Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption
DNA methylation is a critical epigenetic modification that dynamically regulates gene expression in organisms facing abiotic stress. However, few studies have comprehensively examined the role of DNA methylation in marine fish during environmental adaptation. Therefore, this study explored the methy...
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| Format: | Article |
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Frontiers Media S.A.
2023-02-01
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| Series: | Frontiers in Marine Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmars.2023.1082655/full |
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| author | Jian Yang Jian Yang Minhai Liu Tingting Zhou Qi Li Zhihua Lin |
| author_facet | Jian Yang Jian Yang Minhai Liu Tingting Zhou Qi Li Zhihua Lin |
| author_sort | Jian Yang |
| collection | DOAJ |
| description | DNA methylation is a critical epigenetic modification that dynamically regulates gene expression in organisms facing abiotic stress. However, few studies have comprehensively examined the role of DNA methylation in marine fish during environmental adaptation. Therefore, this study explored the methylome dynamics and DNA methylation regulation mechanisms in large yellow croaker (Larimichthys crocea) during low-salinity adaption. The methylation level in the gills was notably raised in the S-group (5‰ salinity) compared to C-group (25‰ salinity). A total of 109 differentially methylated promoter target genes and 581 differentially expressed genes were identified via whole-genome bisulfite sequencing (WGBS) and RNA-seq of gills in the two salinity groups, respectively. Moreover, 23 hypo-methylated/up-regulated differentially methylated genes (DMGs) and 28 hyper-methylated/down-regulated DMGs were identified through integrative analysis, which were mainly enriched in signal transduction, ion exchange, energy metabolism, and cytoskeleton system and other biological processes. Collectively, our findings suggested that low-salinity stress can induce adaptive genome-wide DNA methylation changes, which can in turn affect the transcription of genes in large yellow croaker during low-salinity adaptation. Therefore, our findings provide new insights into the regulatory mechanisms of marine fish in response to rapid environmental changes. |
| first_indexed | 2024-04-10T18:52:04Z |
| format | Article |
| id | doaj.art-022262bd3766482fa6d77032f349e01b |
| institution | Directory Open Access Journal |
| issn | 2296-7745 |
| language | English |
| last_indexed | 2024-04-10T18:52:04Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Marine Science |
| spelling | doaj.art-022262bd3766482fa6d77032f349e01b2023-02-01T06:04:11ZengFrontiers Media S.A.Frontiers in Marine Science2296-77452023-02-011010.3389/fmars.2023.10826551082655Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaptionJian Yang0Jian Yang1Minhai Liu2Tingting Zhou3Qi Li4Zhihua Lin5Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, ChinaKey Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, ChinaNinghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, ChinaNinghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, ChinaKey Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, ChinaNinghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, ChinaDNA methylation is a critical epigenetic modification that dynamically regulates gene expression in organisms facing abiotic stress. However, few studies have comprehensively examined the role of DNA methylation in marine fish during environmental adaptation. Therefore, this study explored the methylome dynamics and DNA methylation regulation mechanisms in large yellow croaker (Larimichthys crocea) during low-salinity adaption. The methylation level in the gills was notably raised in the S-group (5‰ salinity) compared to C-group (25‰ salinity). A total of 109 differentially methylated promoter target genes and 581 differentially expressed genes were identified via whole-genome bisulfite sequencing (WGBS) and RNA-seq of gills in the two salinity groups, respectively. Moreover, 23 hypo-methylated/up-regulated differentially methylated genes (DMGs) and 28 hyper-methylated/down-regulated DMGs were identified through integrative analysis, which were mainly enriched in signal transduction, ion exchange, energy metabolism, and cytoskeleton system and other biological processes. Collectively, our findings suggested that low-salinity stress can induce adaptive genome-wide DNA methylation changes, which can in turn affect the transcription of genes in large yellow croaker during low-salinity adaptation. Therefore, our findings provide new insights into the regulatory mechanisms of marine fish in response to rapid environmental changes.https://www.frontiersin.org/articles/10.3389/fmars.2023.1082655/fulllow salinity stresslarge yellow croakermethylometranscriptomeepigenetic regulation mechanism |
| spellingShingle | Jian Yang Jian Yang Minhai Liu Tingting Zhou Qi Li Zhihua Lin Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption Frontiers in Marine Science low salinity stress large yellow croaker methylome transcriptome epigenetic regulation mechanism |
| title | Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption |
| title_full | Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption |
| title_fullStr | Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption |
| title_full_unstemmed | Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption |
| title_short | Transcriptome and methylome dynamics in the gills of large yellow croaker (Larimichthys crocea) during low-salinity adaption |
| title_sort | transcriptome and methylome dynamics in the gills of large yellow croaker larimichthys crocea during low salinity adaption |
| topic | low salinity stress large yellow croaker methylome transcriptome epigenetic regulation mechanism |
| url | https://www.frontiersin.org/articles/10.3389/fmars.2023.1082655/full |
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