Variation of DNA Methylome of Zebrafish Cells under Cold Pressure

PLOS ONE, Dec 2019

DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure.

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Variation of DNA Methylome of Zebrafish Cells under Cold Pressure

August Variation of DNA Methylome of Zebrafish Cells under Cold Pressure Bingshe Han☯ 0 1 2 Wenhao Li☯ 0 1 2 Zuozhou Chen☯ 0 1 2 Qiongqiong Xu 0 1 2 Juntao Luo 0 1 2 Yingdi Shi 0 1 2 Xiaoxia Li 0 1 2 Xiaonan Yan 0 1 2 Junfang Zhang 0 1 2 0 Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fishery and Life Science, Shanghai Ocean University , Shanghai , China 1 Funding: This study was supported by grants from National Natural Science Foundation of China (grant No. 31372516 awarded to JZ), Shanghai Municipal Education Commission (Oriental scholar program awarded to JZ) and Grant No. 13ZR1419500 from Natural Science Foundation of Shanghai awarded to BH 2 Editor: Zongbin Cui, Chinese Academy of Sciences , CHINA DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIPseq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure. - Data Availability Statement: The data used in this study has been deposited in NCBI’s Gene Expression Omnibus repository and are accessible through GEO accession number GSE71567. Competing Interests: The authors have declared that no competing interests exist. Introduction DNA methylation of cytosine residues is a well-studied epigenetic mechanism implicated in multiple processes, such as genome function, gene transcription, imprinting and X-chromosome inactivation [ 1, 2 ]. Increasing number of studies show that DNA methylation plays an important role under various environmental pressures in some species [ 3–5 ]. In rice, widespread phosphate starvation-induced DNA methylation changes preferentially localize in transposable elements (TEs) close to highly induced genes [3]. In mouse liver and brain, highly Abbreviations: MeDIP, Methylated DNA immunoprecipitation; CGI, CpG island; ChIP, Chromatin immunoprecipitation; GO, Gene ontology; TSS, Transcription start site; RPM, Reads per million; RPKM, Reads Per Kilobase per Million mapped reads; BSP, Bisulfite sequencing PCR; DMR, Differentially methylated regions; ROS, Reactive oxygen species. variably DNA-methylated regions in environmental evolutionary adaptation were identified associated with development and morphogenesis [ 6 ]. In the plant, environmental stresses affect the epigenetic modifications and promote the activity of transposons for adaptation to the changing environment [ 7–10 ]. However, the role of DNA methylation in cold acclimation in fishes is still unclear. Temperature is an important environmental factor that affects the life of fishes including development, sex determination, habit, and so on [ 11 ]. Fishes have been developing various adaptive changes for cold survival, including production of antifreeze glycoproteins (AFGP) [ 12 ], adaptive modification of enzyme protein structures [ 13 ], cold-efficient microtubule assembly [ 14 ], cold-adapted protein translocation [ 15 ], elevated mitochondrial densities [ 16 ], genomic expansion and gene loss [ 17, 18 ]. In addition to the mechanisms mentioned above, expression levels of many genes significantly change, contributing to adaptive changes of multiple processes including anti-oxidant system, apoptosis, development, immune system and so on [18]. In the transcriptomic study of cold acclimation in larval zebrafish, biological processes including RNA splicing, ribosome biogenesis and protein catabolic process were highly overrepresented [ 19, 20 ]. However the mechanisms underlying the regulation of those genes are still not cl (...truncated)


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Bingshe Han, Wenhao Li, Zuozhou Chen, Qiongqiong Xu, Juntao Luo, Yingdi Shi, Xiaoxia Li, Xiaonan Yan, Junfang Zhang. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure, PLOS ONE, 2016, Volume 11, Issue 8, DOI: 10.1371/journal.pone.0160358