pitfalls.
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218
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Du T, Li G, Yang J, Ma K. RNA demethylase Alkbh5 is widely expressed in neurons and decreased during brain development. Brain Res Bull 2020; 163:150-159. [PMID: 32717204 DOI: 10.1016/j.brainresbull.2020.07.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
N6-methyladenosine (m6A) RNA methylation is one of the most abundant internal modifications on mRNAs and highly enriched within the brain. The demethylation of m6A is regulated by demethylases including fat-mass and obesity-associated protein (FTO) and AlkB homolog 5 (Alkbh5). FTO has been shown to play an important role in the brain, but little is known about the expression pattern and role of Alkbh5. Here, we investigated the expression profile of Alkbh5 in the developing mouse brain and its localization in the adult mouse brain. The results showed that Alkbh5 was widely detected throughout the mouse brain, with relatively high levels observed in the cerebellum and olfactory bulb of the adult mouse brain. Furthermore, Alkbh5 is mainly co-localized with neuronal marker NeuN, suggesting that it is primarily expressed in the neurons. Specifically, Alkbh5 could be found primarily in the nucleus of mouse neurons and cell lines. In addition, Alkbh5 protein decreased dramatically during brain development. Our findings detail the expression pattern and subcellular localization of Alkbh5 in the mouse brain. These results provide a neurobiological basis for the participation of Alkbh5 in the regulation of various brain functions, which might shed new light on further functional analysis of Alkbh5 and m6A in the central nervous system (CNS).
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Affiliation(s)
- Tingfu Du
- Center for Drug Safety Evaluation and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China; Medical Primate Research Center & Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, 100005, China; Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Diseases, Kunming, 650118, China
| | - Guoxiang Li
- Center for Drug Safety Evaluation and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Jinling Yang
- Center for Drug Safety Evaluation and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China; Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Diseases, Kunming, 650118, China
| | - Kaili Ma
- Center for Drug Safety Evaluation and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650118, China; Medical Primate Research Center & Neuroscience Center, Chinese Academy of Medical Sciences, Beijing, 100005, China; Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Diseases, Kunming, 650118, China.
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219
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Chellamuthu A, Gray SG. The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer. Cells 2020; 9:cells9081758. [PMID: 32708015 PMCID: PMC7463552 DOI: 10.3390/cells9081758] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine is often associated as an epigenetic modifier in DNA. However, it is also found increasingly in a plethora of RNA species, predominantly transfer RNAs, but increasingly found in cytoplasmic and mitochondrial ribosomal RNAs, enhancer RNAs, and a number of long noncoding RNAs. Moreover, this modification can also be found in messenger RNAs and has led to an increasing appreciation that RNA methylation can functionally regulate gene expression and cellular activities. In mammalian cells, the addition of m5C to RNA cytosines is carried out by enzymes of the NOL1/NOP2/SUN domain (NSUN) family as well as the DNA methyltransferase homologue DNMT2. In this regard, NSUN2 is a critical RNA methyltransferase for adding m5C to mRNA. In this review, using non-small cell lung cancer and other cancers as primary examples, we discuss the recent developments in the known functions of this RNA methyltransferase and its potential critical role in cancer.
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Affiliation(s)
- Anitha Chellamuthu
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
| | - Steven G. Gray
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
- Thoracic Oncology Research Group, St. James’s Hospital, Dublin D08 RX0X, Ireland
- Correspondence:
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220
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Han B, Yao HH. N 6-methyladenosine as a Novel Regulator of Brain Physiology and Diseases. Curr Med Sci 2020; 40:401-406. [PMID: 32681245 DOI: 10.1007/s11596-020-2194-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/02/2020] [Indexed: 01/29/2023]
Abstract
N6-methyladenosine (m6A) is identified as the most widespread and abundant internal chemical modification of RNA in eukaryotes. A series of proteins including methyltransferases (also known as "writers"), demethylases (also known as "erasers"), and m6A-binding proteins (also known as "readers") were indicated to participate in the m6A methylation. m6A has emerged as a regulator of various cellular, developmental, and disease processes. Notably, there is highest abundance of m6A methylation in brain than in other organs, which indicates that m6A plays an essential role in brain functions. Here, we describe the general features, mechanisms, and functions of m6A in the brain, and discuss the emerging roles of m6A in brain physiology and diseases.
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Affiliation(s)
- Bing Han
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Hong-Hong Yao
- Department of Pharmacology, School of Medicine, Southeast University, Nanjing, 210009, China.
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210009, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226019, China.
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221
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Yang YY, Yu K, Li L, Huang M, Wang Y. Proteome-wide Interrogation of Small GTPases Regulated by N6-Methyladenosine Modulators. Anal Chem 2020; 92:10145-10152. [PMID: 32567849 DOI: 10.1021/acs.analchem.0c02203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N6-Methyladenosine (m6A) in messenger RNA (mRNA) regulates its stability, splicing, and translation efficiency. Here, we explored how the expression levels of small GTPase proteins are regulated by m6A modulators. We employed a high-throughput scheduled multiple-reaction monitoring (MRM)-based targeted proteomic approach to quantify systemically the changes in expression of small GTPase proteins in cells upon genetic ablation of METTL3 (the catalytic subunit of the major m6A methyltransferase complex), m6A demethylases (ALKBH5 and FTO), or m6A reader proteins (YTHDF1, YTHDF2, and YTHDF3). Depletions of METTL3 and ALKBH5 resulted in substantially diminished and augmented expression, respectively, of a subset of small GTPase proteins, including RHOB and RHOC. Our results also revealed that the stability of RHOB mRNA is significantly increased in cells depleted of METTL3, suggesting an m6A-elicited destabilization of this mRNA. Those small GTPases that are targeted by METTL3 and/or ALKBH5 also displayed higher discrepancies between protein and mRNA expression in paired primary/metastatic melanoma or colorectal cancer cells than those that are not. Together, this is the first comprehensive analysis of the alterations in small GTPase proteome regulated by epitranscriptomic modulators of m6A, and our study suggests the potential of an alternative therapeutic approach to target the currently "undruggable" small GTPases.
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Affiliation(s)
- Yen-Yu Yang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Kailin Yu
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States.,Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
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222
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Xu N, Chen J, He G, Gao L, Zhang D. Prognostic values of m6A RNA methylation regulators in differentiated Thyroid Carcinoma. J Cancer 2020; 11:5187-5197. [PMID: 32742465 PMCID: PMC7378910 DOI: 10.7150/jca.41193] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/12/2020] [Indexed: 12/24/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent modification of RNA in mammals. m6A RNA methylation levels are dynamically regulated by m6A RNA methylation regulators. While increasing evidence has suggested that m6A RNA methylation is vital in the initiation and progression of human carcinoma, little is known about the expression and effect of m6A RNA methylation regulators in differentiated thyroid carcinoma (DTC). Herein, we demonstrate that most of the thirteen main m6A RNA methylation regulators are differentially expressed in DTC tissues and normal thyroid tissues. Based on consensus clustering of m6A RNA methylation regulators, DTC cases were divided into two subgroups (TC1 and TC2). Compared with the TC1 subgroup, the TC2 subgroup was associated with a poorer prognosis, older age, higher T grade, higher N grade and higher TNM stage. The results indicated that alteration of m6A RNA methylation regulators was closely related to DTC. We further established a risk signature of four m6A RNA methylation regulators that could evaluate prognosis and clinicopathological features in DTC. Finally, the results of the TCGA analysis were verified by other cohorts from Gene Expression Omnibus (GEO) database. In conclusion, m6A RNA methylation regulators play a crucial part in the progression of DTC and are potentially useful for evaluating the prognosis and providing potential novel insights into treatment strategies.
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Affiliation(s)
- Nizhen Xu
- Department of Head and Neck surgery, Institute of Micro-Invasive Surgery of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 3 East Qingchun Road, Hangzhou 310016, P.R. China
| | - Jian Chen
- Department of Head and Neck surgery, Institute of Micro-Invasive Surgery of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 3 East Qingchun Road, Hangzhou 310016, P.R. China
| | - Gaofei He
- Department of Head and Neck surgery, Institute of Micro-Invasive Surgery of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 3 East Qingchun Road, Hangzhou 310016, P.R. China
| | - Li Gao
- Department of Head and Neck surgery, Institute of Micro-Invasive Surgery of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 3 East Qingchun Road, Hangzhou 310016, P.R. China
| | - Deguang Zhang
- Department of Head and Neck surgery, Institute of Micro-Invasive Surgery of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 3 East Qingchun Road, Hangzhou 310016, P.R. China
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Li Y, Guo X, Sun L, Xiao J, Su S, Du S, Li Z, Wu S, Liu W, Mo K, Xia S, Chang Y, Denis D, Tao Y. N 6-Methyladenosine Demethylase FTO Contributes to Neuropathic Pain by Stabilizing G9a Expression in Primary Sensory Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902402. [PMID: 32670741 PMCID: PMC7341103 DOI: 10.1002/advs.201902402] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/27/2020] [Indexed: 05/23/2023]
Abstract
Nerve injury-induced change in gene expression in primary sensory neurons of dorsal root ganglion (DRG) is critical for neuropathic pain genesis. N6-methyladenosine (m6A) modification of RNA represents an additional layer of gene regulation. Here, it is reported that peripheral nerve injury increases the expression of the m6A demethylase fat-mass and obesity-associated proteins (FTO) in the injured DRG via the activation of Runx1, a transcription factor that binds to the Fto gene promoter. Mimicking this increase erases m6A in euchromatic histone lysine methyltransferase 2 (Ehmt2) mRNA (encoding the histone methyltransferase G9a) and elevates the level of G9a in DRG and leads to neuropathic pain symptoms. Conversely, blocking this increase reverses a loss of m6A sites in Ehmt2 mRNA and destabilizes the nerve injury-induced G9a upregulation in the injured DRG and alleviates nerve injury-associated pain hypersensitivities. FTO contributes to neuropathic pain likely through stabilizing nerve injury-induced upregulation of G9a, a neuropathic pain initiator, in primary sensory neurons.
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Affiliation(s)
- Yize Li
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Xinying Guo
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Linlin Sun
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Jifang Xiao
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Songxue Su
- Department of Physiology, Pharmacology & NeuroscienceNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E661NewarkNJ07103USA
| | - Shibin Du
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Zhen Li
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Shaogen Wu
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Weili Liu
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Kai Mo
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Shangzhou Xia
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Yun‐Juan Chang
- The Office of Advanced Research ComputingRutgers, The State University of New Jersey 185 S. Orange Ave., MSB C‐630NewarkNJ07103USA
| | - Daniel Denis
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
| | - Yuan‐Xiang Tao
- Department of AnesthesiologyNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E594NewarkNJ07103USA
- Department of Physiology, Pharmacology & NeuroscienceNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E661NewarkNJ07103USA
- Department of Cell Biology & Molecular MedicineNew Jersey Medical School, RutgersThe State University of New Jersey185 S. Orange Ave., MSB E661NewarkNJ07103USA
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Early-Life m 6A RNA Demethylation by Fat Mass and Obesity-Associated Protein (FTO) Influences Resilience or Vulnerability to Heat Stress Later in Life. eNeuro 2020; 7:ENEURO.0549-19.2020. [PMID: 32554504 PMCID: PMC7329298 DOI: 10.1523/eneuro.0549-19.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 12/20/2022] Open
Abstract
Early life heat stress leads to either resilience or vulnerability to a similar stress later in life. We have previously shown that this tuning of the stress response depends on neural network organization in the preoptic anterior hypothalamus (PO/AH) thermal response center and is regulated by epigenetic mechanisms. Here, we expand our understanding of stress response establishment describing a role for epitranscriptomic regulation of the epigenetic machinery. Specifically, we explore the role of N6-methyladenosine (m6A) RNA methylation in long-term response to heat stress. Heat conditioning of 3-d-old chicks diminished m6A RNA methylation in the hypothalamus, simultaneously with an increase in the mRNA levels of the m6A demethylase, fat mass and obesity-associated protein (FTO). Moreover, a week later, methylation of two heat stress-related transcripts, histone 3 lysine 27 (H3K27) methyltransferase, enhancer of zeste homolog 2 (EZH2) and brain-derived neurotrophic factor (BDNF), were downregulated in harsh-heat-conditioned chicks. During heat challenge a week after conditioning, there was a reduction of m6A levels in mild-heat-conditioned chicks and an elevation in harsh-heat-conditioned ones. This increase in m6A modification was negatively correlated with the expression levels of both BDNF and EZH2. Antisense “knock-down” of FTO caused an elevation of global m6A RNA methylation, reduction of EZH2 and BDNF mRNA levels, and decrease in global H3K27 dimethylation as well as dimethyl H3K27 level along BDNF coding region, and, finally, led to heat vulnerability. These findings emphasize the multilevel regulation of gene expression, including both epigenetic and epitranscriptomic regulatory mechanisms, fine-tuning the neural network organization in a response to stress.
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Abstract
The risk for major depression is both genetically and environmentally determined. It has been proposed that epigenetic mechanisms could mediate the lasting increases in depression risk following exposure to adverse life events and provide a mechanistic framework within which genetic and environmental factors can be integrated. Epigenetics refers to processes affecting gene expression and translation that do not involve changes in the DNA sequence and include DNA methylation (DNAm) and microRNAs (miRNAs) as well as histone modifications. Here we review evidence for a role of epigenetics in the pathogenesis of depression from studies investigating DNAm, miRNAs, and histone modifications using different tissues and various experimental designs. From these studies, a model emerges where underlying genetic and environmental risk factors, and interactions between the two, could drive aberrant epigenetic mechanisms targeting stress response pathways, neuronal plasticity, and other behaviorally relevant pathways that have been implicated in major depression.
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Affiliation(s)
- Signe Penner-Goeke
- Dept of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Dept of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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226
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Xu K, Mo Y, Li D, Yu Q, Wang L, Lin F, Kong C, Balelang MF, Zhang A, Chen S, Dai Q, Wang J. N 6-methyladenosine demethylases Alkbh5/Fto regulate cerebral ischemia-reperfusion injury. Ther Adv Chronic Dis 2020; 11:2040622320916024. [PMID: 32426101 PMCID: PMC7222229 DOI: 10.1177/2040622320916024] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 02/18/2020] [Indexed: 12/20/2022] Open
Abstract
Background Although N6-methyladenosine (m6A) plays a very important role in different biological processes, its function in the brain has not been fully explored. Thus, we investigated the roles of the RNA demethylases Alkbh5/Fto in cerebral ischemia-reperfusion injury. Methods We used a rat model and primary neuronal cell culture to study the role of m6A and Alkbh5/Fto in the cerebral cortex ischemic penumbra after cerebral ischemia-reperfusion injury. We used Alkbh5-shRNA and Lv-Fto (in vitro) to regulate the expression of Alkbh5/Fto to study their regulation of m6A in the cerebral cortex and to study brain function after ischemia-reperfusion injury. Results We found that RNA m6A levels increased consecutive to the increase of Alkbh5 expression in both the cerebral cortex of rats after middle cerebral artery occlusion, and in primary neurons after oxygen deprivation/reoxygenation. In contrast, Fto expression decreased after these perturbations. Our results suggest that knocking down Alkbh5 can aggravate neuronal damage. This is due to the demethylation of Alkbh5 and Fto, which selectively demethylate the Bcl2 transcript, preventing Bcl2 transcript degradation and enhancing Bcl2 protein expression. Conclusion Collectively, our results demonstrate that the demethylases Alkbh5/Fto co-regulate m6A demethylation, which plays a crucial role in cerebral ischemia-reperfusion injury. The results provide novel insights into potential therapeutic mechanisms for stroke.
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Affiliation(s)
- Kaiwei Xu
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yunchang Mo
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dan Li
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qimin Yu
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lu Wang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Feihong Lin
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chang Kong
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meita Felicia Balelang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Anqi Zhang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Sijia Chen
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qinxue Dai
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Junlu Wang
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China Wencheng County People's Hospital, Wenzhou, Zhejiang, China
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227
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Furlan M, Tanaka I, Leonardi T, de Pretis S, Pelizzola M. Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts. Front Genet 2020; 11:394. [PMID: 32425981 PMCID: PMC7212349 DOI: 10.3389/fgene.2020.00394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/30/2020] [Indexed: 01/24/2023] Open
Abstract
It has been known for a few decades that transcripts can be marked by dozens of different modifications. Yet, we are just at the beginning of charting these marks and understanding their functional impact. High-quality methods were developed for the profiling of some of these marks, and approaches to finely study their impact on specific phases of the RNA life-cycle are available, including RNA metabolic labeling. Thanks to these improvements, the most abundant marks, including N6-methyladenosine, are emerging as important determinants of the fate of marked RNAs. However, we still lack approaches to directly study how the set of marks for a given RNA molecule shape its fate. In this perspective, we first review current leading approaches in the field. Then, we propose an experimental and computational setup, based on direct RNA sequencing and mathematical modeling, to decipher the functional consequences of RNA modifications on the fate of individual RNA molecules and isoforms.
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Affiliation(s)
- Mattia Furlan
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
- Department of Physics, National Institute of Nuclear Physics, University of Turin, Turin, Italy
| | - Iris Tanaka
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tommaso Leonardi
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Stefano de Pretis
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science, Istituto Italiano di Tecnologia, Milan, Italy
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228
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Scarrow M, Chen N, Sun G. Insights into the N 6-methyladenosine mechanism and its functionality: progress and questions. Crit Rev Biotechnol 2020; 40:639-652. [PMID: 32321323 DOI: 10.1080/07388551.2020.1751059] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
N6-methyladenosine (m6A) RNA methylation has become a progressively popular area of molecular research since the discovery of its potentially essential regulatory role amongst eukaryotes. m6A marks are observed in the 5'UTR, 3'UTR and coding regions of eukaryotes and its mediation has been associated with various human diseases, RNA stability and translational efficiency. To understand the implications of m6A methylation in molecular governance, its functionality and mechanism must be initially understood. m6A regulation through its readers, writers and erasers as well as an insight into the potential "cross-talk" occurring between m6A and previously well documented regulatory molecular mechanisms have been characterized. The majority of research to date has been limited to few species and has yet to explore the species- and tissue specific nature or mechanistic plasticity of m6A regulation. There is still a tremendous gap in our knowledge surrounding the mechanism and functionality of m6A RNA methylation. Here we review the formation, removal, and decoding of m6A amongst animals, yeast, and plants while noting potential "cross-talk" between various mechanisms and highlighting potential areas of future research.
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Affiliation(s)
| | - Ning Chen
- Biology Department, Saint Mary's University, Halifax, Canada
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, Canada
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229
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McIntyre ABR, Gokhale NS, Cerchietti L, Jaffrey SR, Horner SM, Mason CE. Limits in the detection of m 6A changes using MeRIP/m 6A-seq. Sci Rep 2020; 10:6590. [PMID: 32313079 PMCID: PMC7170965 DOI: 10.1038/s41598-020-63355-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Many cellular mRNAs contain the modified base m6A, and recent studies have suggested that various stimuli can lead to changes in m6A. The most common method to map m6A and to predict changes in m6A between conditions is methylated RNA immunoprecipitation sequencing (MeRIP-seq), through which methylated regions are detected as peaks in transcript coverage from immunoprecipitated RNA relative to input RNA. Here, we generated replicate controls and reanalyzed published MeRIP-seq data to estimate reproducibility across experiments. We found that m6A peak overlap in mRNAs varies from ~30 to 60% between studies, even in the same cell type. We then assessed statistical methods to detect changes in m6A peaks as distinct from changes in gene expression. However, from these published data sets, we detected few changes under most conditions and were unable to detect consistent changes across studies of similar stimuli. Overall, our work identifies limits to MeRIP-seq reproducibility in the detection both of peaks and of peak changes and proposes improved approaches for analysis of peak changes.
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Affiliation(s)
- Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, 10065, USA.
- Tri-Institutional Program in Computational Biology and Medicine, New York City, NY, 10065, USA.
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Leandro Cerchietti
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York City, NY, 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, New York City, NY, 10065, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York City, NY, 10065, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA.
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230
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Sai L, Li Y, Zhang Y, Zhang J, Qu B, Guo Q, Han M, Jia Q, Yu G, Li K, Bo C, Zhang Y, Shao H, Peng C. Distinct m 6A methylome profiles in poly(A) RNA from Xenopus laevis testis and that treated with atrazine. CHEMOSPHERE 2020; 245:125631. [PMID: 31877456 DOI: 10.1016/j.chemosphere.2019.125631] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Recent discovery of reversible N6-methyladenosine (m6A) methylation on messenger RNA (mRNA) and mapping of m6A methylomes in mammals, plant and yeast revealed potential regulatory functions of this RNA modification. However, the role of the m6A methylomes in amphibious is still poorly understood. Here, we examined the m6A transcriptome-wide profile in testis tissues of Xenopus laevis (X. laevis) with and without treatment with 100 μg/L atrazine (AZ) through m6A sequencing analysis using the latest Illumina HiSeq sequencer. The results revealed that m6A is a highly conserved modification of mRNA in X. laevis. Distinct from that in mammals, m6A in X. laevisis enriched around the stop codon and start codon, as is reported in plant. We then investigated the differential expression m6A in testes of AZ-exposed X. laevis and compared that with the X. laevis in the control group by m6A sequencing. The results indicated that AZ leads to altered expression profile in 1380 m6A modification sites (696 upregulated and 684 downregulated). KEGG pathway analysis indicates that the "NOD-like receptors", "tight junction", "Peroxisome proliferator-activated receptors", "adherens junctions", "Glycerophospholipid metabolism" and "Fatty acid biosynthesis" signaling pathways may be associated with abnormal testis development of X. laevis due to exposure to AZ. Analysis results showed a positive correlation between m6A modification and mRNA abundance, suggesting a regulatory role of m6A in amphibious gene expression. Our first report of m6A transcriptome-wide map of an amphibian species X. laevis presented here provides a starting roadmap for uncovering m6A functions that may affect/control amphibian testis development.
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Affiliation(s)
- Linlin Sai
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China.
| | - Yan Li
- Shandong Provincial Chest Hospital, Ji'nan, Shandong, China
| | - Yecui Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Juan Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Binpeng Qu
- Shandong Medical College, Ji'nan, Shandong, China
| | - Qiming Guo
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Mingming Han
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Qiang Jia
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Gongchang Yu
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Kaili Li
- The NO.4 Hospital 1946 Jinan Shandong, Ji'nan, Shandong, China
| | - Cunxiang Bo
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Yu Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China
| | - Hua Shao
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China.
| | - Cheng Peng
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China; The University of Queensland, Queensland Alliance for Environmental Health Sciences (QAEHS), Ji'nan, Shandong, China
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231
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Murik O, Chandran SA, Nevo-Dinur K, Sultan LD, Best C, Stein Y, Hazan C, Ostersetzer-Biran O. Topologies of N 6 -adenosine methylation (m 6 A) in land plant mitochondria and their putative effects on organellar gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1269-1286. [PMID: 31657869 DOI: 10.1111/tpj.14589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Mitochondria serve as major sites of ATP production and play key roles in many other metabolic processes that are critical to the cell. As relicts of an ancient bacterial endosymbiont, mitochondria contain their own hereditary material (i.e. mtDNA, or mitogenome) and a machinery for protein biosynthesis. The expression of the mtDNA in plants is complex, particularly at the post-transcriptional level. Following transcription, the polycistronic pre-RNAs undergo extensive modifications, including trimming, splicing and editing, before being translated by organellar ribosomes. Our study focuses on N6 -methylation of adenosine ribonucleotides (m6 A-RNA) in plant mitochondria. m6 A is a prevalent modification in nuclear-encoded mRNAs. The biological significance of this dynamic modification is under investigation, but it is widely accepted that m6 A mediates structural switches that affect RNA stability and/or activity. Using m6 A-pulldown/RNA-seq (m6 A-RIP-seq) assays of Arabidopsis and cauliflower mitochondria, we provide information on the m6 A-RNA landscapes in Arabidopsis thaliana and Brassica oleracea mitochondria. The results show that m6 A targets different types of mitochondrial transcripts, including known genes, mtORFs, as well as non-coding (transcribed intergenic) RNA species. While ncRNAs undergo multiple m6 A modifications, N6 -methylation of adenosine residues with mRNAs seem preferably positioned near start codons and may modulate their translatability.
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Affiliation(s)
- Omer Murik
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Sam Aldrin Chandran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Keren Nevo-Dinur
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Laure D Sultan
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Corinne Best
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Yuval Stein
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Carina Hazan
- Analytical Chemistry Laboratory, The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Oren Ostersetzer-Biran
- Dept of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
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232
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Koshi-Mano K, Mano T, Morishima M, Murayama S, Tamaoka A, Tsuji S, Toda T, Iwata A. Neuron-specific analysis of histone modifications with post-mortem brains. Sci Rep 2020; 10:3767. [PMID: 32111906 PMCID: PMC7048733 DOI: 10.1038/s41598-020-60775-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/17/2020] [Indexed: 01/25/2023] Open
Abstract
Histone modifications govern chromatin structures and regulate gene expression to orchestrate cellular functions in the central nervous system, where neuronal cells are postmitotic and developmentally inactive, the functional and age-dependent changes also accumulate in the epigenetic states. Because the brain is composed of several types of cells, such as the neurons, glial cells, and vascular cells, the analysis of histone modifications using bulk brain tissue might obscure alterations specific to neuronal cells. Furthermore, among the various epigenetic traits, analysis of the genome-wide distribution of DNA methylation in the bulk brain is predominantly a reflection of DNA methylation of the non-neuronal cells, which may be a potential caveat of previous studies on neurodegenerative diseases using bulk brains. In this study, we established a method of neuron-specific ChIP-seq assay, which allows for the analysis of genome-wide distribution of histone modifications specifically in the neuronal cells derived from post-mortem brains. We successfully enriched neuronal information with high reproducibility and high signal-to-noise ratio. Our method will further facilitate the understanding of neurodegeneration.
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Affiliation(s)
- Kagari Koshi-Mano
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tatsuo Mano
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Maho Morishima
- Department of Neuropathology, Tokyo Metropolitan Geriatric Hospital, 35-2 Sakaecho, Itabashi, Tokyo, 173-0015, Japan
| | - Shigeo Murayama
- Department of Neuropathology, Tokyo Metropolitan Geriatric Hospital, 35-2 Sakaecho, Itabashi, Tokyo, 173-0015, Japan
| | - Akira Tamaoka
- Department of Neurology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Atsushi Iwata
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
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233
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Shafik AM, Allen EG, Jin P. Dynamic N6-methyladenosine RNA methylation in brain and diseases. Epigenomics 2020; 12:371-380. [PMID: 32081027 DOI: 10.2217/epi-2019-0260] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) is a dynamic RNA modification that regulates various aspects of RNA metabolism and has been implicated in many biological processes and transitions. m6A is highly abundant in the brain; however, only recently has the role of m6A in brain development been a focus. The machinery that controls m6A is critically important for proper neurodevelopment, and the precise mechanisms by which m6A regulates these processes are starting to emerge. However, the role of m6A in neurodegenerative and neuropsychiatric diseases still requires much elucidation. This review discusses and summarizes the current body of knowledge surrounding the function of the m6A modification in regulating normal brain development, neurodegenerative diseases and outlines possible future directions.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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234
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Hypoxia Promotes Vascular Smooth Muscle Cell (VSMC) Differentiation of Adipose-Derived Stem Cell (ADSC) by Regulating Mettl3 and Paracrine Factors. Stem Cells Int 2020; 2020:2830565. [PMID: 32148516 PMCID: PMC7053496 DOI: 10.1155/2020/2830565] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/19/2019] [Accepted: 12/31/2019] [Indexed: 12/18/2022] Open
Abstract
Adipose-derived stem cell (ADSC) is an alternative and less invasive source of mesenchymal stem cells which can be used to develop biological treatment strategies for tissue regeneration, and their therapeutic applications hinge on an understanding of their physiological characteristics. N6-Methyladenosine (m6A) is the most common chemical modification of mRNAs and has recently been revealed to play important roles in cell lineage differentiation and development. However, the role of m6A modification in the vascular smooth muscle cell (VSMC) differentiation of ADSCs remains unclear. Herein, we investigated the expression of N6-adenosine methyltransferases (Mettl3) and demethylases (Fto and Alkbh5) and found that Mettl3 was upregulated in ADSCs undergoing vascular smooth muscle differentiation induction. Moreover, silence of Mettle3 reduced the expression level of VSMC-specific markers, including α-SMA, SM22α, calponin, and SM-MHC. Meanwhile, Mettl3 knockdown also decreased the expression of paracrine factors, including VEGF, HGF, TGF-β, GM-CSF, bFGF, and SDF-1. In addition, our results suggested that hypoxia stress promotes the ADSC differentiate into VMSCs and regulates the secretion of VEGF, HGF, TGF-β, GM-CSF, bFGF, and SDF-1 by mediating Mettl3 gene expression. These observations might contribute to novel progress in understanding the role of epitranscriptomic regulation in the VSMC differentiation of ADSCs and provide a promising perspective for new therapeutic strategies for tissue regeneration.
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235
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Gokhale NS, McIntyre ABR, Mattocks MD, Holley CL, Lazear HM, Mason CE, Horner SM. Altered m 6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection. Mol Cell 2020; 77:542-555.e8. [PMID: 31810760 PMCID: PMC7007864 DOI: 10.1016/j.molcel.2019.11.007] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/11/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
The RNA modification N6-methyladenosine (m6A) modulates mRNA fate and thus affects many biological processes. We analyzed m6A across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters m6A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral infection, the addition of m6A to RIOK3 promotes its translation, while loss of m6A in CIRBP promotes alternative splicing. Importantly, viral activation of innate immune sensing or the endoplasmic reticulum (ER) stress response contributes to the changes in m6A in RIOK3 or CIRBP, respectively. Further, several transcripts with infection-altered m6A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, and HCV infection. Overall, this work reveals that cellular signaling pathways activated during viral infection lead to alterations in m6A modification of host mRNAs to regulate infection.
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Affiliation(s)
- Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27705, USA
| | - Alexa B R McIntyre
- Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Melissa D Mattocks
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher L Holley
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27705, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Helen M Lazear
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27705, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA.
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236
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Hu Y, Wang S, Liu J, Huang Y, Gong C, Liu J, Xiao Y, Yang S. New sights in cancer: Component and function of N6-methyladenosine modification. Biomed Pharmacother 2019; 122:109694. [PMID: 31918269 DOI: 10.1016/j.biopha.2019.109694] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 12/30/2022] Open
Abstract
M6A is the most prevalent modification among epigenetics. M6A occurs on different sites of RNA and exerts important functions in specific circumstances, such as mRNA splicing, stability, nuclear export, translation or damage response. Different aspects of the concrete machinery of m6A modification have been studied, including its writing, erasing and reading capabilities. The molecular and biological functions of the m6A modification and enzymes, as well as their functions in different cancers have been substantially published. The present review summarizes these findings and provides clear description of the problems involved. The probable roles of m6A modification may acts on other cancers, suggesting that it may be a treatment target for these cancers.
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Affiliation(s)
- Yiyang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Sumin Wang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Jiao Liu
- Department of Endoscope, The General Hospital of Shenyang Military Region, China
| | - Yu Huang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Chunli Gong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Jingjing Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Yufeng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China.
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237
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Roy R, Shiina N, Wang DO. More dynamic, more quantitative, unexpectedly intricate: Advanced understanding on synaptic RNA localization in learning and memory. Neurobiol Learn Mem 2019; 168:107149. [PMID: 31881355 DOI: 10.1016/j.nlm.2019.107149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/25/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Synaptic signaling exhibits great diversity, complexity, and plasticity which necessitates maintenance and rapid modification of a local proteome. One solution neurons actively exploit to meet such demands is the strategic deposition of mRNAs encoding proteins for both basal and experience-driven activities into ribonucleoprotein complexes at the synapse. Transcripts localized in this manner can be rapidly accessed for translation in response to a diverse range of stimuli in a temporal- and spatially-restricted manner. Here we review recent findings on localized RNAs and RNA binding proteins in the context of learning and memory, as revealed by cutting-edge in-vitro and in-vivo technologies capable of yielding quantitative and dynamic information. The new technologies include proteomic and transcriptomic analyses, high-resolution multiplexed RNA imaging, single-molecule RNA tracking in living neurons, animal models and human neuron cell models. Among many recent advances in the field, RNA chemical modification has emerged as one of the new regulatory layers of gene expression at synapse that is complex and yet largely unexplored. These exciting new discoveries have enhanced our understanding of the modulation mechanisms of synaptic gene expression and their roles in cognition.
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Affiliation(s)
- Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, SOKENDAI, Okazaki, Japan; Exploratory Research Center on Life and Living Systems, Okazaki, Japan.
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto, Japan.
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238
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Zhang Z, Zhan Q, Eckert M, Zhu A, Chryplewicz A, De Jesus DF, Ren D, Kulkarni RN, Lengyel E, He C, Chen M. RADAR: differential analysis of MeRIP-seq data with a random effect model. Genome Biol 2019; 20:294. [PMID: 31870409 PMCID: PMC6927177 DOI: 10.1186/s13059-019-1915-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/08/2019] [Indexed: 12/22/2022] Open
Abstract
Epitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data. RADAR enables accurate identification of altered methylation sites by accommodating variability of pre-immunoprecipitation expression level and post-immunoprecipitation count using different strategies. In addition, it is compatible with complex study design when covariates need to be incorporated in the analysis. Through simulation and real dataset analyses, we show that RADAR leads to more accurate and reproducible differential methylation analysis results than alternatives, which is available at https://github.com/scottzijiezhang/RADAR.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Qi Zhan
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Mark Eckert
- Section of Gynecologic Oncology, Department of Obstetrics and Gynecology, The University of Chicago, Chicago, IL, 60637, USA
| | - Allen Zhu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Agnieszka Chryplewicz
- Section of Gynecologic Oncology, Department of Obstetrics and Gynecology, The University of Chicago, Chicago, IL, 60637, USA
| | - Dario F De Jesus
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Decheng Ren
- Section of Endocrinology, Diabetes & Metabolism, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Ernst Lengyel
- Section of Gynecologic Oncology, Department of Obstetrics and Gynecology, The University of Chicago, Chicago, IL, 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA.
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA.
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239
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The m 6A epitranscriptome: transcriptome plasticity in brain development and function. Nat Rev Neurosci 2019; 21:36-51. [PMID: 31804615 DOI: 10.1038/s41583-019-0244-z] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 02/08/2023]
Abstract
The field of epitranscriptomics examines the recently deciphered form of gene expression regulation that is mediated by type- and site-specific RNA modifications. Similarly to the role played by epigenetic mechanisms - which operate via DNA and histone modifications - epitranscriptomic modifications are involved in the control of the delicate gene expression patterns that are needed for the development and activity of the nervous system and are essential for basic and higher brain functions. Here we describe the mechanisms that are involved in the writing, erasing and reading of N6-methyladenosine, the most prevalent internal mRNA modification, and the emerging roles played by N6-methyladenosine in the nervous system.
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240
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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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241
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Flamand MN, Meyer KD. The epitranscriptome and synaptic plasticity. Curr Opin Neurobiol 2019; 59:41-48. [PMID: 31108373 PMCID: PMC6858947 DOI: 10.1016/j.conb.2019.04.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/18/2019] [Indexed: 12/22/2022]
Abstract
RNA modifications, collectively referred to as 'the epitranscriptome,' have recently emerged as a pervasive feature of cellular mRNAs which have diverse impacts on gene expression. In the last several years, technological advances improving our ability to identify mRNA modifications, coupled with the discovery of proteins that add and remove these marks, have substantially expanded our knowledge of how the epitranscriptome shapes gene expression. Efforts to uncover functional roles for mRNA modifications have begun to reveal important roles for some marks within the nervous system, and animal models have emerged which demonstrate severe neurodevelopmental and neurocognitive abnormalities resulting from the loss of mRNA modification machinery. Here, we review the recent advances in the field of neuroepitranscriptomics, with a particular emphasis on how modifications to mRNAs within the brain contribute to synaptic activity.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, United States.
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242
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Zhang C, Wang Y, Peng Y, Xu H, Zhou X. METTL3 regulates inflammatory pain by modulating m 6A-dependent pri-miR-365-3p processing. FASEB J 2019; 34:122-132. [PMID: 31914601 DOI: 10.1096/fj.201901555r] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/15/2019] [Accepted: 10/15/2019] [Indexed: 01/24/2023]
Abstract
N6-methyladenosine (m6A) modification in RNA has been implicated in diverse biological processes. However, very little is currently known about its role in nociceptive modulation. Here, we found that the level of spinal m6A modification was significantly increased in a mouse model of Complete Freund's Adjuvant (CFA)-induced chronic inflammatory pain, which was accompanied with the augmentation of methyltransferase-like 3 (METTL3) expression in the spinal cord. Knockdown of spinal METTL3 prevented and reversed CFA-induced pain behaviors and spinal neuronal sensitization. In contrast, overexpression of spinal METTL3 produced pain behaviors and neuronal sensitization in naive mice. Moreover, we found that METTL3 positively modulated the pri-miR-65-3p processing in a microprocessor protein DiGeorge critical region 8-dependent manner. Collectively, our findings reveal an important role of METTL3-mediated m6A modification in nociceptive sensitization and provide a novel perspective on m6A modification in the development of pathological pain.
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Affiliation(s)
- Chenjing Zhang
- Department of Gastroenterology, Zhejiang Province People's Hospital, Hangzhou, China
| | - Yin Wang
- Department of Anesthesiology, Taizhou People's Hospital, Taizhou, China
| | - Yunan Peng
- Department of Anesthesiology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Hongjiao Xu
- Department of Anesthesiology, the First People's Hospital of Shanghai Transportation University, Shanghai, China
| | - Xuelong Zhou
- Department of Anesthesiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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243
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Rockwell AL, Hongay CF. The m 6A Dynamics of Profilin in Neurogenesis. Front Genet 2019; 10:987. [PMID: 31798620 PMCID: PMC6862867 DOI: 10.3389/fgene.2019.00987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/17/2019] [Indexed: 01/22/2023] Open
Abstract
Our understanding of the biological role of N6-methyladenosine (m6A), a ubiquitous non-editing RNA modification, has increased greatly since 2011. More recently, work from several labs revealed that m6A methylation regulates several aspects of mRNA metabolism. The “writer” protein METTL3, known as MT-A70 in humans, DmIme4 in flies, and MTA in plants, has the catalytic site of the METTL3/14/16 subunit of the methyltransferase complex that includes many other proteins. METTL3 is evolutionarily conserved and essential for development in multicellular organisms. However, until recently, no study has been able to provide a mechanism that explains the essentiality of METTL3. The addition of m6A to gene transcripts has been compared with the epigenetic code of histone modifications because of its effects on gene expression and its reversibility, giving birth to the field of epitranscriptomics, the study of the biological role of this and similar RNA modifications. Here, we focus on METTL3 and its likely conserved role in profilin regulation in neurogenesis. However, this and many other subunits of the methyltransferase complex are starting to be identified in several developmental processes and diseases. A recent plethora of studies about the biological role of METTL3 and other components of the methyltransferase complex that erase (FTO) or recognize (YTH proteins) this modification on transcripts revealed that this RNA modification plays a variety of roles in many biological processes like neurogenesis. Our work in Drosophila shows that the ancient and evolutionarily conserved gene profilin (chic in Drosophila) is a target of the m6A writer. Here, we discuss the implications of our study in Drosophila and how it unveils a conserved mechanism in support of the essential function of METTL3 in metazoan development. Profilin (chic) is an essential gene of ancient evolutionary origins, present in sponges (Porifera), the oldest still extant metazoan phylum of the common metazoan ancestor Urmetazoa. We propose that the relationship between profilin and METTL3 is conserved in metazoans and it provides insights into possible regulatory roles of m6A modification of profilin transcripts in processes such as neurogenesis.
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Affiliation(s)
| | - Cintia F Hongay
- Department of Biology, Clarkson University, Potsdam, NY, United States
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244
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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245
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Chokkalla AK, Mehta SL, Kim T, Chelluboina B, Kim JY, Vemuganti R. Transient Focal Ischemia Significantly Alters the m 6A Epitranscriptomic Tagging of RNAs in the Brain. Stroke 2019; 50:2912-2921. [PMID: 31436138 PMCID: PMC6759411 DOI: 10.1161/strokeaha.119.026433] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background and Purpose- Adenosine in many types of RNAs can be converted to m6A (N6-methyladenosine) which is a highly dynamic epitranscriptomic modification that regulates RNA metabolism and function. Of all organs, the brain shows the highest abundance of m6A methylation of RNAs. As recent studies showed that m6A modification promotes cell survival after adverse conditions, we currently evaluated the effect of stroke on cerebral m6A methylation in mRNAs and lncRNAs. Methods- Adult C57BL/6J mice were subjected to transient middle cerebral artery occlusion. In the peri-infarct cortex, m6A levels were measured by dot blot analysis, and transcriptome-wide m6A changes were profiled using immunoprecipitated methylated RNAs with microarrays (44 122 mRNAs and 12 496 lncRNAs). Gene ontology analysis was conducted to understand the functional implications of m6A changes after stroke. Expression of m6A writers, readers, and erasers was also estimated in the ischemic brain. Results- Global m6A levels increased significantly at 12 hours and 24 hours of reperfusion compared with sham. While 139 transcripts (122 mRNAs and 17 lncRNAs) were hypermethylated, 8 transcripts (5 mRNAs and 3 lncRNAs) were hypomethylated (>5-fold compared with sham) in the ischemic brain at 12 hours reperfusion. Inflammation, apoptosis, and transcriptional regulation are the major biological processes modulated by the poststroke differentially m6A methylated mRNAs. The m6A writers were unaltered, but the m6A eraser (fat mass and obesity-associated protein) decreased significantly after stroke compared with sham. Conclusions- This is the first study to show that stroke alters the cerebral m6A epitranscriptome, which might have functional implications in poststroke pathophysiology. Visual Overview- An online visual overview is available for this article.
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Affiliation(s)
- Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Suresh L. Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - TaeHee Kim
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Bharath Chelluboina
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Joo Yong Kim
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA
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Han P, Ivanovski S. Effect of Saliva Collection Methods on the Detection of Periodontium-Related Genetic and Epigenetic Biomarkers-A Pilot Study. Int J Mol Sci 2019; 20:ijms20194729. [PMID: 31554202 PMCID: PMC6801527 DOI: 10.3390/ijms20194729] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/17/2019] [Accepted: 09/23/2019] [Indexed: 12/11/2022] Open
Abstract
Different collection methods may influence the ability to detect and quantify biomarker levels in saliva, particularly in the expression of DNA/RNA methylation regulators of several inflammations and tissue turnover markers. This pilot study recruited five participants and unstimulated saliva were collected by either spitting or drooling, and the relative preference for each method was evaluated using a visual analogue scale. Subsequently, total RNA, gDNA and proteins were isolated using the Trizol method. Thereafter, a systematic evaluation was carried out on the potential effects of different saliva collection methods on periodontium-associated genes, DNA/RNA epigenetic factors and periodontium-related DNA methylation levels. The quantity and quality of DNA and RNA were comparable from different collection methods. Periodontium-related genes, DNA/RNA methylation epigenetic factors and periodontium-associated DNA methylation could be detected in the saliva sample, with a similar expression for both methods. The methylation of tumour necrosis factor-alpha gene promoter from drooling method showed a significant positive correlation (TNF α, r = 0.9) with clinical parameter (bleeding on probing-BOP). In conclusion, the method of saliva collection has a minimal impact on detecting periodontium-related genetic and epigenetic regulators in saliva. The pilot data shows that TNF α methylation may be correlated with clinical parameters.
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Affiliation(s)
- Pingping Han
- School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia.
| | - Sašo Ivanovski
- School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia.
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247
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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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248
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Li J, Yang X, Qi Z, Sang Y, Liu Y, Xu B, Liu W, Xu Z, Deng Y. The role of mRNA m 6A methylation in the nervous system. Cell Biosci 2019; 9:66. [PMID: 31452869 PMCID: PMC6701067 DOI: 10.1186/s13578-019-0330-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/14/2019] [Indexed: 11/21/2022] Open
Abstract
Epitranscriptomics, also known as “RNA epigenetics”, is a chemical modification for RNA regulation. Ribonucleic acid (RNA) methylation is considered to be a major discovery following the deoxyribonucleic acid (DNA) and histone methylation. Messenger RNA (mRNA) methylation modification accounts for more than 60% of all RNA modifications and N6-methyladenosine (m6A) is known as one of the most common type of eukaryotic mRNA methylation modifications in current. The m6A modification is a dynamic reversible modification, which can directly or indirectly affect biological processes, such as RNA degradation, translation and splicing, and can play important biological roles in vivo. This article introduces the mRNA m6A methylation modification enzymes and binding proteins, and reviews the research progress and related mechanisms of the role of mRNA m6A methylation in the nervous system from the aspects of neural stem cells, learning and memory, brain development, axon growth and glioblastoma.
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Affiliation(s)
- Jiashuo Li
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Xinxin Yang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhipeng Qi
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanqi Sang
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yanan Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Bin Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Wei Liu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Zhaofa Xu
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
| | - Yu Deng
- School of Public Health, China Medical University, Shenyang, 110122 Liaoning China
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249
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Transcriptome-wide dynamics of extensive m 6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol 2019; 4:2246-2259. [PMID: 31384004 DOI: 10.1038/s41564-019-0521-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/20/2019] [Indexed: 01/17/2023]
Abstract
Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-h life cycle. Although substantial post-transcriptional regulation of this hardwired program has been observed, it remains unclear how these processes are mediated on a transcriptome-wide level. To this end, we identified mRNA modifications in the P. falciparum transcriptome and performed a comprehensive characterization of N6-methyladenosine (m6A) over the course of blood-stage development. Using mass spectrometry and m6A RNA sequencing, we demonstrate that m6A is highly developmentally regulated, exceeding m6A levels known in any other eukaryote. We characterize a distinct m6A writer complex and show that knockdown of the putative m6A methyltransferase, PfMT-A70, by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A methylation and mRNA stability or translational efficiency. We further identify two putative m6A-binding YTH proteins that are likely to be involved in the regulation of these processes across the parasite's life cycle. Our data demonstrate unique features of an extensive m6A mRNA methylation programme in malaria parasites and reveal its crucial role in dynamically fine-tuning the transcriptional cascade of a unicellular eukaryote.
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250
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Yoon KJ, Ming GL, Song H. Epitranscriptomes in the Adult Mammalian Brain: Dynamic Changes Regulate Behavior. Neuron 2019; 99:243-245. [PMID: 30048610 DOI: 10.1016/j.neuron.2018.07.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epitranscriptomic modification of mRNA affects its metabolism and has recently been shown to regulate brain development. Two studies in this issue of Neuron, Koranda et al. (2018) and Engel et al. (2018), uncover dynamic and critical roles of m6A/m RNA modifications in the adult mammalian brain in regulating physiological and stress-induced behaviors.
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Affiliation(s)
- Ki-Jun Yoon
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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