151
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Cao Y, Zhuang Y, Chen J, Xu W, Shou Y, Huang X, Shu Q, Li X. Dynamic effects of Fto in regulating the proliferation and differentiation of adult neural stem cells of mice. Hum Mol Genet 2021; 29:727-735. [PMID: 31751468 DOI: 10.1093/hmg/ddz274] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/13/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
N 6-methyladenosine (m6A) modification of RNA is deposited by the methyltransferase complex consisting of Mettl3 and Mettl14 and erased by demethylase Fto and Alkbh5 and is involved in diverse biological processes. However, it remains largely unknown the specific function and mechanism of Fto in regulating adult neural stem cells (aNSCs). In the present study, utilizing a conditional knockout (cKO) mouse model, we show that the specific ablation of Fto in aNSCs transiently increases the proliferation of aNSCs and promotes neuronal differentiation both in vitro and in vivo, but in a long term, the specific ablation of Fto inhibits adult neurogenesis and neuronal development. Mechanistically, Fto deficiency results in a significant increase in m6A modification in Pdgfra and Socs5. The increased expression of Pdgfra and decreased expression of Socs5 synergistically promote the phosphorylation of Stat3. The modulation of Pdgfra and Socs5 can rescue the neurogenic deficits induced by Fto depletion. Our results together reveal an important function of Fto in regulating aNSCs through modulating Pdgfra/Socs5-Stat3 pathway.
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Affiliation(s)
- Yuhang Cao
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
| | - Yingliang Zhuang
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
| | - Junchen Chen
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
| | - Weize Xu
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
| | - Yikai Shou
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
| | - Xiaoli Huang
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
| | - Qiang Shu
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
| | - Xuekun Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310051, China.,The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310029, China.,National Clinical Research Center for Child Health, 3333 Binsheng Road, Hangzhou, Zhejiang 310051, China
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152
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Salisbury DA, Casero D, Zhang Z, Wang D, Kim J, Wu X, Vergnes L, Mirza AH, Leon-Mimila P, Williams KJ, Huertas-Vazquez A, Jaffrey SR, Reue K, Chen J, Sallam T. Transcriptional regulation of N 6-methyladenosine orchestrates sex-dimorphic metabolic traits. Nat Metab 2021; 3:940-953. [PMID: 34282353 PMCID: PMC8422857 DOI: 10.1038/s42255-021-00427-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Males and females exhibit striking differences in the prevalence of metabolic traits including hepatic steatosis, a key driver of cardiometabolic morbidity and mortality. RNA methylation is a widespread regulatory mechanism of transcript turnover. Here, we show that presence of the RNA modification N6-methyladenosine (m6A) triages lipogenic transcripts for degradation and guards against hepatic triglyceride accumulation. In male but not female mice, this protective checkpoint stalls under lipid-rich conditions. Loss of m6A control in male livers increases hepatic triglyceride stores, leading to a more 'feminized' hepatic lipid composition. Crucially, liver-specific deletion of the m6A complex protein Mettl14 from male and female mice significantly diminishes sex-specific differences in steatosis. We further surmise that the m6A installing machinery is subject to transcriptional control by the sex-responsive BCL6-STAT5 axis in response to dietary conditions. These data show that m6A is essential for precise and synchronized control of lipogenic enzyme activity and provide insights into the molecular basis for the existence of sex-specific differences in hepatic lipid traits.
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Affiliation(s)
- David A Salisbury
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zhengyi Zhang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dan Wang
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jason Kim
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiaohui Wu
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Vergnes
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aashiq H Mirza
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Paola Leon-Mimila
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kevin J Williams
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Huertas-Vazquez
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Karen Reue
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, The Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA.
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153
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The role of epigenetics in psychological resilience. Lancet Psychiatry 2021; 8:620-629. [PMID: 33915083 PMCID: PMC9561637 DOI: 10.1016/s2215-0366(20)30515-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022]
Abstract
There is substantial variation in people's responses to adversity, with a considerable proportion of individuals displaying psychological resilience. Epigenetic mechanisms are hypothesised to be one molecular pathway of how adverse and traumatic events can become biologically embedded and contribute to individual differences in resilience. However, not much is known regarding the role of epigenetics in the development of psychological resilience. In this Review, we propose a new conceptual model for the different functions of epigenetic mechanisms in psychological resilience. The model considers the initial establishment of the epigenome, epigenetic modification due to adverse and protective environments, the role of protective factors in counteracting adverse influences, and genetic moderation of environmentally induced epigenetic modifications. After reviewing empirical evidence for the various components of the model, we identify research that should be prioritised and discuss practical implications of the proposed model for epigenetic research on resilience.
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154
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Albik S, Tao YX. Emerging role of RNA m6A modification in chronic pain. Pain 2021; 162:1897-1898. [PMID: 33675633 PMCID: PMC8205953 DOI: 10.1097/j.pain.0000000000002219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/04/2021] [Indexed: 01/25/2023]
Affiliation(s)
- Sfian Albik
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Yuan-Xiang Tao
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Department of Physiology, Pharmacology & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Department of Cell Biology & Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
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155
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Methyltransferase-like 3 contributes to inflammatory pain by targeting TET1 in YTHDF2-dependent manner. Pain 2021; 162:1960-1976. [PMID: 34130310 DOI: 10.1097/j.pain.0000000000002218] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/03/2020] [Indexed: 11/26/2022]
Abstract
ABSTRACT The methyltransferase-like 3 (Mettl3) is a key component of the large N6-adenosine-methyltransferase complex in mammalian responsible for RNA N6-methyladenosine (m6A) modification, which plays an important role in gene post-transcription modulation. Although RNA m6A is enriched in mammalian neurons, its regulatory function in nociceptive information processing remains elusive. Here, we reported that Complete Freund's Adjuvant (CFA)-induced inflammatory pain significantly decreased global m6A level and m6A writer Mettl3 in the spinal cord. Mimicking this decease by knocking down or conditionally deleting spinal Mettl3 elevated the levels of m6A in ten-eleven translocation methylcytosine dioxygenases 1 (Tet1) mRNA and TET1 protein in the spinal cord, leading to production of pain hypersensitivity. By contrast, overexpressing Mettl3 reversed a loss of m6A in Tet1 mRNA and blocked the CFA-induced increase of TET1 in the spinal cord, resulting in the attenuation of pain behavior. Furthermore, the decreased level of spinal YT521-B homology domain family protein 2 (YTHDF2), an RNA m6A reader, stabilized upregulation of spinal TET1 because of the reduction of Tet1 mRNA decay by the binding to m6A in Tet1 mRNA in the spinal cord after CFA. This study reveals a novel mechanism for downregulated spinal cord METTL3 coordinating with YTHDF2 contributes to the modulation of inflammatory pain through stabilizing upregulation of TET1 in spinal neurons.
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156
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Kino T, Burd I, Segars JH. Dexamethasone for Severe COVID-19: How Does It Work at Cellular and Molecular Levels? Int J Mol Sci 2021; 22:ijms22136764. [PMID: 34201797 PMCID: PMC8269070 DOI: 10.3390/ijms22136764] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by infection of the severe respiratory syndrome coronavirus-2 (SARS-CoV-2) significantly impacted human society. Recently, the synthetic pure glucocorticoid dexamethasone was identified as an effective compound for treatment of severe COVID-19. However, glucocorticoids are generally harmful for infectious diseases, such as bacterial sepsis and severe influenza pneumonia, which can develop respiratory failure and systemic inflammation similar to COVID-19. This apparent inconsistency suggests the presence of pathologic mechanism(s) unique to COVID-19 that renders this steroid effective. We review plausible mechanisms and advance the hypothesis that SARS-CoV-2 infection is accompanied by infected cell-specific glucocorticoid insensitivity as reported for some other viruses. This alteration in local glucocorticoid actions interferes with undesired glucocorticoid to facilitate viral replication but does not affect desired anti-inflammatory properties in non-infected organs/tissues. We postulate that the virus coincidentally causes glucocorticoid insensitivity in the process of modulating host cell activities for promoting its replication in infected cells. We explore this tenet focusing on SARS-CoV-2-encoding proteins and potential molecular mechanisms supporting this hypothetical glucocorticoid insensitivity unique to COVID-19 but not characteristic of other life-threatening viral diseases, probably due to a difference in specific virally-encoded molecules and host cell activities modulated by them.
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Affiliation(s)
- Tomoshige Kino
- Laboratory of Molecular and Genomic Endocrinology, Sidra Medicine, Doha 26999, Qatar
- Correspondence: ; Tel.: +974-4003-7566
| | - Irina Burd
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (I.B.); (J.H.S.)
| | - James H. Segars
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (I.B.); (J.H.S.)
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157
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Floriou-Servou A, von Ziegler L, Waag R, Schläppi C, Germain PL, Bohacek J. The Acute Stress Response in the Multiomic Era. Biol Psychiatry 2021; 89:1116-1126. [PMID: 33722387 DOI: 10.1016/j.biopsych.2020.12.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/13/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022]
Abstract
Studying the stress response is a major pillar of neuroscience research not only because stress is a daily reality but also because the exquisitely fine-tuned bodily changes triggered by stress are a neuroendocrinological marvel. While the genome-wide changes induced by chronic stress have been extensively studied, we know surprisingly little about the complex molecular cascades triggered by acute stressors, the building blocks of chronic stress. The acute stress (or fight-or-flight) response mobilizes organismal energy resources to meet situational demands. However, successful stress coping also requires the efficient termination of the stress response. Maladaptive coping-particularly in response to severe or repeated stressors-can lead to allostatic (over)load, causing wear and tear on tissues, exhaustion, and disease. We propose that deep molecular profiling of the changes triggered by acute stressors could provide molecular correlates for allostatic load and predict healthy or maladaptive stress responses. We present a theoretical framework to interpret multiomic data in light of energy homeostasis and activity-dependent gene regulation, and we review the signaling cascades and molecular changes rapidly induced by acute stress in different cell types in the brain. In addition, we review and reanalyze recent data from multiomic screens conducted mainly in the rodent hippocampus and amygdala after acute psychophysical stressors. We identify challenges surrounding experimental design and data analysis, and we highlight promising new research directions to better understand the stress response on a multiomic level.
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Affiliation(s)
- Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Lukas von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Rebecca Waag
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Christa Schläppi
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland
| | - Pierre-Luc Germain
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland; Laboratory of Statistical Bioinformatics, Department for Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Switzerland; Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zürich, Switzerland.
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158
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Identification of an m6A-Related Signature as Biomarker for Hepatocellular Carcinoma Prognosis and Correlates with Sorafenib and Anti-PD-1 Immunotherapy Treatment Response. DISEASE MARKERS 2021; 2021:5576683. [PMID: 34221187 PMCID: PMC8213471 DOI: 10.1155/2021/5576683] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
Background N6-methyladenosine (m6A) modification plays an essential role in diverse key biological processes and may take part in the development and progression of hepatocellular carcinoma (HCC). Here, we systematically analyzed the expression profiles and prognostic values of 13 widely reported m6A modification-related genes in HCC. Methods The mRNA expression of 13 m6A modification-related genes and clinical parameters of HCC patients were downloaded from TCGA, ICGC, GSE109211, and GSE78220. Univariate and LASSO analyses were used to develop risk signature. Time-dependent ROC was performed to assess the predictive accuracy and sensitivity of risk signature. Results FTO, YTHDC1, YTHDC2, ALKBH5, KIAA1429, HNRNPC, METTL3, RBM15, YTHDF2, YTHDF1, and WTAP were significantly overexpressed in HCC patients. YTHDF1, HNRNPC, RBM15, METTL3, and YTHDF2 were independent prognostic factors for OS and DFS in HCC patients. Next, a risk signature was also developed and validated with five m6A modification-related genes in TCGA and ICGC HCC cohort. It could effectively stratify HCC patients into high-risk patients with shorter OS and DFS and low-risk patients with longer OS and DFS and showed good predictive efficiency in predicting OS and DFS. Moreover, significantly higher proportions of macrophages M0 cells, neutrophils, and Tregs were found to be enriched in HCC patients with high risk scores, while significantly higher proportions of memory CD4 T cells, gamma delta T cells, and naive B cells were found to be enriched in HCC patients with low scores. Finally, significantly lower risk scores were found at sorafenib treatment responders and anti-PD-1 immunotherapy responders compared to that in nonresponders, and anti-PD-1 immunotherapy-treated patients with lower risk scores had better OS than patients with higher risk scores. Conclusion A risk signature developed with the expression of 5 m6A-related genes could improve the prediction of prognosis of HCC and correlated with sorafenib treatment and anti-PD-1 immunotherapy response.
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159
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Han X, Liu J, Cheng G, Cui S. Gene Signatures and Prognostic Values of m6A RNA Methylation Regulators in Ovarian Cancer. Cancer Control 2021; 27:1073274820960460. [PMID: 32951457 PMCID: PMC7791456 DOI: 10.1177/1073274820960460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the most common form of mRNA modification under the field of "RNA epigenetics." However, its role in ovarian cancer (OC) development is poorly understood. In the current study, we aimed to identify gene signatures and prognostic values of m6A RNA methylation regulators. METHOD Specifically, we downloaded Mutations and Copy number variant (CNV) data from the TCGA database for 579 OC patients, then analyzed gene expression and prognosis value using integrative bioinformatics. Thereafter, we verified the related biological processes of Wilms' tumor 1-associating protein (WTAP) gene using Gene set enrichment analysis (GSEA). RESULTS Results showed that almost all ovarian cancer patients (99.31%) have CNVs with at least 1 m6A regulatory gene, whereas 83.76% of cases exhibited concurrence of CNVs in more than 4 m6A regulatory genes. Additionally, alteration of m6A regulators was associated with historical grade, whereas integrative bioinformatics and Cox multivariate model analysis revealed a significant correlation between high WTAP expression and worse ovarian cancer outcomes. Moreover, GSEA revealed that high WTAP expression was associated with cell cycle regulation and MYC targets. CONCLUSION Overall, our findings demonstrate the significance of high-frequency genetic alterations of m6A RNA methylation regulators and WTAP's poor prognosis value in OC. These findings provide valuable insights into the role of m6A methylation in OC, and will be vital in guiding development of novel treatment therapies.
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Affiliation(s)
- Xiao Han
- Department of Obstetrics and Gynecology, 117977The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Liu
- Department of Internal Medicine, 117977The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou, China
| | - Guomei Cheng
- Department of Obstetrics and Gynecology, 117977The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shihong Cui
- Department of Obstetrics and Gynecology, 117977The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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160
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The m 6A-epitranscriptome in brain plasticity, learning and memory. Semin Cell Dev Biol 2021; 125:110-121. [PMID: 34053866 DOI: 10.1016/j.semcdb.2021.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
Activity-dependent gene expression and protein translation underlie the ability of neurons to dynamically adjust their synaptic strength in response to sensory experience and during learning. The emerging field of epitranscriptomics (RNA modifications) has rapidly shifted our views on the mechanisms that regulate gene expression. Among hundreds of biochemical modifications on RNA, N6-methyladenosine (m6A) is the most abundant reversible mRNA modification in the brain. Its dynamic nature and ability to regulate all aspects of mRNA processing have positioned m6A as an important and versatile regulator of nervous system functions, including neuronal plasticity, learning and memory. In this review, we summarise recent experimental evidence that supports the role of m6A signalling in learning and memory, as well as providing an overview of the underlying molecular mechanisms in neurons. We also discuss the consequences of perturbed m6A signalling and/or its regulatory networks which are increasingly being linked to various cognitive disorders in humans.
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161
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Yu J, She Y, Ji SJ. m 6A Modification in Mammalian Nervous System Development, Functions, Disorders, and Injuries. Front Cell Dev Biol 2021; 9:679662. [PMID: 34113622 PMCID: PMC8185210 DOI: 10.3389/fcell.2021.679662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/03/2021] [Indexed: 01/27/2023] Open
Abstract
N 6-methyladenosine (m6A) modification, as the most prevalent internal modification on mRNA, has been implicated in many biological processes through regulating mRNA metabolism. Given that m6A modification is highly enriched in the mammalian brain, this dynamic modification provides a crucial new layer of epitranscriptomic regulation of the nervous system. Here, in this review, we summarize the recent progress on studies of m6A modification in the mammalian nervous system ranging from neuronal development to basic and advanced brain functions. We also highlight the detailed underlying mechanisms in each process mediated by m6A writers, erasers, and readers. Besides, the involvement of dysregulated m6A modification in neurological disorders and injuries is discussed as well.
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Affiliation(s)
- Jun Yu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,SUSTech-HKU Joint Ph.D. Program, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuanchu She
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Sheng-Jian Ji
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
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162
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Sokpor G, Xie Y, Nguyen HP, Tuoc T. Emerging Role of m 6 A Methylome in Brain Development: Implications for Neurological Disorders and Potential Treatment. Front Cell Dev Biol 2021; 9:656849. [PMID: 34095121 PMCID: PMC8170044 DOI: 10.3389/fcell.2021.656849] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/07/2021] [Indexed: 12/22/2022] Open
Abstract
Dynamic modification of RNA affords proximal regulation of gene expression triggered by non-genomic or environmental changes. One such epitranscriptomic alteration in RNA metabolism is the installation of a methyl group on adenosine [N6-methyladenosine (m6A)] known to be the most prevalent modified state of messenger RNA (mRNA) in the mammalian cell. The methylation machinery responsible for the dynamic deposition and recognition of m6A on mRNA is composed of subunits that play specific roles, including reading, writing, and erasing of m6A marks on mRNA to influence gene expression. As a result, peculiar cellular perturbations have been linked to dysregulation of components of the mRNA methylation machinery or its cofactors. It is increasingly clear that neural tissues/cells, especially in the brain, make the most of m6A modification in maintaining normal morphology and function. Neurons in particular display dynamic distribution of m6A marks during development and in adulthood. Interestingly, such dynamic m6A patterns are responsive to external cues and experience. Specific disturbances in the neural m6A landscape lead to anomalous phenotypes, including aberrant stem/progenitor cell proliferation and differentiation, defective cell fate choices, and abnormal synaptogenesis. Such m6A-linked neural perturbations may singularly or together have implications for syndromic or non-syndromic neurological diseases, given that most RNAs in the brain are enriched with m6A tags. Here, we review the current perspectives on the m6A machinery and function, its role in brain development and possible association with brain disorders, and the prospects of applying the clustered regularly interspaced short palindromic repeats (CRISPR)–dCas13b system to obviate m6A-related neurological anomalies.
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Affiliation(s)
- Godwin Sokpor
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Yuanbin Xie
- Department of Biochemistry and Molecular Biology, Gannan Medical University, Ganzhou, China
| | - Huu P Nguyen
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
| | - Tran Tuoc
- Department of Human Genetics, Ruhr University of Bochum, Bochum, Germany
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163
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Zarza-Rebollo JA, Molina E, Rivera M. The role of the FTO gene in the relationship between depression and obesity. A systematic review. Neurosci Biobehav Rev 2021; 127:630-637. [PMID: 34019853 DOI: 10.1016/j.neubiorev.2021.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/23/2022]
Abstract
Depression and obesity are major global health problems that frequently co-occur. The FTO gene has one of the strongest links with obesity and high body mass index (BMI) in humans. Besides, this gene is highly expressed in the brain, may play a role in the nervous system, and could confer risk for depression, although scarce literature is available in this respect. We perform a systematic review of the relationship between FTO and both conditions. We selected original articles with observational design or reviews, where depression was assessed with ICD-10, DSM-5 or previous versions, published from 2012 (when the first related paper was published) to November 2020, performed in adults, in English or Spanish and having an optimal methodological quality (evaluated with SIGN checklist). Five original studies were finally included. The results regarding the role of FTO in depression-obesity comorbidity were inconclusive. This leads us to endorse further research covering the role of this gene on both conditions, emphasising a more precise characterization of depression, in order to confirm this role.
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Affiliation(s)
- Juan Antonio Zarza-Rebollo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Spain; Institute of Neurosciences 'Federico Olóriz', Biomedical Research Centre (CIBM), University of Granada, Spain
| | - Esther Molina
- Institute of Neurosciences 'Federico Olóriz', Biomedical Research Centre (CIBM), University of Granada, Spain; Department of Nursing, Faculty of Health Sciences, University of Granada, Spain.
| | - Margarita Rivera
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Spain; Institute of Neurosciences 'Federico Olóriz', Biomedical Research Centre (CIBM), University of Granada, Spain
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164
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Mathoux J, Henshall DC, Brennan GP. Regulatory Mechanisms of the RNA Modification m 6A and Significance in Brain Function in Health and Disease. Front Cell Neurosci 2021; 15:671932. [PMID: 34093133 PMCID: PMC8170084 DOI: 10.3389/fncel.2021.671932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
RNA modifications have emerged as an additional layer of regulatory complexity governing the function of almost all species of RNA. N6-methyladenosine (m6A), the addition of methyl groups to adenine residues, is the most abundant and well understood RNA modification. The current review discusses the regulatory mechanisms governing m6A, how this influences neuronal development and function and how aberrant m6A signaling may contribute to neurological disease. M6A is known to regulate the stability of mRNA, the processing of microRNAs and function/processing of tRNAs among other roles. The development of antibodies against m6A has facilitated the application of next generation sequencing to profile methylated RNAs in both health and disease contexts, revealing the extent of this transcriptomic modification. The mechanisms by which m6A is deposited, processed, and potentially removed are increasingly understood. Writer enzymes include METTL3 and METTL14 while YTHDC1 and YTHDF1 are key reader proteins, which recognize and bind the m6A mark. Finally, FTO and ALKBH5 have been identified as potential erasers of m6A, although there in vivo activity and the dynamic nature of this modification requires further study. M6A is enriched in the brain and has emerged as a key regulator of neuronal activity and function in processes including neurodevelopment, learning and memory, synaptic plasticity, and the stress response. Changes to m6A have recently been linked with Schizophrenia and Alzheimer disease. Elucidating the functional consequences of m6A changes in these and other brain diseases may lead to novel insight into disease pathomechanisms, molecular biomarkers and novel therapeutic targets.
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Affiliation(s)
- Justine Mathoux
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.,FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.,FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Gary P Brennan
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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165
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Kunovac A, Hathaway QA, Pinti MV, Durr AJ, Taylor AD, Goldsmith WT, Garner KL, Nurkiewicz TR, Hollander JM. Enhanced antioxidant capacity prevents epitranscriptomic and cardiac alterations in adult offspring gestationally-exposed to ENM. Nanotoxicology 2021; 15:812-831. [PMID: 33969789 DOI: 10.1080/17435390.2021.1921299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Maternal engineered nanomaterial (ENM) exposure during gestation has been associated with negative long-term effects on cardiovascular health in progeny. Here, we evaluate an epitranscriptomic mechanism that contributes to these chronic ramifications and whether overexpression of mitochondrial phospholipid hydroperoxide glutathione peroxidase (mPHGPx) can preserve cardiovascular function and bioenergetics in offspring following gestational nano-titanium dioxide (TiO2) inhalation exposure. Wild-type (WT) and mPHGPx (Tg) dams were exposed to nano-TiO2 aerosols with a mass concentration of 12.01 ± 0.50 mg/m3 starting from gestational day (GD) 5 for 360 mins/day for 6 nonconsecutive days over 8 days. Echocardiography was performed in pregnant dams, adult (11-week old) and fetal (GD 14) progeny. Mitochondrial function and global N6-methyladenosine (m6A) content were assessed in adult progeny. MPHGPx enzymatic function was further evaluated in adult progeny and m6A-RNA immunoprecipitation (RIP) was combined with RT-qPCR to evaluate m6A content in the 3'-UTR. Following gestational ENM exposure, global longitudinal strain (GLS) was 32% lower in WT adult offspring of WT dams, with preservation in WT offspring of Tg dams. MPHGPx activity was significantly reduced in WT offspring (29%) of WT ENM-exposed dams, but preserved in the progeny of Tg dams. M6A-RIP-qPCR for the SEC insertion sequence region of mPHGPx revealed hypermethylation in WT offspring from ENM-exposed WT dams, which was thwarted in the presence of the maternal transgene. Our findings implicate that m6A hypermethylation of mPHGPx may be culpable for diminished antioxidant capacity and resultant mitochondrial and cardiac deficits that persist into adulthood following gestational ENM inhalation exposure.
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Affiliation(s)
- Amina Kunovac
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA.,Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA.,Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA.,Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA.,Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
| | - Mark V Pinti
- Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA.,West Virginia University School of Pharmacy, Morgantown, WV, USA
| | - Andrya J Durr
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA.,Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Andrew D Taylor
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA.,Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA
| | - William T Goldsmith
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA.,Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Krista L Garner
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA.,Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Timothy R Nurkiewicz
- Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA.,Department of Physiology & Pharmacology, West Virginia University School of Medicine, Morgantown, WV, USA
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University School of Medicine, Morgantown, WV, USA.,Mitochondria, Metabolism & Bioenergetics Working Group, West Virginia University School of Medicine, Morgantown, WV, USA.,Center for Inhalation Toxicology (iTOX), West Virginia University School of Medicine, Morgantown, WV, USA
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166
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Song D, Hou J, Wu J, Wang J. Role of N 6-Methyladenosine RNA Modification in Cardiovascular Disease. Front Cardiovasc Med 2021; 8:659628. [PMID: 34026872 PMCID: PMC8138049 DOI: 10.3389/fcvm.2021.659628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
Despite treatments being improved and many risk factors being identified, cardiovascular disease (CVD) is still a leading cause of mortality and disability worldwide. N6-methyladenosine (m6A) is the most common, abundant, and conserved internal modification in RNAs and plays an important role in the development of CVD. Many studies have shown that aabnormal m6A modifications of coding RNAs are involved in the development of CVD. In addition, non-coding RNAs (ncRNAs) exert post-transcriptional regulation in many diseases including CVD. Although ncRNAs have also been found to be modified by m6A, the studies on m6A modifications of ncRNAs in CVD are currently lacking. In this review, we summarized the recent progress in understanding m6A modifications in the context of coding RNAs and ncRNAs, as well as their regulatory roles in CVD.
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Affiliation(s)
- Dandan Song
- Department of Clinical Laboratory, Second Hospital of Jilin University, Changchun, China.,State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, China
| | - Jianhua Hou
- Department of Orthodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Junduo Wu
- Department of Cardiology, Second Hospital of Jilin University, Changchun, China
| | - Junnan Wang
- Department of Cardiology, Second Hospital of Jilin University, Changchun, China
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167
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Xu S, Xu X, Zhang Z, Yan L, Zhang L, Du L. The role of RNA m 6A methylation in the regulation of postnatal hypoxia-induced pulmonary hypertension. Respir Res 2021; 22:121. [PMID: 33902609 PMCID: PMC8074209 DOI: 10.1186/s12931-021-01728-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pulmonary hypertension (PH) is a complex pulmonary vascular disease characterized by an imbalance in vasoconstrictor/vasodilator signaling within the pulmonary vasculature. Recent evidence suggests that exposure to hypoxia early in life can cause alterations in the pulmonary vasculature and lead to the development of PH. However, the long-term impact of postnatal hypoxia on lung development and pulmonary function remains unknown. N6-methyladenosine (m6A) regulates gene expression and governs many important biological processes. However, the function of m6A in the development of PH remains poorly characterized. Thus, the purpose of this investigation was to test the two-fold hypothesis that (1) postnatal exposure to hypoxia would alter lung development leading to PH in adult rats, and (2) m6A modification would change in rats exposed to hypoxia, suggesting it plays a role in the development of PH. METHODS Twenty-four male Sprague-Dawley rats were exposed to a hypoxic environment (FiO2: 12%) within 24 h after birth for 2 weeks. PH was defined as an increased right ventricular pressure (RVP) and pathologic changes of pulmonary vasculature measured by α-SMA immunohistochemical staining. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was performed to analyze m6A modification changes in lung tissue in 2- and 9-week-old rats that were exposed to postnatal hypoxia. RESULTS Mean pulmonary arterial pressure, lung/body weight ratio, and the Fulton index was significantly greater in rats exposed to hypoxia when compared to control and the difference persisted into adulthood. m6A methyltransferase and demethylase proteins were significantly downregulated in postnatal hypoxia-induced PH. Distinct m6A modification peak-related genes differed between the two groups, and these genes were associated with lung development. CONCLUSIONS Our results indicate postnatal hypoxia can cause PH, which can persist into adulthood. The development and persistence of PH may be because of the continuous low expression of methyltransferase like 3 affecting the m6A level of PH-related genes. Our findings provide new insights into the impact of postnatal hypoxia and the role of m6A in the development of pulmonary vascular pathophysiology.
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Affiliation(s)
- Shanshan Xu
- Department of Neonatology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People's Republic of China
| | - Xuefeng Xu
- Department of Rheumatology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People's Republic of China
| | - Ziming Zhang
- Department of Neonatology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People's Republic of China
| | - Lingling Yan
- Department of Neonatology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People's Republic of China
| | - Liyan Zhang
- Fuzhou Children Hospital of Fujian Medical University, Fuzhou, 350005, People's Republic of China
| | - Lizhong Du
- Department of Neonatology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People's Republic of China.
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168
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Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
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169
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Richter JD, Zhao X. The molecular biology of FMRP: new insights into fragile X syndrome. Nat Rev Neurosci 2021; 22:209-222. [PMID: 33608673 PMCID: PMC8094212 DOI: 10.1038/s41583-021-00432-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 01/31/2023]
Abstract
Fragile X mental retardation protein (FMRP) is the product of the fragile X mental retardation 1 gene (FMR1), a gene that - when epigenetically inactivated by a triplet nucleotide repeat expansion - causes the neurodevelopmental disorder fragile X syndrome (FXS). FMRP is a widely expressed RNA-binding protein with activity that is essential for proper synaptic plasticity and architecture, aspects of neural function that are known to go awry in FXS. Although the neurophysiology of FXS has been described in remarkable detail, research focusing on the molecular biology of FMRP has only scratched the surface. For more than two decades, FMRP has been well established as a translational repressor; however, recent whole transcriptome and translatome analyses in mouse and human models of FXS have shown that FMRP is involved in the regulation of nearly all aspects of gene expression. The emerging mechanistic details of the mechanisms by which FMRP regulates gene expression may offer ways to design new therapies for FXS.
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Affiliation(s)
- Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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170
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Zhao Y, Chen Y, Jin M, Wang J. The crosstalk between m 6A RNA methylation and other epigenetic regulators: a novel perspective in epigenetic remodeling. Am J Cancer Res 2021; 11:4549-4566. [PMID: 33754077 PMCID: PMC7977459 DOI: 10.7150/thno.54967] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/07/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic regulation involves a range of sophisticated processes which contribute to heritable alterations in gene expression without altering DNA sequence. Regulatory events predominantly include DNA methylation, chromatin remodeling, histone modifications, non-coding RNAs (ncRNAs), and RNA modification. As the most prevalent RNA modification in eukaryotic cells, N6-methyladenosine (m6A) RNA methylation actively participates in the modulation of RNA metabolism. Notably, accumulating evidence has revealed complicated interrelations occurring between m6A and other well-known epigenetic modifications. Their crosstalk conspicuously triggers epigenetic remodeling, further yielding profound impacts on a variety of physiological and pathological processes, especially tumorigenesis. Herein, we provide an up-to-date review of this emerging hot area of biological research, summarizing the interplay between m6A RNA methylation and other epigenetic regulators, and highlighting their underlying functions in epigenetic reprogramming.
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171
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Jiang X, Liu B, Nie Z, Duan L, Xiong Q, Jin Z, Yang C, Chen Y. The role of m6A modification in the biological functions and diseases. Signal Transduct Target Ther 2021; 6:74. [PMID: 33611339 PMCID: PMC7897327 DOI: 10.1038/s41392-020-00450-x] [Citation(s) in RCA: 755] [Impact Index Per Article: 251.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent, abundant and conserved internal cotranscriptional modification in eukaryotic RNAs, especially within higher eukaryotic cells. m6A modification is modified by the m6A methyltransferases, or writers, such as METTL3/14/16, RBM15/15B, ZC3H3, VIRMA, CBLL1, WTAP, and KIAA1429, and, removed by the demethylases, or erasers, including FTO and ALKBH5. It is recognized by m6A-binding proteins YTHDF1/2/3, YTHDC1/2 IGF2BP1/2/3 and HNRNPA2B1, also known as "readers". Recent studies have shown that m6A RNA modification plays essential role in both physiological and pathological conditions, especially in the initiation and progression of different types of human cancers. In this review, we discuss how m6A RNA methylation influences both the physiological and pathological progressions of hematopoietic, central nervous and reproductive systems. We will mainly focus on recent progress in identifying the biological functions and the underlying molecular mechanisms of m6A RNA methylation, its regulators and downstream target genes, during cancer progression in above systems. We propose that m6A RNA methylation process offer potential targets for cancer therapy in the future.
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Affiliation(s)
- Xiulin Jiang
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, 650223 Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Baiyang Liu
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, 650223 Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhi Nie
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, 650223 Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China ,grid.285847.40000 0000 9588 0960Kunming Medical University, 650500 Kunming, China
| | - Lincan Duan
- grid.285847.40000 0000 9588 0960Kunming Medical University, 650500 Kunming, China
| | - Qiuxia Xiong
- grid.285847.40000 0000 9588 0960Kunming Medical University, 650500 Kunming, China
| | - Zhixian Jin
- grid.285847.40000 0000 9588 0960Kunming Medical University, 650500 Kunming, China
| | - Cuiping Yang
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, 650223 Kunming, Yunnan China
| | - Yongbin Chen
- grid.419010.d0000 0004 1792 7072Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, 650223 Kunming, Yunnan China ,grid.9227.e0000000119573309Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, Yunnan China
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172
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Wilkinson E, Cui YH, He YY. Context-Dependent Roles of RNA Modifications in Stress Responses and Diseases. Int J Mol Sci 2021; 22:ijms22041949. [PMID: 33669361 PMCID: PMC7920320 DOI: 10.3390/ijms22041949] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
RNA modifications are diverse post-transcriptional modifications that regulate RNA metabolism and gene expression. RNA modifications, and the writers, erasers, and readers that catalyze these modifications, serve as important signaling machineries in cellular stress responses and disease pathogenesis. In response to stress, RNA modifications are mobilized to activate or inhibit the signaling pathways that combat stresses, including oxidative stress, hypoxia, therapeutic stress, metabolic stress, heat shock, DNA damage, and ER stress. The role of RNA modifications in response to these cellular stressors is context- and cell-type-dependent. Due to their pervasive roles in cell biology, RNA modifications have been implicated in the pathogenesis of different diseases, including cancer, neurologic and developmental disorders and diseases, and metabolic diseases. In this review, we aim to summarize the roles of RNA modifications in molecular and cellular stress responses and diseases.
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173
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Jonkhout N, Cruciani S, Santos Vieira HG, Tran J, Liu H, Liu G, Pickford R, Kaczorowski D, Franco GR, Vauti F, Camacho N, Abedini SS, Najmabadi H, Ribas de Pouplana L, Christ D, Schonrock N, Mattick JS, Novoa EM. Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation. RNA Biol 2021; 18:1905-1919. [PMID: 33499731 DOI: 10.1080/15476286.2021.1881291] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.
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Affiliation(s)
- Nicky Jonkhout
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Sonia Cruciani
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Julia Tran
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Huanle Liu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Ganqiang Liu
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Current Address: School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia
| | | | - Gloria R Franco
- Departamento De Bioquímica E Imunologia, Universidade Federal De Minas Gerais,Belo Horizonte,Minas Gerais, Brazil
| | - Franz Vauti
- Division of Cellular & Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Noelia Camacho
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain
| | - Seyedeh Sedigheh Abedini
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nicole Schonrock
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Eva Maria Novoa
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
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174
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Fang Z, Jiang C, Li S. The Potential Regulatory Roles of Circular RNAs in Tumor Immunology and Immunotherapy. Front Immunol 2021; 11:617583. [PMID: 33613544 PMCID: PMC7886782 DOI: 10.3389/fimmu.2020.617583] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/14/2020] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules in eukaryotes with features of high stability, tissue-specific and cell-specific expression. According to their biogenesis, circRNAs are mainly classified into five types, i.e. exonic circRNAs (EciRNAs), exon-intron circRNAs (EIciRNAs), intronic RNAs (CiRNAs), fusion circRNAs (f-circRNAs), and read-through circRNAs (rt-circRNAs). CircRNAs have been emerging as important non-coding regulatory RNAs in a variety of human cancers. CircRNA4s were revealed to exert regulatory function through multiple mechanisms, such as sponges/decoys of miRNAs and proteins, enhancers of protein functions, protein scaffolds, protein recruitment, or protein translation templates. Furthermore, some circRNAs are intensively associated with immune cells in tumor immune microenvironment (TIME), e.g. circARSP91 and natural killer cells. Through regulating immune checkpoint genes, circRNAs are demonstrated to modulate the immune checkpoint blockade immunotherapy, e.g. circCPA4 could up-regulate PD-L1 expression. In summary, we reviewed the molecular features of circRNAs and mechanisms how they exert functions. We further summarized functional implications of circRNA regulations in tumor immunology and immunotherapy. Further understanding of the regulatory roles of circRNAs in tumor immunology and immunotherapy will benefit tumor treatment.
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Affiliation(s)
- Zhixiao Fang
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Shengli Li
- Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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175
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Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A, Soldano A, Roignant JY. Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J 2021; 40:e104975. [PMID: 33428246 PMCID: PMC7883056 DOI: 10.15252/embj.2020104975] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
N6‐methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. This modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior, albeit the underlying molecular mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6A reader in the nervous system, being required to limit axonal growth. Mechanistically, we show that the m6A reader Ythdf directly interacts with Fmr1, the fly homolog of Fragile X mental retardation RNA binding protein (FMRP), to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system and modulates Fmr1 target transcript selection.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Tina Lence
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Hans-Hermann Wessels
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department CIBIO, University of Trento, Trento, Italy
| | - Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anke Busch
- Bioinformatics Core Facility, IMB, Mainz, Germany
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Michela Notarangelo
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Heidelberg-Mannheim, Heidelberg, Germany
| | - Alessandro Quattrone
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessia Soldano
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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176
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Gu J, Zhan Y, Zhuo L, Zhang Q, Li G, Li Q, Qi S, Zhu J, Lv Q, Shen Y, Guo Y, Liu S, Xie T, Sui X. Biological functions of m 6A methyltransferases. Cell Biosci 2021; 11:15. [PMID: 33431045 PMCID: PMC7798219 DOI: 10.1186/s13578-020-00513-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022] Open
Abstract
M6A methyltransferases, acting as a writer in N6-methyladenosine, have attracted wide attention due to their dynamic regulation of life processes. In this review, we first briefly introduce the individual components of m6A methyltransferases and explain their close connections to each other. Then, we concentrate on the extensive biological functions of m6A methyltransferases, which include cell growth, nerve development, osteogenic differentiation, metabolism, cardiovascular system homeostasis, infection and immunity, and tumour progression. We summarize the currently unresolved problems in this research field and propose expectations for m6A methyltransferases as novel targets for preventive and curative strategies for disease treatment in the future.
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Affiliation(s)
- Jianzhong Gu
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, China
| | - Yu Zhan
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, China
| | - Lvjia Zhuo
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Qin Zhang
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Guohua Li
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Qiujie Li
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Shasha Qi
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Jinyu Zhu
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China
| | - Qun Lv
- Department of Respiratory medicine, the Affiliated Hospital of Hangzhou Normal University, School of Medicine, Hangzhou Normal University, Hangzhou, 310015, Zhejiang, China
| | - Yingying Shen
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, China
| | - Yong Guo
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, China
| | - Shuiping Liu
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China. .,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
| | - Tian Xie
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China. .,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
| | - Xinbing Sui
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China. .,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, Zhejiang, China.
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177
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Tang Y, Chen K, Song B, Ma J, Wu X, Xu Q, Wei Z, Su J, Liu G, Rong R, Lu Z, de Magalhães J, Rigden DJ, Meng J. m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. Nucleic Acids Res 2021; 49:D134-D143. [PMID: 32821938 PMCID: PMC7779050 DOI: 10.1093/nar/gkaa692] [Citation(s) in RCA: 182] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 12/25/2022] Open
Abstract
N 6-Methyladenosine (m6A) is the most prevalent RNA modification on mRNAs and lncRNAs. It plays a pivotal role during various biological processes and disease pathogenesis. We present here a comprehensive knowledgebase, m6A-Atlas, for unraveling the m6A epitranscriptome. Compared to existing databases, m6A-Atlas features a high-confidence collection of 442 162 reliable m6A sites identified from seven base-resolution technologies and the quantitative (rather than binary) epitranscriptome profiles estimated from 1363 high-throughput sequencing samples. It also offers novel features, such as; the conservation of m6A sites among seven vertebrate species (including human, mouse and chimp), the m6A epitranscriptomes of 10 virus species (including HIV, KSHV and DENV), the putative biological functions of individual m6A sites predicted from epitranscriptome data, and the potential pathogenesis of m6A sites inferred from disease-associated genetic mutations that can directly destroy m6A directing sequence motifs. A user-friendly graphical user interface was constructed to support the query, visualization and sharing of the m6A epitranscriptomes annotated with sites specifying their interaction with post-transcriptional machinery (RBP-binding, microRNA interaction and splicing sites) and interactively display the landscape of multiple RNA modifications. These resources provide fresh opportunities for unraveling the m6A epitranscriptomes. m6A-Atlas is freely accessible at: www.xjtlu.edu.cn/biologicalsciences/atlas.
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Affiliation(s)
- Yujiao Tang
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Kunqi Chen
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX Liverpool, UK
| | - Bowen Song
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Jiongming Ma
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Xiangyu Wu
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX Liverpool, UK
| | - Qingru Xu
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Zhen Wei
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Jionglong Su
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Gang Liu
- Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Rong Rong
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Zhiliang Lu
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | | | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Jia Meng
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
- AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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178
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Aluru N, Karchner SI. PCB126 Exposure Revealed Alterations in m6A RNA Modifications in Transcripts Associated With AHR Activation. Toxicol Sci 2021; 179:84-94. [PMID: 33064826 PMCID: PMC8453794 DOI: 10.1093/toxsci/kfaa158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3' UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3' UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
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Affiliation(s)
- Neelakanteswar Aluru
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543
| | - Sibel I Karchner
- Biology Department and Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543
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179
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Anreiter I, Mir Q, Simpson JT, Janga SC, Soller M. New Twists in Detecting mRNA Modification Dynamics. Trends Biotechnol 2021; 39:72-89. [PMID: 32620324 PMCID: PMC7326690 DOI: 10.1016/j.tibtech.2020.06.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/28/2022]
Abstract
Modified nucleotides in mRNA are an essential addition to the standard genetic code of four nucleotides in animals, plants, and their viruses. The emerging field of epitranscriptomics examines nucleotide modifications in mRNA and their impact on gene expression. The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions. Selective chemical and immunological identification of modified nucleotides has revealed global candidate topology maps for many modifications in mRNA, but further technical advances to increase confidence will be necessary. Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel sequencing technology.
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Affiliation(s)
- Ina Anreiter
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Sarath C Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, 5021 Health Information and Translational Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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180
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Su Y, Xu R, Zhang R, Qu Y, Zuo W, Ji Z, Geng H, Pan M, Ma G. N6-methyladenosine methyltransferase plays a role in hypoxic preconditioning partially through the interaction with lncRNA H19. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1306-1315. [PMID: 33197240 DOI: 10.1093/abbs/gmaa130] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 11/13/2022] Open
Abstract
N6-methyladenosine (m6A), a methylation in the N6 position of adenosine especially in the mRNA, exerts diverse physiological and pathological functions. However, the precise role of m6A methylation in hypoxic preconditioning (HPC) is still unknown. Here, we observed that HPC treatment protected H9c2 cells against H2O2-induced injury, upregulated the m6A level in the total RNA and the expression of methyltransferase like 3 (METTL3), methyltransferase like 14 (METTL14), and long noncoding RNA (lncRNA) H19. Either knockdown of METTL3 or METTL14 notably reversed the HPC-induced enhancement of cell viability, anti-apoptosis ability, and H19 expression. Methylated RNA immunoprecipitation (IP) indicated that knockdown of METTL3 or METTL14 decreased m6A level in the lncRNA H19. Gain-of-function assay demonstrated that H19 overexpression could partially rescue the decreased protection mediated by METTL3 or METTL14 knockdown in HPC-treated H9c2 cells. RNA binding protein immunoprecipitation (RIP) assay showed that METTL3 and METTL14 could directly bind with H19. Our study identified a novel pattern of posttranscriptional regulation in HPC treatment. Since METTL3, METTL14, and lncRNA H19 were involved in HPC protection, they could be considered as potential biomarkers and therapeutic targets in HPC-derived cardiac rehabilitation and therapeutic approaches.
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Affiliation(s)
- Yamin Su
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Rongfeng Xu
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Rui Zhang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Yangyang Qu
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Wenjie Zuo
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Zhenjun Ji
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Haihua Geng
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Min Pan
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Genshan Ma
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
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181
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Das Mandal S, Ray PS. Transcriptome-wide analysis reveals spatial correlation between N6-methyladenosine and binding sites of microRNAs and RNA-binding proteins. Genomics 2020; 113:205-216. [PMID: 33340693 DOI: 10.1016/j.ygeno.2020.12.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/02/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022]
Abstract
N6-methyladenosine (m6A), the most prevalent epitranscriptomic modification in eukaryotes, is enriched in 3'-untranslated regions (3'UTRs) of mRNAs. As 3'UTRs are major binding sites of RNA-binding proteins (RBPs) and microRNAs (miRNAs), m6A-dependent local RNA structure change may alter the accessibility of RBPs and miRNAs to their target sites and regulate mRNA function. Using a human transcriptome-wide computational analysis to investigate the relation between m6A, RBPs and miRNAs, we find a strong positive correlation between number of m6A sites, miRNAs and RBPs binding to mRNAs, suggesting m6A-modified mRNAs are more targeted by miRNAs and RBPs. Moreover, m6A sites are located proximally to miRNA target sites and binding sites of multiple RBPs. Further, miRNA target sites and RBP-binding sites located close to each other are also located proximally to m6A. This study indicates three-way interplay between m6A, microRNA and RBP binding, suggesting the influence of mRNA modifications on the miRNA and RBP interactomes.
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Affiliation(s)
- Sukhen Das Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, Nadia, 741246, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, Mohanpur, Nadia, 741246, West Bengal, India.
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182
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Yang F, Zhang F, Ji X, Jiang X, Xue M, Yu H, Hu X, Bao Z. Secretory galectin-3 induced by glucocorticoid stress triggers stemness exhaustion of hepatic progenitor cells. J Biol Chem 2020; 295:16852-16862. [PMID: 32989051 PMCID: PMC7864077 DOI: 10.1074/jbc.ra120.012974] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 09/17/2020] [Indexed: 12/18/2022] Open
Abstract
Adult progenitor cell populations typically exist in a quiescent state within a controlled niche environment. However, various stresses or forms of damage can disrupt this state, which often leads to dysfunction and aging. We built a glucocorticoid (GC)-induced liver damage model of mice, found that GC stress induced liver damage, leading to consequences for progenitor cells expansion. However, the mechanisms by which niche factors cause progenitor cells proliferation are largely unknown. We demonstrate that, within the liver progenitor cells niche, Galectin-3 (Gal-3) is responsible for driving a subset of progenitor cells to break quiescence. We show that GC stress causes aging of the niche, which induces the up-regulation of Gal-3. The increased Gal-3 population increasingly interacts with the progenitor cell marker CD133, which triggers focal adhesion kinase (FAK)/AMP-activated kinase (AMPK) signaling. This results in the loss of quiescence and leads to the eventual stemness exhaustion of progenitor cells. Conversely, blocking Gal-3 with the inhibitor TD139 prevents the loss of stemness and improves liver function. These experiments identify a stress-dependent change in progenitor cell niche that directly influence liver progenitor cell quiescence and function.
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Affiliation(s)
- Fan Yang
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Fan Zhang
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Xueying Ji
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Xin Jiang
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Mengjuan Xue
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Huiyuan Yu
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Xiaona Hu
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Zhijun Bao
- Department of Geriatric Medicine, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China; Research Center on Aging and Medicine, Fudan University, Shanghai, China.
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183
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Chokkalla AK, Mehta SL, Vemuganti R. Epitranscriptomic regulation by m 6A RNA methylation in brain development and diseases. J Cereb Blood Flow Metab 2020; 40:2331-2349. [PMID: 32967524 PMCID: PMC7820693 DOI: 10.1177/0271678x20960033] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
Cellular RNAs are pervasively tagged with diverse chemical moieties, collectively called epitranscriptomic modifications. The methylation of adenosine at N6 position generates N6-methyladenosine (m6A), which is the most abundant and reversible epitranscriptomic modification in mammals. The m6A signaling is mediated by a dedicated set of proteins comprised of writers, erasers, and readers. Contrary to the activation-repression binary view of gene regulation, emerging evidence suggests that the m6A methylation controls multiple aspects of mRNA metabolism, such as splicing, export, stability, translation, and degradation, culminating in the fine-tuning of gene expression. Brain shows the highest abundance of m6A methylation in the body, which is developmentally altered. Within the brain, m6A methylation is biased toward neuronal transcripts and sensitive to neuronal activity. In a healthy brain, m6A maintains several developmental and physiological processes such as neurogenesis, axonal growth, synaptic plasticity, circadian rhythm, cognitive function, and stress response. The m6A imbalance contributes to the pathogenesis of acute and chronic CNS insults, brain cancer, and neuropsychiatric disorders. This review discussed the molecular mechanisms of m6A regulation and its implication in the developmental, physiological, and pathological processes of the brain.
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Affiliation(s)
- Anil K Chokkalla
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin–Madison, Madison, WI, USA
- Department of Neurological Surgery, University of Wisconsin–Madison, Madison, WI, USA
| | - Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin–Madison, Madison, WI, USA
| | - Raghu Vemuganti
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin–Madison, Madison, WI, USA
- Department of Neurological Surgery, University of Wisconsin–Madison, Madison, WI, USA
- William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA
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184
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Madugalle SU, Meyer K, Wang DO, Bredy TW. RNA N 6-Methyladenosine and the Regulation of RNA Localization and Function in the Brain. Trends Neurosci 2020; 43:1011-1023. [PMID: 33041062 PMCID: PMC7688512 DOI: 10.1016/j.tins.2020.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022]
Abstract
A major challenge in neurobiology in the 21st century is to understand how the brain adapts with experience. Activity-dependent gene expression is integral to the synaptic plasticity underlying learning and memory; however, this process cannot be explained by a simple linear trajectory of transcription to translation within a specific neuronal population. Many other regulatory mechanisms can influence RNA metabolism and the capacity of neurons to adapt. In particular, the RNA modification N6-methyladenosine (m6A) has recently been shown to regulate RNA processing through alternative splicing, RNA stability, and translation. Here, we discuss the emerging idea that m6A could also coordinate the transport, localization, and local translation of key mRNAs in learning and memory and expand on the notion of dynamic functional RNA states in the brain.
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Affiliation(s)
- Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Kate Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA; Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
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185
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Park CW, Lee SM, Yoon KJ. Epitranscriptomic regulation of transcriptome plasticity in development and diseases of the brain. BMB Rep 2020. [PMID: 33148378 PMCID: PMC7704224 DOI: 10.5483/bmbrep.2020.53.11.204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Proper development of the nervous system is critical for its function, and deficits in neural development have been impli-cated in many brain disorders. A precise and predictable developmental schedule requires highly coordinated gene expression programs that orchestrate the dynamics of the developing brain. Especially, recent discoveries have been showing that various mRNA chemical modifications can affect RNA metabolism including decay, transport, splicing, and translation in cell type- and tissue-specific manner, leading to the emergence of the field of epitranscriptomics. Moreover, accumulating evidences showed that certain types of RNA modifications are predominantly found in the developing brain and their dysregulation disrupts not only the developmental processes, but also neuronal activities, suggesting that epitranscriptomic mechanisms play critical post-transcriptional regulatory roles in development of the brain and etiology of brain disorders. Here, we review recent advances in our understanding of molecular regulation on transcriptome plasticity by RNA modifications in neurodevelopment and how alterations in these RNA regulatory programs lead to human brain disorders.
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Affiliation(s)
- Chan-Woo Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sung-Min Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ki-Jun Yoon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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186
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Song N, Du J, Gao Y, Yang S. Epitranscriptome of the ventral tegmental area in a deep brain-stimulated chronic unpredictable mild stress mouse model. Transl Neurosci 2020; 11:402-418. [PMID: 33343932 PMCID: PMC7724003 DOI: 10.1515/tnsci-2020-0146] [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: 06/30/2020] [Revised: 09/08/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
Deep brain stimulation (DBS) applied to the nucleus accumbens (NAc) alleviates the depressive symptoms of major depressive disorders. We investigated the mechanism of this effect by assessing gene expression and RNA methylation changes in the ventral tegmental area (VTA) following NAc-DBS in a chronic unpredictable mild stress (CUMS) mouse model of depression. Gene expression and N 6-methyladenosine (m6A) levels in the VTA were measured in mice subjected to CUMS and then DBS, and transcriptome-wide m6A changes were profiled using immunoprecipitated methylated RNAs with microarrays, prior to gene ontology analysis. The expression levels of genes linked to neurotransmitter receptors, transporters, transcription factors, neuronal activities, synaptic functions, and mitogen-activated protein kinase and dopamine signaling were upregulated in the VTA upon NAc-DBS. Furthermore, m6A modifications included both hypermethylation and hypomethylation, and changes were positively correlated with the upregulation of some genes. Moreover, the effects of CUMS on gene expression and m6A-mRNA modification were reversed by DBS for some genes. Interestingly, while the expression of certain genes was not changed by DBS, long-term stimulation did alter their m6A modifications. NAc-DBS-induced modifications are correlated largely with upregulation but sometimes downregulation of genes in CUMS mice. Our findings improve the current understanding of the molecular mechanisms underlying DBS effects on depression.
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Affiliation(s)
- Nan Song
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
| | - Jun Du
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
| | - Yan Gao
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
| | - Shenglian Yang
- Center of Military Brain Science, Institute of Military Cognition and Brain Sciences, Academy of Military Medical Sciences (AMMS), The Academy of Military Sciences, No. 27 Taiping Road, Haidian District, Beijing, China, 100850
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187
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Kupsco A, Gonzalez G, Baker BH, Knox JM, Zheng Y, Wang S, Chang D, Schwartz J, Hou L, Wang Y, Baccarelli AA. Associations of smoking and air pollution with peripheral blood RNA N 6-methyladenosine in the Beijing truck driver air pollution study. ENVIRONMENT INTERNATIONAL 2020; 144:106021. [PMID: 32791345 PMCID: PMC7572654 DOI: 10.1016/j.envint.2020.106021] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Post-transcriptional modifications of RNA constitute fundamental mechanisms of gene regulation. N6-methyladenosine (m6A) is critical for health and disease and is modulated by cellular stressors. However, associations between environmental exposures and m6A have not been studied in humans. We aimed to examine associations between tobacco smoking and particulate air pollution with m6A and mRNA expression levels of its reader, writer and eraser (RWE) genes in blood. METHODS Using the Beijing Truck Driver Air Pollution Study, we investigated global m6A in RNA from peripheral blood collected from 106 human subjects in Beijing, China, in 2008. We measured m6A with nano-flow liquid chromatography-tandem mass spectrometry and investigated gene expression of six m6A RWEs with real-time-quantitative PCR. Using linear models, we examined associations with smoking status, pack-years, and smoking on day of visit in men, and with environmental tobacco smoke in nonsmokers. We also examined associations with ambient PM10 (particulate matter ≤ 10 µm in diameter), and personal black carbon (BC) and PM2.5 measured with a portable monitor. RESULTS Smoking in men was significantly associated with a relative 10.7% decrease in global m6A levels in comparison to nonsmokers (p = 0.02). In men, smoking greater than 3.8 pack-years was associated with a 14.9% lower m6A than in nonsmokers. BC exposure trended towards positive associations with m6A (5.95% per 10 μg/m3 increase in BC; 95% CI: -0.96, 13.3). Global m6A levels were not correlated with RWE gene expression levels. No associations were detected between smoking or air pollutants and m6A RWE gene expression. DISCUSSION m6A was negatively associated with long-term smoking, yet positively associated with short-term BC exposure. These results indicate variable m6A responses to environmental stressors, providing early evidence into the impacts of toxicants on RNA modifications and suggesting potential for m6A as a biomarker or mechanism in environmental health research.
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Affiliation(s)
- Allison Kupsco
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA.
| | - Gwendolyn Gonzalez
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, CA, USA
| | - Brennan H Baker
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Julia M Knox
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Yinan Zheng
- Department of Preventative Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sheng Wang
- Department of Occupational and Environmental Health, Peking University Health Science Center; Beijing, China
| | - Dou Chang
- Department of Safety Engineering, China Institute of Industrial Relations, Beijing, China
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Lifang Hou
- Department of Preventative Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, CA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
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188
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Vissers C, Sinha A, Ming GL, Song H. The epitranscriptome in stem cell biology and neural development. Neurobiol Dis 2020; 146:105139. [PMID: 33065280 DOI: 10.1016/j.nbd.2020.105139] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 12/26/2022] Open
Abstract
The blossoming field of epitranscriptomics has recently garnered attention across many fields by findings that chemical modifications on RNA have immense biological consequences. Methylation of nucleotides in RNA, including N6-methyladenosine (m6A), 2-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), and isomerization of uracil to pseudouridine (Ψ), have the potential to alter RNA processing events and contribute to developmental processes and different diseases. Though the abundance and roles of some RNA modifications remain contentious, the epitranscriptome is thought to be especially relevant in stem cell biology and neurobiology. In particular, m6A occurs at the highest levels in the brain and plays major roles in embryonic stem cell differentiation, brain development, and neurodevelopmental disorders. However, studies in these areas have reported conflicting results on epitranscriptomic regulation of stem cell pluripotency and mechanisms in neural development. In this review we provide an overview of the current understanding of several RNA modifications and disentangle the various findings on epitranscriptomic regulation of stem cell biology and neural development.
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Affiliation(s)
- Caroline Vissers
- Biochemistry, Cellular and Molecular Biology Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biochemistry and Biophysics, Department of Psychiatry, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Aniketa Sinha
- Department of Biochemistry and Biophysics, Department of Psychiatry, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, 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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189
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An Emerging Role of m6A in Memory: A Case for Translational Priming. Int J Mol Sci 2020; 21:ijms21207447. [PMID: 33050279 PMCID: PMC7589748 DOI: 10.3390/ijms21207447] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022] Open
Abstract
Investigation into the role of methylation of the adenosine base (m6A) of RNA has only recently begun, but it quickly became apparent that m6A is able to control and fine-tune many aspects of mRNA, from splicing to translation. The ability of m6A to regulate translation distally, away from traditional sites near the nucleus, quickly caught the eye of neuroscientists because of implications for selective protein translation at synapses. Work in the brain has demonstrated how m6A is functionally required for many neuronal functions, but two in particular are covered at length here: The role of m6A in 1) neuron development; and 2) memory formation. The purpose of this review is not to cover all data about m6A in the brain. Instead, this review will focus on connecting mechanisms of m6A function in neuron development, with m6A’s known function in memory formation. We will introduce the concept of “translational priming” and discuss how current data fit into this model, then speculate how m6A-mediated translational priming during memory consolidation can regulate learning and memory locally at the synapse.
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190
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Gheller BJ, Blum JE, Fong EHH, Malysheva OV, Cosgrove BD, Thalacker-Mercer AE. A defined N6-methyladenosine (m 6A) profile conferred by METTL3 regulates muscle stem cell/myoblast state transitions. Cell Death Discov 2020; 6:95. [PMID: 33083017 PMCID: PMC7524727 DOI: 10.1038/s41420-020-00328-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/01/2020] [Accepted: 09/02/2020] [Indexed: 01/20/2023] Open
Abstract
Muscle-specific adult stem cells (MuSCs) are required for skeletal muscle regeneration. To ensure efficient skeletal muscle regeneration after injury, MuSCs must undergo state transitions as they are activated from quiescence, give rise to a population of proliferating myoblasts, and continue either to terminal differentiation, to repair or replace damaged myofibers, or self-renewal to repopulate the quiescent population. Changes in MuSC/myoblast state are accompanied by dramatic shifts in their transcriptional profile. Previous reports in other adult stem cell systems have identified alterations in the most abundant internal mRNA modification, N6-methyladenosine (m6A), conferred by its active writer, METTL3, to regulate cell state transitions through alterations in the transcriptional profile of these cells. Our objective was to determine if m6A-modification deposition via METTL3 is a regulator of MuSC/myoblast state transitions in vitro and in vivo. Using liquid chromatography/mass spectrometry we identified that global m6A levels increase during the early stages of skeletal muscle regeneration, in vivo, and decline when C2C12 myoblasts transition from proliferation to differentiation, in vitro. Using m6A-specific RNA-sequencing (MeRIP-seq), a distinct profile of m6A-modification was identified, distinguishing proliferating from differentiating C2C12 myoblasts. RNAi studies show that reducing levels of METTL3, the active m6A methyltransferase, reduced global m6A levels and forced C2C12 myoblasts to prematurely differentiate. Reducing levels of METTL3 in primary mouse MuSCs prior to transplantation enhanced their engraftment capacity upon primary transplantation, however their capacity for serial transplantation was lost. In conclusion, METTL3 regulates m6A levels in MuSCs/myoblasts and controls the transition of MuSCs/myoblasts to different cell states. Furthermore, the first transcriptome wide map of m6A-modifications in proliferating and differentiating C2C12 myoblasts is provided and reveals a number of genes that may regulate MuSC/myoblast state transitions which had not been previously identified.
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Affiliation(s)
| | - Jamie E. Blum
- Division of Nutritional Sciences, Cornell University, Ithaca, NY USA
| | | | - Olga V. Malysheva
- Division of Nutritional Sciences, Cornell University, Ithaca, NY USA
| | | | - Anna E. Thalacker-Mercer
- Division of Nutritional Sciences, Cornell University, Ithaca, NY USA
- Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL USA
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191
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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: 9] [Impact Index Per Article: 2.3] [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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192
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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: 109] [Impact Index Per Article: 27.3] [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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193
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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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194
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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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195
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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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196
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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: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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197
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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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198
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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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199
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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: 98] [Impact Index Per Article: 24.5] [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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200
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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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