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Tegowski M, Meyer KD. Studying m 6A in the brain: a perspective on current methods, challenges, and future directions. Front Mol Neurosci 2024; 17:1393973. [PMID: 38711483 PMCID: PMC11070500 DOI: 10.3389/fnmol.2024.1393973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024] Open
Abstract
A major mechanism of post-transcriptional RNA regulation in cells is the addition of chemical modifications to RNA nucleosides, which contributes to nearly every aspect of the RNA life cycle. N6-methyladenosine (m6A) is a highly prevalent modification in cellular mRNAs and non-coding RNAs, and it plays important roles in the control of gene expression and cellular function. Within the brain, proper regulation of m6A is critical for neurodevelopment, learning and memory, and the response to injury, and m6A dysregulation has been implicated in a variety of neurological disorders. Thus, understanding m6A and how it is regulated in the brain is important for uncovering its roles in brain function and potentially identifying novel therapeutic pathways for human disease. Much of our knowledge of m6A has been driven by technical advances in the ability to map and quantify m6A sites. Here, we review current technologies for characterizing m6A and highlight emerging methods. We discuss the advantages and limitations of current tools as well as major challenges going forward, and we provide our perspective on how continued developments in this area can propel our understanding of m6A in the brain and its role in brain disease.
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Affiliation(s)
- Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Kate D. Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, United States
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2
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Chen HS, Wang F, Chen JG. Epigenetic mechanisms in depression: Implications for pathogenesis and treatment. Curr Opin Neurobiol 2024; 85:102854. [PMID: 38401316 DOI: 10.1016/j.conb.2024.102854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/26/2024]
Abstract
The risk of depression is influenced by both genetic and environmental factors. It has been suggested that epigenetic mechanisms may mediate the risk of depression following exposure to adverse life events. Epigenetics encompasses stable alterations in gene expression that are controlled through transcriptional, post-transcriptional, translational, or post-translational processes, including DNA modifications, chromatin remodeling, histone modifications, RNA modifications, and non-coding RNA (ncRNA) regulation, without any changes in the DNA sequence. In this review, we explore recent research advancements in the realm of epigenetics concerning depression. Furthermore, we evaluate the potential of epigenetic changes as diagnostic and therapeutic biomarkers for depression.
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Affiliation(s)
- Hong-Sheng Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China
| | - Fang Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China
| | - Jian-Guo Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan 430030, China; The Research Center for Depression, Tongji Medical College, Huazhong University of Science, Wuhan 430030, China; The Key Laboratory of Neurological Diseases (HUST), Ministry of Education of China, Wuhan 430030, China.
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3
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Marayati BF, Thompson MG, Holley CL, Horner SM, Meyer KD. Programmable protein expression using a genetically encoded m 6A sensor. Nat Biotechnol 2024:10.1038/s41587-023-01978-3. [PMID: 38168988 PMCID: PMC11217150 DOI: 10.1038/s41587-023-01978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/01/2023] [Indexed: 01/05/2024]
Abstract
The N6-methyladenosine (m6A) modification is found in thousands of cellular mRNAs and is a critical regulator of gene expression and cellular physiology. m6A dysregulation contributes to several human diseases, and the m6A methyltransferase machinery has emerged as a promising therapeutic target. However, current methods for studying m6A require RNA isolation and do not provide a real-time readout of mRNA methylation in living cells. Here we present a genetically encoded m6A sensor (GEMS) technology, which couples a fluorescent signal with cellular mRNA methylation. GEMS detects changes in m6A caused by pharmacological inhibition of the m6A methyltransferase, giving it potential utility for drug discovery efforts. Additionally, GEMS can be programmed to achieve m6A-dependent delivery of custom protein payloads in cells. Thus, GEMS is a versatile platform for m6A sensing that provides both a simple readout for m6A methylation and a system for m6A-coupled protein expression.
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Affiliation(s)
- Bahjat F Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Matthew G Thompson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Christopher L Holley
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Stacy M Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
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4
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Jeong S, Chokkalla AK, Davis CK, Vemuganti R. Post-stroke depression: epigenetic and epitranscriptomic modifications and their interplay with gut microbiota. Mol Psychiatry 2023; 28:4044-4055. [PMID: 37188778 PMCID: PMC10646155 DOI: 10.1038/s41380-023-02099-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Epigenetic and epitranscriptomic modifications that regulate physiological processes of an organism at the DNA and RNA levels, respectively, are novel therapeutic candidates for various neurological diseases. Gut microbiota and its metabolites are known to modulate DNA methylation and histone modifications (epigenetics), as well as RNA methylation especially N6-methyladenosine (epitranscriptomics). As gut microbiota as well as these modifications are highly dynamic across the lifespan of an organism, they are implicated in the pathogenesis of stroke and depression. The lack of specific therapeutic interventions for managing post-stroke depression emphasizes the need to identify novel molecular targets. This review highlights the interaction between the gut microbiota and epigenetic/epitranscriptomic pathways and their interplay in modulating candidate genes that are involved in post-stroke depression. This review further focuses on the three candidates, including brain-derived neurotrophic factor, ten-eleven translocation family proteins, and fat mass and obesity-associated protein based on their prevalence and pathoetiologic role in post-stroke depression.
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Affiliation(s)
- Soomin Jeong
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Charles K Davis
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA.
- William S. Middleton Veterans Hospital, Madison, WI, USA.
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5
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Wright AL, Konen LM, Mockett BG, Morris GP, Singh A, Burbano LE, Milham L, Hoang M, Zinn R, Chesworth R, Tan RP, Royle GA, Clark I, Petrou S, Abraham WC, Vissel B. The Q/R editing site of AMPA receptor GluA2 subunit acts as an epigenetic switch regulating dendritic spines, neurodegeneration and cognitive deficits in Alzheimer's disease. Mol Neurodegener 2023; 18:65. [PMID: 37759260 PMCID: PMC10537207 DOI: 10.1186/s13024-023-00632-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/03/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND RNA editing at the Q/R site of GluA2 occurs with ~99% efficiency in the healthy brain, so that the majority of AMPARs contain GluA2(R) instead of the exonically encoded GluA2(Q). Reduced Q/R site editing infcreases AMPA receptor calcium permeability and leads to dendritic spine loss, neurodegeneration, seizures and learning impairments. Furthermore, GluA2 Q/R site editing is impaired in Alzheimer's disease (AD), raising the possibility that unedited GluA2(Q)-containing AMPARs contribute to synapse loss and neurodegeneration in AD. If true, then inhibiting expression of unedited GluA2(Q), while maintaining expression of GluA2(R), may be a novel strategy of preventing synapse loss and neurodegeneration in AD. METHODS We engineered mice with the 'edited' arginine codon (CGG) in place of the unedited glutamine codon (CAG) at position 607 of the Gria2 gene. We crossbred this line with the J20 mouse model of AD and conducted anatomical, electrophysiological and behavioural assays to determine the impact of eliminating unedited GluA2(Q) expression on AD-related phenotypes. RESULTS Eliminating unedited GluA2(Q) expression in AD mice prevented dendritic spine loss and hippocampal CA1 neurodegeneration as well as improved working and reference memory in the radial arm maze. These phenotypes were improved independently of Aβ pathology and ongoing seizure susceptibility. Surprisingly, our data also revealed increased spine density in non-AD mice with exonically encoded GluA2(R) as compared to their wild-type littermates, suggesting an unexpected and previously unknown role for unedited GluA2(Q) in regulating dendritic spines. CONCLUSION The Q/R editing site of the AMPA receptor subunit GluA2 may act as an epigenetic switch that regulates dendritic spines, neurodegeneration and memory deficits in AD.
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Affiliation(s)
- Amanda L Wright
- St Vincent's Clinical School, St Vincent's Hospital Sydney, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia
- School of Rural Medicine, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Lyndsey M Konen
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
| | - Bruce G Mockett
- Department of Psychology, Brain Health Research Centre, Brain Research New Zealand, University of Otago, Box 56, Dunedin, 9054, New Zealand
| | - Gary P Morris
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Anurag Singh
- Department of Psychology, Brain Health Research Centre, Brain Research New Zealand, University of Otago, Box 56, Dunedin, 9054, New Zealand
| | - Lisseth Estefania Burbano
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Luke Milham
- St Vincent's Clinical School, St Vincent's Hospital Sydney, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
| | - Monica Hoang
- School of Pharmacy, University of Waterloo, Kitchener, ON, N2G 1C5, Canada
| | - Raphael Zinn
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
| | - Rose Chesworth
- School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia
| | - Richard P Tan
- Chronic Diseases, School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, 2050, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Gordon A Royle
- Middlemore Hospital, Counties Manukau DHB, Otahuhu, Auckland, 1062, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Grafton, Auckland, 1023, New Zealand
| | - Ian Clark
- Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
| | - Steven Petrou
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Wickliffe C Abraham
- Department of Psychology, Brain Health Research Centre, Brain Research New Zealand, University of Otago, Box 56, Dunedin, 9054, New Zealand
| | - Bryce Vissel
- St Vincent's Clinical School, St Vincent's Hospital Sydney, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia.
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia.
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Breger K, Kunkler CN, O'Leary NJ, Hulewicz JP, Brown JA. Ghost authors revealed: The structure and function of human N 6 -methyladenosine RNA methyltransferases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1810. [PMID: 37674370 PMCID: PMC10915109 DOI: 10.1002/wrna.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 09/08/2023]
Abstract
Despite the discovery of modified nucleic acids nearly 75 years ago, their biological functions are still being elucidated. N6 -methyladenosine (m6 A) is the most abundant modification in eukaryotic messenger RNA (mRNA) and has also been detected in non-coding RNAs, including long non-coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6 A marks can alter RNA secondary structure and initiate unique RNA-protein interactions that can alter splicing, mRNA turnover, and translation, just to name a few. Although m6 A marks in human RNAs have been known to exist since 1974, the structures and functions of methyltransferases responsible for writing m6 A marks have been established only recently. Thus far, there are four confirmed human methyltransferases that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the N6 position of adenosine, producing m6 A: methyltransferase-like protein (METTL) 3/METTL14 complex, METTL16, METTL5, and zinc-finger CCHC-domain-containing protein 4. Though the methyltransferases have unique RNA targets, all human m6 A RNA methyltransferases contain a Rossmann fold with a conserved SAM-binding pocket, suggesting that they utilize a similar catalytic mechanism for methyl transfer. For each of the human m6 A RNA methyltransferases, we present the biological functions and links to human disease, RNA targets, catalytic and kinetic mechanisms, and macromolecular structures. We also discuss m6 A marks in human viruses and parasites, assigning m6 A marks in the transcriptome to specific methyltransferases, small molecules targeting m6 A methyltransferases, and the enzymes responsible for hypermodified m6 A marks and their biological functions in humans. Understanding m6 A methyltransferases is a critical steppingstone toward establishing the m6 A epitranscriptome and more broadly the RNome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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7
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Kastellakis G, Tasciotti S, Pandi I, Poirazi P. The dendritic engram. Front Behav Neurosci 2023; 17:1212139. [PMID: 37576932 PMCID: PMC10412934 DOI: 10.3389/fnbeh.2023.1212139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Accumulating evidence from a wide range of studies, including behavioral, cellular, molecular and computational findings, support a key role of dendrites in the encoding and recall of new memories. Dendrites can integrate synaptic inputs in non-linear ways, provide the substrate for local protein synthesis and facilitate the orchestration of signaling pathways that regulate local synaptic plasticity. These capabilities allow them to act as a second layer of computation within the neuron and serve as the fundamental unit of plasticity. As such, dendrites are integral parts of the memory engram, namely the physical representation of memories in the brain and are increasingly studied during learning tasks. Here, we review experimental and computational studies that support a novel, dendritic view of the memory engram that is centered on non-linear dendritic branches as elementary memory units. We highlight the potential implications of dendritic engrams for the learning and memory field and discuss future research directions.
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Affiliation(s)
- George Kastellakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece
| | - Simone Tasciotti
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Ioanna Pandi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Panayiota Poirazi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece
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8
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Abstract
Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, N6-methyladenosine (m6A). We first describe the discovery of the key enzymes that deposit and remove m6A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m6A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, USA
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9
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Yin H, Ju Z, Zheng M, Zhang X, Zuo W, Wang Y, Ding X, Zhang X, Peng Y, Li J, Yang A, Zhang R. Loss of the m6A methyltransferase METTL3 in monocyte-derived macrophages ameliorates Alzheimer's disease pathology in mice. PLoS Biol 2023; 21:e3002017. [PMID: 36881554 PMCID: PMC9990945 DOI: 10.1371/journal.pbio.3002017] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
Alzheimer's disease (AD) is a heterogeneous disease with complex clinicopathological characteristics. To date, the role of m6A RNA methylation in monocyte-derived macrophages involved in the progression of AD is unknown. In our study, we found that methyltransferase-like 3 (METTL3) deficiency in monocyte-derived macrophages improved cognitive function in an amyloid beta (Aβ)-induced AD mouse model. The mechanistic study showed that that METTL3 ablation attenuated the m6A modification in DNA methyltransferase 3A (Dnmt3a) mRNAs and consequently impaired YTH N6-methyladenosine RNA binding protein 1 (YTHDF1)-mediated translation of DNMT3A. We identified that DNMT3A bound to the promoter region of alpha-tubulin acetyltransferase 1 (Atat1) and maintained its expression. METTL3 depletion resulted in the down-regulation of ATAT1, reduced acetylation of α-tubulin and subsequently enhanced migration of monocyte-derived macrophages and Aβ clearance, which led to the alleviated symptoms of AD. Collectively, our findings demonstrate that m6A methylation could be a promising target for the treatment of AD in the future.
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Affiliation(s)
- Huilong Yin
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
- The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi’an, Shaanxi, China
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Zhuan Ju
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Minhua Zheng
- The State Key Laboratory of Cancer Biology, Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiang Zhang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Wenjie Zuo
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
- Xinxiang Key Laboratory of Tumor Microenvironment and Immunotherapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yidi Wang
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaochen Ding
- Department of Experimental Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaofang Zhang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yingran Peng
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jiadi Li
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
| | - Angang Yang
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China
- The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi’an, Shaanxi, China
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi, China
- * E-mail: (AY); (RZ)
| | - Rui Zhang
- The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi’an, Shaanxi, China
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi’an, Shaanxi, China
- * E-mail: (AY); (RZ)
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10
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Zhang X, Yang S, Han S, Sun Y, Han M, Zheng X, Li F, Wei Y, Wang Y, Bi J. Differential methylation of circRNA m6A in an APP/PS1 Alzheimer's disease mouse model. Mol Med Rep 2023; 27:55. [PMID: 36660942 PMCID: PMC9879070 DOI: 10.3892/mmr.2023.12942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/25/2022] [Indexed: 01/19/2023] Open
Abstract
Alzheimer's disease (AD) is a chronic neurological disease characterized by memory loss and progressive cognitive impairment. The characteristic AD pathologies include extracellular senile plaques formed by β‑amyloid protein deposition, neurofibrillary tangles formed by hyper‑phosphorylation of τ protein and neuronal loss caused by glial cell proliferation. However, the pathogenesis of AD is still unclear. Dysregulation of RNA methylation is associated with biological processes, including neurodevelopment and neurodegenerative disease. N6‑methyladenosine (m6A) is the main modification in eukaryotic RNA and may be associated with the pathophysiology of AD. Circular RNA (circRNA) is a new type of evolutionarily conserved non‑coding RNA without 5'‑cap and 3'‑polyadenylic acid tail. circRNA undergoes m6A RNA methylation and may be involved in the pathogenesis of AD. In the present study, high‑throughput sequencing was performed to assess the degree of circRNA m6A methylation in APP/PS1 AD and C57BL/6 mice. These results suggested that circRNA m6A methylation in AD mice was markedly altered compared to the control group. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis was used to predict associated pathways; genes with different circRNA m6A methylation in AD mice were associated with 'axon guidance', 'long‑term potentiation', 'glutamatergic synapse', 'cholinergic synapse', 'GABAergic synapse' and 'long‑term depression'. Methylated RNA immunoprecipitation reverse transcription‑quantitative PCR demonstrated that among the eight selected circRNA m6A genes, there were five genes that demonstrated significantly increased methylation and three demonstrated significantly decreased methylation. In summary, the present study indicated that circRNA m6A methylation may be associated with pathogenesis of AD.
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Affiliation(s)
- Xiao Zhang
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Suge Yang
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Song Han
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yuan Sun
- Department of Outpatients, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Min Han
- Department of Geriatric Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Xiaolei Zheng
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Fan Li
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yan Wei
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Yun Wang
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China,Correspondence to: Dr Yun Wang, Department of Neurological Medicine, The Second Hospital of Shandong University, 247 Beiyuan Road, Jinan, Shandong 250033, P.R. China, E-mail:
| | - Jianzhong Bi
- Department of Neurological Medicine, The Second Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
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11
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Vinogradov S, Chafee MV, Lee E, Morishita H. Psychosis spectrum illnesses as disorders of prefrontal critical period plasticity. Neuropsychopharmacology 2023; 48:168-185. [PMID: 36180784 PMCID: PMC9700720 DOI: 10.1038/s41386-022-01451-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 01/05/2023]
Abstract
Emerging research on neuroplasticity processes in psychosis spectrum illnesses-from the synaptic to the macrocircuit levels-fill key gaps in our models of pathophysiology and open up important treatment considerations. In this selective narrative review, we focus on three themes, emphasizing alterations in spike-timing dependent and Hebbian plasticity that occur during adolescence, the critical period for prefrontal system development: (1) Experience-dependent dysplasticity in psychosis emerges from activity decorrelation within neuronal ensembles. (2) Plasticity processes operate bidirectionally: deleterious environmental and experiential inputs shape microcircuits. (3) Dysregulated plasticity processes interact across levels of scale and time and include compensatory mechanisms that have pathogenic importance. We present evidence that-given the centrality of progressive dysplastic changes, especially in prefrontal cortex-pharmacologic or neuromodulatory interventions will need to be supplemented by corrective learning experiences for the brain if we are to help people living with these illnesses to fully thrive.
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Affiliation(s)
- Sophia Vinogradov
- Department of Psychiatry & Behavioral Science, University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Matthew V Chafee
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Erik Lee
- Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Hirofumi Morishita
- Department of Psychiatry, Neuroscience, & Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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12
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Sokolov PL, Chebanenko NV, Mednaya DM. [Epigenetic influences and brain development]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:12-19. [PMID: 36946391 DOI: 10.17116/jnevro202312303112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
In recent years, the amount of scientific data on the involvement of epigenetic processes in the regulation of brain development in postnatal ontogenesis has been rapidly growing. The article provides an overview of scientific research on the mechanisms of epigenetic influences on brain development. Information was searched in the Scopus, Web of Science, MedLine, The Cochrane Library, PubMed, Pedro, Scholar, eLibrary, CyberLeninka and RSCI databases for the period 1940-2022 by keywords: brain development, epigenetics, neuroontogenesis, methylation, histone modifications, chromatin remodeling, non-coding RNAs. Today, the mechanisms of epigenetic influence on the genome include DNA and RNA methylation, covalent modification of histones, chromatin remodeling, and the influence of non-coding RNAs. Epigenetic modifications are often reversible and provide the necessary plasticity for the response of progenitor cells to environmental signals. The influence of each of these factors on the neurodevelopment is considered. The possibility of transsynaptic transmission of hereditary material by means of circular RNA is indicated. The main ways of microRNA influence on brain development are presented and their universality as an «overgenic» regulator of organism adaptation to external conditions is indicated. Data on the relationship of long non-coding RNAs with the regulation of the functional activity of oligodendroglia are presented. Also, the data presented indicate the paths to the pathogenetically determined prevention of congenital brain pathology.
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Affiliation(s)
- P L Sokolov
- Voyno-Yasenetsky Scientific and Practical Center for Specialized Assistance for Children, Moscow, Russia
| | - N V Chebanenko
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - D M Mednaya
- Pirogov Russian National Research Medical University, Moscow, Russia
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13
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Zou J, Liu H, Tan W, Chen YQ, Dong J, Bai SY, Wu ZX, Zeng Y. Dynamic regulation and key roles of ribonucleic acid methylation. Front Cell Neurosci 2022; 16:1058083. [PMID: 36601431 PMCID: PMC9806184 DOI: 10.3389/fncel.2022.1058083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Ribonucleic acid (RNA) methylation is the most abundant modification in biological systems, accounting for 60% of all RNA modifications, and affects multiple aspects of RNA (including mRNAs, tRNAs, rRNAs, microRNAs, and long non-coding RNAs). Dysregulation of RNA methylation causes many developmental diseases through various mechanisms mediated by N 6-methyladenosine (m6A), 5-methylcytosine (m5C), N 1-methyladenosine (m1A), 5-hydroxymethylcytosine (hm5C), and pseudouridine (Ψ). The emerging tools of RNA methylation can be used as diagnostic, preventive, and therapeutic markers. Here, we review the accumulated discoveries to date regarding the biological function and dynamic regulation of RNA methylation/modification, as well as the most popularly used techniques applied for profiling RNA epitranscriptome, to provide new ideas for growth and development.
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Affiliation(s)
- Jia Zou
- Community Health Service Center, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China,Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Hui Liu
- Community Health Service Center, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China,Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Wei Tan
- Community Health Service Center, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Yi-qi Chen
- Community Health Service Center, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China,Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Jing Dong
- Community Health Service Center, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China,Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Shu-yuan Bai
- Community Health Service Center, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China,Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Zhao-xia Wu
- Community Health Service Center, Wuchang Hospital, Wuhan, China
| | - Yan Zeng
- Community Health Service Center, Geriatric Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China,Brain Science and Advanced Technology Institute, School of Medicine, Wuhan University of Science and Technology, Wuhan, China,School of Public Health, Wuhan University of Science and Technology, Wuhan, China,*Correspondence: Yan Zeng,
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14
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Vinogradov S, Hamid AA, Redish AD. Etiopathogenic Models of Psychosis Spectrum Illnesses Must Resolve Four Key Features. Biol Psychiatry 2022; 92:514-522. [PMID: 35931575 PMCID: PMC9809152 DOI: 10.1016/j.biopsych.2022.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 01/07/2023]
Abstract
Etiopathogenic models for psychosis spectrum illnesses are converging on a number of key processes, such as the influence of specific genes on the synthesis of proteins important in synaptic functioning, alterations in how neurons respond to synaptic inputs and engage in synaptic pruning, and microcircuit dysfunction that leads to more global cortical information processing vulnerabilities. Disruptions in prefrontal operations then accumulate and propagate over time, interacting with environmental factors, developmental processes, and homeostatic mechanisms, eventually resulting in symptoms of psychosis and disability. However, there are 4 key features of psychosis spectrum illnesses that are of primary clinical relevance but have been difficult to assimilate into a single model and have thus far received little direct attention: 1) the bidirectionality of the causal influences for the emergence of psychosis, 2) the catastrophic clinical threshold seen in first episodes of psychosis and why it is irreversible in some individuals, 3) observed biotypes that are neurophysiologically distinct but clinically both convergent and divergent, and 4) a reconciliation of the role of striatal dopaminergic dysfunction with models of prefrontal cortical state instability. In this selective review, we briefly describe these 4 hallmark features and we argue that theoretically driven computational perspectives making use of both algorithmic and neurophysiologic models are needed to reduce this complexity and variability of psychosis spectrum illnesses in a principled manner.
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Affiliation(s)
- Sophia Vinogradov
- Department of Psychiatry & Behavioral Sciences, University of Minnesota Medical School, Minneapolis, Minnesota.
| | - Arif A Hamid
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota
| | - A David Redish
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota
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15
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Choi SH, Flamand MN, Liu B, Zhu H, Hu M, Wang M, Sewell J, Holley CL, Al-Hashimi HM, Meyer KD. RBM45 is an m 6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs. Cell Rep 2022; 40:111293. [PMID: 36044854 PMCID: PMC9472474 DOI: 10.1016/j.celrep.2022.111293] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/14/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the brain and is critical for neurodevelopment. However, the mechanisms through which m6A contributes to brain development are incompletely understood. RBM45 acts as an m6A-binding protein that is highly expressed during neurodevelopment. We find that RBM45 binds to thousands of cellular RNAs, predominantly within intronic regions. Rbm45 depletion disrupts the constitutive splicing of a subset of target pre-mRNAs, leading to altered mRNA and protein levels through both m6A-dependent and m6A-independent mechanisms. Finally, we find that RBM45 is necessary for neuroblastoma cell differentiation and that its depletion impacts the expression of genes involved in several neurodevelopmental signaling pathways. Altogether, our findings show a role for RBM45 in controlling mRNA processing and neuronal differentiation, mediated in part by the recognition of methylated RNA. Choi et al. identify RBM45 as an m6A-binding protein enriched in the developing brain. RBM45 binds to thousands of cellular RNAs, primarily within introns, and regulates constitutive splicing of target transcripts. Loss of RBM45 causes altered expression of neurodevelopmental genes and defects in the proliferation and differentiation of neuroblastoma cells.
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Affiliation(s)
- Seung H Choi
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Huanyu Zhu
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Meghan Hu
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA
| | - Melanie Wang
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA
| | - Jonathon Sewell
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Christopher L Holley
- Department of Medicine (Cardiology Division), Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA; Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
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16
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Alagia A, Gullerova M. The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine. Front Cell Dev Biol 2022; 10:915685. [PMID: 35721489 PMCID: PMC9204050 DOI: 10.3389/fcell.2022.915685] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m5C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m5C deposition and removal, and the role m5C plays within the cell, remains to be fully understood.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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17
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Flamand MN, Meyer KD. m6A and YTHDF proteins contribute to the localization of select neuronal mRNAs. Nucleic Acids Res 2022; 50:4464-4483. [PMID: 35438793 PMCID: PMC9071445 DOI: 10.1093/nar/gkac251] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/11/2022] [Accepted: 03/30/2022] [Indexed: 01/08/2023] Open
Abstract
The transport of mRNAs to distal subcellular compartments is an important component of spatial gene expression control in neurons. However, the mechanisms that control mRNA localization in neurons are not completely understood. Here, we identify the abundant base modification, m6A, as a novel regulator of this process. Transcriptome-wide analysis following genetic loss of m6A reveals hundreds of transcripts that exhibit altered subcellular localization in hippocampal neurons. Additionally, using a reporter system, we show that mutation of specific m6A sites in select neuronal transcripts diminishes their localization to neurites. Single molecule fluorescent in situ hybridization experiments further confirm our findings and identify the m6A reader proteins YTHDF2 and YTHDF3 as mediators of this effect. Our findings reveal a novel function for m6A in controlling mRNA localization in neurons and enable a better understanding of the mechanisms through which m6A influences gene expression in the brain.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
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18
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Gene expression and epigenetic markers of prion diseases. Cell Tissue Res 2022; 392:285-294. [PMID: 35307791 PMCID: PMC10113299 DOI: 10.1007/s00441-022-03603-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/24/2022] [Indexed: 12/19/2022]
Abstract
Epigenetics, meaning the variety of mechanisms underpinning gene regulation and chromatin states, plays a key role in normal development as well as in disease initiation and progression. Epigenetic mechanisms like alteration of DNA methylation, histone modifications, and non-coding RNAs, have been proposed as biomarkers for diagnosis, classification, or monitoring of responsiveness to treatment in many diseases. In prion diseases, the profound associations with human aging, the effects of cell type and differentiation on in vitro susceptibility, and recently identified human risk factors, all implicate causal epigenetic mechanisms. Here, we review the current state of the art of epigenetics in prion diseases and its interaction with genetic determinants. In particular, we will review recent advances made by several groups in the field profiling DNA methylation and microRNA expression in mammalian prion diseases and the potential for these discoveries to be exploited as biomarkers.
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19
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Dastidar SG, Nair D. A Ribosomal Perspective on Neuronal Local Protein Synthesis. Front Mol Neurosci 2022; 15:823135. [PMID: 35283723 PMCID: PMC8904363 DOI: 10.3389/fnmol.2022.823135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/17/2022] [Indexed: 11/15/2022] Open
Abstract
Continued mRNA translation and protein production are critical for various neuronal functions. In addition to the precise sorting of proteins from cell soma to distant locations, protein synthesis allows a dynamic remodeling of the local proteome in a spatially variable manner. This spatial heterogeneity of protein synthesis is shaped by several factors such as injury, guidance cues, developmental cues, neuromodulators, and synaptic activity. In matured neurons, thousands of synapses are non-uniformly distributed throughout the dendritic arbor. At any given moment, the activity of individual synapses varies over a wide range, giving rise to the variability in protein synthesis. While past studies have primarily focused on the translation factors or the identity of translated mRNAs to explain the source of this variation, the role of ribosomes in this regard continues to remain unclear. Here, we discuss how several stochastic mechanisms modulate ribosomal functions, contributing to the variability in neuronal protein expression. Also, we point out several underexplored factors such as local ion concentration, availability of tRNA or ATP during translation, and molecular composition and organization of a compartment that can influence protein synthesis and its variability in neurons.
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20
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He S, Gu C, Su T, Qiu Q. Research Progress of circRNAs in Inflammatory Mechanisms of Diabetic Retinopathy: An Emerging Star with Potential Therapeutic Targets. Curr Eye Res 2021; 47:165-178. [PMID: 34963381 DOI: 10.1080/02713683.2021.1995002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE We summarized the existing studies to elaborate the biogenesis and function of circRNAs, the effect of aberrant circRNAs expression in the mechanism of inflammation and diabetic retinopathy (DR) respectively and further explored the vital roles of circRNAs in inflammation involved in DR. Methods: We conducted a systematical literature search of abundant electronic databases (PubMed, GeneMedical and MEDLINE) up to August 2021. Results: In this review, we exhibited the biogenesis and function of circRNAs and highlighted the components of inflammatory mediators implicated in DR. Numerous circRNAs, such as circHIPK3, circZNF609, circRNA_0084043, circ_0002570, circ_0041795, circEhmt1 and circ-ITCH were discovered to play vital roles in inflammation involved in DR, which provided new ideas for diagnosis and treatment of DR. Moreover, we proposed not only the epigenetic functions of circRNAs but also novel forms of the inflammatory response, including pyroptosis, to inspire further exploration and creative research in this field. Conclusion: CircRNAs were implicated in the progression and development of inflammation in DR via aberrant expression and modulation of gene expression, serving as an emerging star with potential therapeutic targets.
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Affiliation(s)
- Shuai He
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases; Shanghai Key Laboratory of Ocular Fundus Diseases; Shanghai Engineering Center for Visual Science and Photomedicine; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Department of Ophthalmology, Shanghai, PR China
| | - Chufeng Gu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases; Shanghai Key Laboratory of Ocular Fundus Diseases; Shanghai Engineering Center for Visual Science and Photomedicine; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Department of Ophthalmology, Shanghai, PR China
| | - Tong Su
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases; Shanghai Key Laboratory of Ocular Fundus Diseases; Shanghai Engineering Center for Visual Science and Photomedicine; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Department of Ophthalmology, Shanghai, PR China
| | - Qinghua Qiu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases; Shanghai Key Laboratory of Ocular Fundus Diseases; Shanghai Engineering Center for Visual Science and Photomedicine; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Department of Ophthalmology, Shanghai, PR China.,Department of Ophthalmology, Shigatse People's Hospital, Shigatse, Xizang, PR China
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21
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Detecting m 6A with In Vitro DART-Seq. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2404:363-374. [PMID: 34694620 DOI: 10.1007/978-1-0716-1851-6_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recent studies have uncovered that cellular mRNAs contain a diverse epitranscriptome comprising chemically modified bases which play important roles in gene expression regulation. Among these is m6A, which is a highly prevalent modification that contributes to several aspects of RNA regulation and cellular function. Traditional methods for m6A profiling have used m6A antibodies to immunoprecipitate methylated RNAs. Although powerful, such methods require high amounts of input material. Recently, we developed DART-seq, an antibody-free method for m6A profiling from low-input RNA samples. DART-seq relies on deamination of cytidines that invariably follow m6A sites and can be performed using a simple in vitro assay with only 50 ng of total RNA. Here, we describe the in vitro DART method and present a detailed protocol for highly sensitive m6A profiling from any RNA sample of interest.
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22
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Issah MA, Wu D, Zhang F, Zheng W, Liu Y, Fu H, Zhou H, Chen R, Shen J. Epigenetic modifications in acute myeloid leukemia: The emerging role of circular RNAs (Review). Int J Oncol 2021; 59:107. [PMID: 34792180 PMCID: PMC8651224 DOI: 10.3892/ijo.2021.5287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/13/2021] [Indexed: 11/06/2022] Open
Abstract
Canonical epigenetic modifications, which include histone modification, chromatin remodeling and DNA methylation, play key roles in numerous cellular processes. Epigenetics underlies how cells that posses DNA with similar sequences develop into different cell types with different functions in an organism. Earlier epigenetic research has primarily been focused at the chromatin level. However, the number of studies on epigenetic modifications of RNA, such as N1‑methyladenosine, 2'‑O‑ribosemethylation, inosine, 5‑methylcytidine, N6‑methyladenosine (m6A) and pseudouridine, has seen an increase. Circular RNAs (circRNAs), a type of RNA species that lacks a 5' cap or 3' poly(A) tail, are abundantly expressed in acute myeloid leukemia (AML) and may regulate disease progression. circRNAs possess various functions, including microRNA sponging, gene transcription regulation and RNA‑binding protein interaction. Furthermore, circRNAs are m6A methylated in other types of cancer, such as colorectal and hypopharyngeal squamous cell cancers. Therefore, the critical roles of circRNA epigenetic modifications, particularly m6A, and their possible involvement in AML are discussed in the present review. Epigenetic modification of circRNAs may become a diagnostic and therapeutic target for AML in the future.
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Affiliation(s)
- Mohammed Awal Issah
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Dansen Wu
- Medical Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Feng Zhang
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Weili Zheng
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Yanquan Liu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Haiying Fu
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Huarong Zhou
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Rong Chen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Jianzhen Shen
- Fujian Institute of Hematology, Fujian Medical Center of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fuzhou, Fujian 350001, P.R. China
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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23
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Deng Y, Zhu H, Xiao L, Liu C, Liu YL, Gao W. Identification of the function and mechanism of m6A reader IGF2BP2 in Alzheimer's disease. Aging (Albany NY) 2021; 13:24086-24100. [PMID: 34705667 PMCID: PMC8610118 DOI: 10.18632/aging.203652] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/03/2021] [Indexed: 01/06/2023]
Abstract
Alzheimer’s disease, the most common form of dementia in the elderly, is a kind of neurodegenerative disease. However, its pathogenesis and diagnosis remain unclear. M6A is related to nervous system development and neurodegenerative diseases. Here in this study, using multiple RNA-seq datasets of Alzheimer’s brain tissues, along with bioinformatic analysis, we innovatively found that m6A reader protein IGF2BP2 was abnormally highly expressed in Alzheimer’s patients. After compared between Alzheimer’s and normal brain samples, and between IGF2BP2- high and IGF2BP2- low subgroups of Alzheimer’s patients, we took the shared differentially expressed genes as the relevant gene sets of IGF2PB2 affecting Alzheimer’s disease occurrence for subsequent analysis. Then, weight gene correlation analysis was conducted and 17 functional modules were identified. The module that most positively correlated with Alzheimer’s disease and IGF2PB2-high subgroups were mainly participated in ECM receptor interaction, focal adhesion, cytokine-cytokine receptor interaction, and TGF-beta signaling pathway. Afterwards, a hub gene-based model including 20 genes was constructed by LASSO regression and validated by ROC curve for Alzheimer diagnosis. Finally, we preliminarily elucidated that IGF2BP2 could bind with mRNAs in a m6A-dependent manner. This study first elucidates the pathogenic role of IGF2BP2 in Alzheimer’s disease. IGF2BP2 and its relevant m6A modifications are potential to be new diagnostic and therapeutic targets for Alzheimer’s patients.
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Affiliation(s)
- Yanyao Deng
- Department of Neurology, The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Hongwei Zhu
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Le Xiao
- Department of Neurology, The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Chao Liu
- Department of Neurology, The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Ya-Lin Liu
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China.,Xiangya School of Medicine, Central South University, Changsha, Hunan Province, China
| | - Wenzhe Gao
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, Hunan Province, China
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24
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Wang J, Sha Y, Sun T. m 6A Modifications Play Crucial Roles in Glial Cell Development and Brain Tumorigenesis. Front Oncol 2021; 11:611660. [PMID: 33718165 PMCID: PMC7943831 DOI: 10.3389/fonc.2021.611660] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/11/2021] [Indexed: 01/27/2023] Open
Abstract
RNA methylation is a reversible post-transcriptional modification to RNA and has a significant impact on numerous biological processes. N6-methyladenosine (m6A) is known as one of the most common types of eukaryotic mRNA methylation modifications, and exists in a wide variety of organisms, including viruses, yeast, plants, mice, and humans. Widespread and dynamic m6A methylation is identified in distinct developmental stages in the brain, and controls development of neural stem cells and their differentiation into neurons, glial cells such as oligodendrocytes and astrocytes. Here we summarize recent advances in our understanding of RNA methylation regulation in brain development, neurogenesis, gliogenesis, and its dysregulation in brain tumors. This review will highlight biological roles of RNA methylation in development and function of neurons and glial cells, and provide insights into brain tumor formation, and diagnostic and treatment strategies.
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Affiliation(s)
- Jing Wang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China.,College of Materials Science and Engineering, Huaqiao University, Xiamen, China
| | - Yongqiang Sha
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, China
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25
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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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26
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Ulmke PA, Xie Y, Sokpor G, Pham L, Shomroni O, Berulava T, Rosenbusch J, Basu U, Fischer A, Nguyen HP, Staiger JF, Tuoc T. Post-transcriptional regulation by the exosome complex is required for cell survival and forebrain development via repression of P53 signaling. Development 2021; 148:dev.188276. [PMID: 33462115 DOI: 10.1242/dev.188276] [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: 01/16/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Fine-tuned gene expression is crucial for neurodevelopment. The gene expression program is tightly controlled at different levels, including RNA decay. N6-methyladenosine (m6A) methylation-mediated degradation of RNA is essential for brain development. However, m6A methylation impacts not only RNA stability, but also other RNA metabolism processes. How RNA decay contributes to brain development is largely unknown. Here, we show that Exosc10, a RNA exonuclease subunit of the RNA exosome complex, is indispensable for forebrain development. We report that cortical cells undergo overt apoptosis, culminating in cortical agenesis upon conditional deletion of Exosc10 in mouse cortex. Mechanistically, Exosc10 directly binds and degrades transcripts of the P53 signaling-related genes, such as Aen and Bbc3. Overall, our findings suggest a crucial role for Exosc10 in suppressing the P53 pathway, in which the rapid turnover of the apoptosis effectors Aen and Bbc3 mRNAs is essential for cell survival and normal cortical histogenesis.
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Affiliation(s)
- Pauline Antonie Ulmke
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Yuanbin Xie
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Gannan Medical University, 341000 Ganzhou, The People's Republic of China
| | - Godwin Sokpor
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Linh Pham
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Orr Shomroni
- Microarray and Deep-Sequencing Core Facility, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Tea Berulava
- German Center for Neurodegenerative Diseases, Goettingen 37075, Germany
| | - Joachim Rosenbusch
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Andre Fischer
- German Center for Neurodegenerative Diseases, Goettingen 37075, Germany.,Department for Psychiatry and Psychotherapy, University Medical Center, Georg-August-University Goettingen, Goettingen 37075, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen 37075, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Jochen F Staiger
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Tran Tuoc
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany .,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
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27
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Yang Y, Okada S, Sakurai M. Adenosine-to-inosine RNA editing in neurological development and disease. RNA Biol 2021; 18:999-1013. [PMID: 33393416 DOI: 10.1080/15476286.2020.1867797] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) editing is one of the most prevalent post-transcriptional RNA modifications in metazoan. This reaction is catalysed by enzymes called adenosine deaminases acting on RNA (ADARs). RNA editing is involved in the regulation of protein function and gene expression. The numerous A-to-I editing sites have been identified in both coding and non-coding RNA transcripts. These editing sites are also found in various genes expressed in the central nervous system (CNS) and play an important role in neurological development and brain function. Aberrant regulation of RNA editing has been associated with the pathogenesis of neurological and psychiatric disorders, suggesting the physiological significance of RNA editing in the CNS. In this review, we discuss the current knowledge of editing on neurological disease and development.
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Affiliation(s)
- Yuxi Yang
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda-shi, Chiba, Japan
| | - Shunpei Okada
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda-shi, Chiba, Japan
| | - Masayuki Sakurai
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda-shi, Chiba, Japan
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28
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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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29
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Roy R, Shiina N, Wang DO. More dynamic, more quantitative, unexpectedly intricate: Advanced understanding on synaptic RNA localization in learning and memory. Neurobiol Learn Mem 2019; 168:107149. [PMID: 31881355 DOI: 10.1016/j.nlm.2019.107149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/25/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Synaptic signaling exhibits great diversity, complexity, and plasticity which necessitates maintenance and rapid modification of a local proteome. One solution neurons actively exploit to meet such demands is the strategic deposition of mRNAs encoding proteins for both basal and experience-driven activities into ribonucleoprotein complexes at the synapse. Transcripts localized in this manner can be rapidly accessed for translation in response to a diverse range of stimuli in a temporal- and spatially-restricted manner. Here we review recent findings on localized RNAs and RNA binding proteins in the context of learning and memory, as revealed by cutting-edge in-vitro and in-vivo technologies capable of yielding quantitative and dynamic information. The new technologies include proteomic and transcriptomic analyses, high-resolution multiplexed RNA imaging, single-molecule RNA tracking in living neurons, animal models and human neuron cell models. Among many recent advances in the field, RNA chemical modification has emerged as one of the new regulatory layers of gene expression at synapse that is complex and yet largely unexplored. These exciting new discoveries have enhanced our understanding of the modulation mechanisms of synaptic gene expression and their roles in cognition.
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Affiliation(s)
- Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, SOKENDAI, Okazaki, Japan; Exploratory Research Center on Life and Living Systems, Okazaki, Japan.
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto, Japan.
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30
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Meng S, Zhou H, Feng Z, Xu Z, Tang Y, Wu M. Epigenetics in Neurodevelopment: Emerging Role of Circular RNA. Front Cell Neurosci 2019; 13:327. [PMID: 31379511 PMCID: PMC6658887 DOI: 10.3389/fncel.2019.00327] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/03/2019] [Indexed: 01/16/2023] Open
Abstract
Canonical epigenetic modifications, including DNA methylation, histone modification and chromatin remodeling, play a role in numerous life processes, particularly neurodevelopment. Epigenetics explains the development of cells in an organism with the same DNA sequence into different cell types with various functions. However, previous studies on epigenetics have only focused on the chromatin level. Recently, epigenetic modifications of RNA, which mainly include 6-methyladenosine (m6A), pseudouridine, 5-methylcytidine (m5C), inosine (I), 2′-O-ribosemethylation, and 1-methyladenosine (m1A), have gained increasing attention. Circular RNAs (circRNAs), which are a type of non-coding RNA without a 5′ cap or 3′ poly (A) tail, are abundantly found in the brain and might respond to and regulate synaptic function. Also, circRNAs have various functions, such as microRNA sponge, regulation of gene transcription and interaction with RNA binding protein. In addition, circRNAs are methylated by N6-methyladenosine (m6A). In this review, we discuss the crucial roles of epigenetic modifications of circRNAs, such as m6A, in the genesis and development of neurons and in synaptic function and plasticity. Thus, this type of changes in circRNAs might be a therapeutic target in central nervous system (CNS) disorders and could aid the diagnosis and treatment of these disorders.
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Affiliation(s)
- Shujuan Meng
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Hecheng Zhou
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Ziyang Feng
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Zihao Xu
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Ying Tang
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
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