• Integrated analysis of DNA met...

*Result*: Integrated analysis of DNA methylome and transcriptome reveals key regulatory genes and immune pathways in Opsariichthys bidens against Aeromonas veronii infection.

Title:
Integrated analysis of DNA methylome and transcriptome reveals key regulatory genes and immune pathways in Opsariichthys bidens against Aeromonas veronii infection.
Authors:
Fang W; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, 321004, China., Ye J; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, 321004, China., Wu Z; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China., Li Y; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, 321004, China., Tong W; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, 321004, China., Hu M; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, 321004, China., Li Q; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, 321004, China., Wu Z; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China., Zheng S; College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China; Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, 321004, China. Electronic address: zhengsj@zjnu.cn.
Source:
Fish & shellfish immunology [Fish Shellfish Immunol] 2026 Feb; Vol. 169, pp. 111061. Date of Electronic Publication: 2025 Dec 05.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Academic Press Country of Publication: England NLM ID: 9505220 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1095-9947 (Electronic) Linking ISSN: 10504648 NLM ISO Abbreviation: Fish Shellfish Immunol Subsets: MEDLINE
Imprint Name(s):
Original Publication: London ; New York : Academic Press, c1991-
MeSH Terms:
DNA Methylation*/immunology , Fish Diseases*/immunology , Fish Diseases*/genetics , Fish Diseases*/microbiology , Gram-Negative Bacterial Infections*/veterinary , Gram-Negative Bacterial Infections*/immunology , Gram-Negative Bacterial Infections*/genetics , Transcriptome*/immunology , Immunity, Innate*/genetics , Epigenome* , Perciformes*/immunology , Perciformes*/genetics, Animals ; Aeromonas veronii/physiology ; Gene Expression Profiling/veterinary ; Epigenesis, Genetic
Contributed Indexing:
Keywords: Aeromonas veronii; DNA methylation; Immune response; Opsariichthys bidens; Transcriptome
Entry Date(s):
Date Created: 20251207 Date Completed: 20260110 Latest Revision: 20260110
Update Code:
20260130
DOI:
10.1016/j.fsi.2025.111061
PMID:
41354111
Database:
MEDLINE

*Further Information*

*DNA methylation is an important epigenetic modification closely associated with various biological processes, including immune responses. Opsariichthys bidens is an emerging economic fish species in China. However, a disease caused by Aeromonas veronii poses a serious threat to the development of its aquaculture industry. To elucidate the epigenetic regulatory mechanisms underlying the resistance of O. bidens to A. veronii infection, this study employed an integrated approach. We conducted whole-genome bisulfite sequencing (WGBS) on midgut tissues at 48 h post-infection and comprehensively analyzed these data alongside histological examinations, immune parameters, and transcriptome profiles from both midgut and liver. The results demonstrated that infected O. bidens exhibited significant tissue damage in both midgut and liver, along with substantial alterations in immune parameters. WGBS analysis identified a total of 10,597 differentially methylated regions (DMRs), with the CG context being the predominant type. KEGG pathway analysis revealed that differentially methylated genes (DMGs) were significantly enriched in biological processes related to immunity, metabolism, and epigenetic modification. Integrated transcriptome and methylome analysis identified 101 genes exhibiting both differential methylation and differential expression. These genes showed significant enrichment in several immune-related pathways, including focal adhesion, ECM-receptor interaction, TNF signaling pathway, NF-κB signaling pathway, and apoptosis. Further analysis indicated a significant down-regulation in the overall methylation level of the focal adhesion and ECM-receptor interaction pathways, accompanied by cross-talk among multiple genes. Furthermore, the NF-κB pathway was found to be activated through tumor necrosis factor receptor 1 (TNFR1). Based on these findings, we propose that these two pathways represent key mechanisms of DNA methylation regulation in response to A. veronii infection. This study represents the first application of WGBS to analyze whole-genome methylation in the midgut of O. bidens following infection with A. veronii, providing novel epigenetic insights for breeding disease-resistant varieties and preventing A. veronii infections.
(Copyright © 2025 Elsevier Ltd. All rights reserved.)*

*Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.*