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Xia W, Liu Y, Lu J, Cheung HH, Meng Q, Huang B. RNA methylation in neurodevelopment and related diseases. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39344412 DOI: 10.3724/abbs.2024159] [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: 10/01/2024] Open
Abstract
Biological development and genetic information transfer are governed by genetic, epigenetic, transcriptional, and posttranscriptional mechanisms. RNA methylation, the attachment of methyl (-CH 3) groups to RNA molecules, is a posttranscriptional modification that has gained increasing attention in recent years because of its role in RNA epitranscriptomics. RNA modifications (RMs) influence various aspects of RNA metabolism and are involved in the regulation of diverse biological processes and diseases. Neural cell types emerge at specific stages of brain development, and recent studies have revealed that neurodevelopment, aging, and disease are tightly linked to transcriptome dysregulation. In this review, we discuss the roles of N6-methyladenine (m6A) and 5-methylcytidine (m5C) RNA modifications in neurodevelopment, physiological functions, and related diseases.
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Affiliation(s)
- Wenjuan Xia
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Yue Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Jiafeng Lu
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Hoi-Hung Cheung
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Qingxia Meng
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine and Offspring Health (Suzhou), Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
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Xu X, Johnson Z, Wang A, Padget RL, Smyth JW, Xie H. Folate regulates RNA m 5C modification and translation in neural stem cells. BMC Biol 2022; 20:261. [PMID: 36424632 PMCID: PMC9686110 DOI: 10.1186/s12915-022-01467-0] [Citation(s) in RCA: 6] [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: 04/15/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Folate is an essential B-group vitamin and a key methyl donor with important biological functions including DNA methylation regulation. Normal neurodevelopment and physiology are sensitive to the cellular folate levels. Either deficiency or excess of folate may lead to neurological disorders. Recently, folate has been linked to tRNA cytosine-5 methylation (m5C) and translation in mammalian mitochondria. However, the influence of folate intake on neuronal mRNA m5C modification and translation remains largely unknown. Here, we provide transcriptome-wide landscapes of m5C modification in poly(A)-enriched RNAs together with mRNA transcription and translation profiles for mouse neural stem cells (NSCs) cultured in three different concentrations of folate. RESULTS NSCs cultured in three different concentrations of folate showed distinct mRNA methylation profiles. Despite uncovering only a few differentially expressed genes, hundreds of differentially translated genes were identified in NSCs with folate deficiency or supplementation. The differentially translated genes induced by low folate are associated with cytoplasmic translation and mitochondrial function, while the differentially translated genes induced by high folate are associated with increased neural stem cell proliferation. Interestingly, compared to total mRNAs, polysome mRNAs contained high levels of m5C. Furthermore, an integrative analysis indicated a transcript-specific relationship between RNA m5C methylation and mRNA translation efficiency. CONCLUSIONS Altogether, our study reports a transcriptome-wide influence of folate on mRNA m5C methylation and translation in NSCs and reveals a potential link between mRNA m5C methylation and mRNA translation.
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Affiliation(s)
- Xiguang Xu
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Zachary Johnson
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Amanda Wang
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Rachel L Padget
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, 24061, USA
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, 24016, USA
| | - James W Smyth
- Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA, 24061, USA
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, 24061, USA
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, 24016, USA
- Virginia Tech Carilion School of Medicine, Roanoke, VA, 24016, USA
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
- Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA, 24061, USA.
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, 24061, USA.
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA, 24061, USA.
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA, 24061, USA.
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Liu J. 5-Methylcytosine profiles in mouse transcriptomes suggest the randomness of m 5C formation catalyzed by RNA methyltransferase. BMC Res Notes 2022; 15:81. [PMID: 35197120 PMCID: PMC8867762 DOI: 10.1186/s13104-022-05968-7] [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: 11/01/2021] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE 5-Methylcytosine (m5C) is a type of chemical modification on the nucleotides and is widespread in both DNA and RNA. Although the DNA m5C has been extensively studied over the past years, the distribution and biological function of RNA m5C still remain to be elucidated. Here, I explored the profiles of RNA m5C in four mouse tissues by applying a RNA cytosine methylation data analysis tool to public mouse RNA m5C data. RESULTS I found that the methylation rates of cytosine were the same with the averages of methylation level at single-nucleotide level. Furthermore, I gave a mathematical formula to describe the observed relationship and analyzed it deeply. The sufficient necessary condition for the given formula suggests that the methylation levels at most m5C sites are the same in four mouse tissues. Therefore, I proposed a hypothesis that the m5C formation catalyzed by RNA methyltransferase is random and with the same probability at most m5C sites, which is the methylation rate of cytosine. My hypothesis can be used to explain the observed profiles of RNA m5C in four mouse tissues and will be benefit to future studies of the distribution and biological function of RNA m5C in mammals.
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Affiliation(s)
- Junfeng Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,China National Center for Bioinformation, Beijing, 100101, China. .,Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
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Zhang SY, Zhang SW, Zhang T, Fan XN, Meng J. Recent advances in functional annotation and prediction of the epitranscriptome. Comput Struct Biotechnol J 2021; 19:3015-3026. [PMID: 34136099 PMCID: PMC8175281 DOI: 10.1016/j.csbj.2021.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
RNA modifications, in particular N6-methyladenosine (m6A), participate in every stages of RNA metabolism and play diverse roles in essential biological processes and disease pathogenesis. Thanks to the advances in sequencing technology, tens of thousands of RNA modification sites can be identified in a typical high-throughput experiment; however, it remains a major challenge to decipher the functional relevance of these sites, such as, affecting alternative splicing, regulation circuit in essential biological processes or association to diseases. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, we review here recent progress in functional annotation and prediction of RNA modification sites from a bioinformatics perspective. The review covers naïve annotation with associated biological events, e.g., single nucleotide polymorphism (SNP), RNA binding protein (RBP) and alternative splicing, prediction of key sites and their regulatory functions, inference of disease association, and mining the diagnosis and prognosis value of RNA modification regulators. We further discussed the limitations of existing approaches and some future perspectives.
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Affiliation(s)
- Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Teng Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xiao-Nan Fan
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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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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Liu L, Song B, Ma J, Song Y, Zhang SY, Tang Y, Wu X, Wei Z, Chen K, Su J, Rong R, Lu Z, de Magalhães JP, Rigden DJ, Zhang L, Zhang SW, Huang Y, Lei X, Liu H, Meng J. Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. Comput Struct Biotechnol J 2020; 18:1587-1604. [PMID: 32670500 PMCID: PMC7334300 DOI: 10.1016/j.csbj.2020.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional RNA modification occurs on all types of RNA and plays a vital role in regulating every aspect of RNA function. Thanks to the development of high-throughput sequencing technologies, transcriptome-wide profiling of RNA modifications has been made possible. With the accumulation of a large number of high-throughput datasets, bioinformatics approaches have become increasing critical for unraveling the epitranscriptome. We review here the recent progress in bioinformatics approaches for deciphering the epitranscriptomes, including epitranscriptome data analysis techniques, RNA modification databases, disease-association inference, general functional annotation, and studies on RNA modification site prediction. We also discuss the limitations of existing approaches and offer some future perspectives.
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Affiliation(s)
- Lian Liu
- School of Computer Sciences, Shannxi Normal University, Xi’an, Shaanxi 710119, China
| | - Bowen Song
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Jiani Ma
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Yi Song
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Yujiao Tang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - 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, United Kingdom
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - 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, United Kingdom
| | - Jionglong Su
- 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 Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Zhiliang Lu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - João Pedro de Magalhães
- Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX, Liverpool, United Kingdom
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Shao-Wu Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Yufei Huang
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, 78249, USA
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiujuan Lei
- School of Computer Sciences, Shannxi Normal University, Xi’an, Shaanxi 710119, China
| | - Hui Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
- AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
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