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Liu Y, Wang Y, Bao D, Chen H, Gong M, Sun S, Zou G. Cross-Kingdom DNA Methylation Dynamics: Comparative Mechanisms of 5mC/6mA Regulation and Their Implications in Epigenetic Disorders. BIOLOGY 2025; 14:461. [PMID: 40427651 PMCID: PMC12108942 DOI: 10.3390/biology14050461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2025] [Revised: 04/17/2025] [Accepted: 04/22/2025] [Indexed: 05/29/2025]
Abstract
DNA methylation, a cornerstone of epigenetic regulation, governs critical biological processes including transcriptional modulation, genomic imprinting, and transposon suppression through chromatin architecture remodeling. Recent advances have revealed that aberrant methylation patterns-characterized by spatial-temporal dysregulation and stochastic molecular noise-serve as key drivers of diverse pathological conditions, from oncogenesis to neurodegenerative disorders. However, the field faces dual challenges: (1) current understanding remains fragmented due to the inherent spatiotemporal heterogeneity of methylation landscapes across tissues and developmental stages, and (2) mechanistic insights into non-canonical methylation pathways (particularly 6mA) in non-mammalian systems are conspicuously underdeveloped. This review systematically synthesizes the evolutionary-conserved versus species-specific features of 5-methylcytosine (5mC) and N6-methyladenine (6mA) regulatory networks across three biological kingdoms. Through comparative analysis of methylation/demethylation enzymatic cascades (DNMTs/TETs in mammals, CMTs/ROS1 in plants, and DIM-2/DNMTA in fungi), we propose a unified framework for targeting methylation-associated diseases through precision epigenome editing, while identifying critical knowledge gaps in fungal methylome engineering that demand urgent investigation.
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Affiliation(s)
- Yu Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Ying Wang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Hongyu Chen
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Ming Gong
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
| | - Shujing Sun
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Gen Zou
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd., Shanghai 201403, China; (Y.W.); (D.B.)
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Xiao F, Rui K, Shi X, Wu H, Cai X, Lui KO, Lu Q, Ballestar E, Tian J, Zou H, Lu L. Epigenetic regulation of B cells and its role in autoimmune pathogenesis. Cell Mol Immunol 2022; 19:1215-1234. [PMID: 36220996 PMCID: PMC9622816 DOI: 10.1038/s41423-022-00933-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022] Open
Abstract
B cells play a pivotal role in the pathogenesis of autoimmune diseases. Although previous studies have shown many genetic polymorphisms associated with B-cell activation in patients with various autoimmune disorders, progress in epigenetic research has revealed new mechanisms leading to B-cell hyperactivation. Epigenetic mechanisms, including those involving histone modifications, DNA methylation, and noncoding RNAs, regulate B-cell responses, and their dysregulation can contribute to the pathogenesis of autoimmune diseases. Patients with autoimmune diseases show epigenetic alterations that lead to the initiation and perpetuation of autoimmune inflammation. Moreover, many clinical and animal model studies have shown the promising potential of epigenetic therapies for patients. In this review, we present an up-to-date overview of epigenetic mechanisms with a focus on their roles in regulating functional B-cell subsets. Furthermore, we discuss epigenetic dysregulation in B cells and highlight its contribution to the development of autoimmune diseases. Based on clinical and preclinical evidence, we discuss novel epigenetic biomarkers and therapies for patients with autoimmune disorders.
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Affiliation(s)
- Fan Xiao
- Department of Pathology, Shenzhen Institute of Research and Innovation and Shenzhen Hospital, The University of Hong Kong, Hong Kong; Chongqing International Institute for Immunology, Chongqing, China
| | - Ke Rui
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaofei Shi
- Department of Rheumatology and Immunology, The First Affiliated Hospital and School of Medicine, Henan University of Science and Technology, Luoyang, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Xiaoyan Cai
- Department of Rheumatology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Kathy O Lui
- Department of Chemical Pathology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute, Badalona, 08916, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center, East China Normal University, Shanghai, China
| | - Jie Tian
- Institute of Medical Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China.
| | - Hejian Zou
- Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Liwei Lu
- Department of Pathology, Shenzhen Institute of Research and Innovation and Shenzhen Hospital, The University of Hong Kong, Hong Kong; Chongqing International Institute for Immunology, Chongqing, China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong, China.
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DNA Methylation and Immune Memory Response. Cells 2021; 10:cells10112943. [PMID: 34831166 PMCID: PMC8616503 DOI: 10.3390/cells10112943] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/16/2022] Open
Abstract
The generation of memory is a cardinal feature of the adaptive immune response, involving different factors in a complex process of cellular differentiation. This process is essential for protecting the second encounter with pathogens and is the mechanism by which vaccines work. Epigenetic changes play important roles in the regulation of cell differentiation events. There are three types of epigenetic regulation: DNA methylation, histone modification, and microRNA expression. One of these epigenetic changes, DNA methylation, occurs in cytosine residues, mainly in CpG dinucleotides. This brief review aimed to analyse the literature to verify the involvement of DNA methylation during memory T and B cell development. Several studies have highlighted the importance of the DNA methyltransferases, enzymes that catalyse the methylation of DNA, during memory differentiation, maintenance, and function. The methylation profile within different subsets of naïve activated and memory cells could be an interesting tool to help monitor immune memory response.
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