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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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