Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection
IntroductionThe large yellow croaker iridovirus (LYCIV) poses a significant threat to the aquaculture industry of Larimichthys crocea. Understanding the host defense response to LYCIV infection is crucial for developing effective strategies to mitigate its impact.MethodsIn this study, an epigenetic...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1513966/full |
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| author | Chaowei Song Ying Huang Fang Han Zhiyong Wang Zhiyong Wang |
| author_facet | Chaowei Song Ying Huang Fang Han Zhiyong Wang Zhiyong Wang |
| author_sort | Chaowei Song |
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| description | IntroductionThe large yellow croaker iridovirus (LYCIV) poses a significant threat to the aquaculture industry of Larimichthys crocea. Understanding the host defense response to LYCIV infection is crucial for developing effective strategies to mitigate its impact.MethodsIn this study, an epigenetic approach was employed to investigate dynamic changes in chromatin accessibility using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Additionally, RNA sequencing (RNA-seq) was used to analyze the expression pattern of immune response genes upon LYCIV infection.ResultsSubstantial alterations in chromatin accessibility were observed, particularly in the regulatory regions of key immune-related genes. Significant changes in the expression of AP-1 transcription factors, including the Batf gene, were noted. CUT&Tag results revealed that AP-1 was significantly enriched in the open chromatin regions of cytokine genes, with Batf potentially regulating the cytokine genes LIF and CLCF1.DiscussionThese findings suggest that AP-1 may play a crucial role in the defense response against viral infection by modulating inflammatory cytokines and contributing to cellular inflammatory responses. This study provides a comprehensive analysis of the epigenomic landscape and gene expression regulation during iridovirus infection in L. crocea, offering valuable insights for breeding programs aimed at combating iridovirus infections. |
| format | Article |
| id | doaj-art-c408565580da4121a0691f66502920ce |
| institution | Kabale University |
| issn | 1664-3224 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj-art-c408565580da4121a0691f66502920ce2025-01-30T06:22:38ZengFrontiers Media S.A.Frontiers in Immunology1664-32242025-01-011610.3389/fimmu.2025.15139661513966Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infectionChaowei Song0Ying Huang1Fang Han2Zhiyong Wang3Zhiyong Wang4State Key Laboratory of Mariculture Breeding, Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen, ChinaState Key Laboratory of Mariculture Breeding, Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen, ChinaState Key Laboratory of Mariculture Breeding, Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen, ChinaState Key Laboratory of Mariculture Breeding, Key Laboratory of Healthy Mariculture for the East China Sea, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-Environment, Fisheries College, Jimei University, Xiamen, ChinaLaboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, ChinaIntroductionThe large yellow croaker iridovirus (LYCIV) poses a significant threat to the aquaculture industry of Larimichthys crocea. Understanding the host defense response to LYCIV infection is crucial for developing effective strategies to mitigate its impact.MethodsIn this study, an epigenetic approach was employed to investigate dynamic changes in chromatin accessibility using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Additionally, RNA sequencing (RNA-seq) was used to analyze the expression pattern of immune response genes upon LYCIV infection.ResultsSubstantial alterations in chromatin accessibility were observed, particularly in the regulatory regions of key immune-related genes. Significant changes in the expression of AP-1 transcription factors, including the Batf gene, were noted. CUT&Tag results revealed that AP-1 was significantly enriched in the open chromatin regions of cytokine genes, with Batf potentially regulating the cytokine genes LIF and CLCF1.DiscussionThese findings suggest that AP-1 may play a crucial role in the defense response against viral infection by modulating inflammatory cytokines and contributing to cellular inflammatory responses. This study provides a comprehensive analysis of the epigenomic landscape and gene expression regulation during iridovirus infection in L. crocea, offering valuable insights for breeding programs aimed at combating iridovirus infections.https://www.frontiersin.org/articles/10.3389/fimmu.2025.1513966/fullchromatin accessibilityiridovirus infectionepigeneticsimmune gene expressionATAC-seq |
| spellingShingle | Chaowei Song Ying Huang Fang Han Zhiyong Wang Zhiyong Wang Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection Frontiers in Immunology chromatin accessibility iridovirus infection epigenetics immune gene expression ATAC-seq |
| title | Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection |
| title_full | Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection |
| title_fullStr | Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection |
| title_full_unstemmed | Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection |
| title_short | Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection |
| title_sort | chromatin accessibility and differentially expressed genes profiling in large yellow croaker larimichthys crocea head kidney cells following iridovirus infection |
| topic | chromatin accessibility iridovirus infection epigenetics immune gene expression ATAC-seq |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1513966/full |
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