Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
BMC Genomics. 2023 Aug 28;24(1):491. doi: 10.1186/s12864-023-09616-7.
DNA methylation plays an important role in life processes by affecting gene expression, but it is still unclear how DNA methylation is controlled and how it regulates gene transcription under high temperature stress conditions in Strongylocentrotus intermedius. The potential link between DNA methylation variation and gene expression changes in response to heat stress in S. intermedius was investigated by MethylRAD-seq and RNA-seq analysis. We screened DNA methylation driver genes in order to comprehensively elucidate the regulatory mechanism of its high temperature adaptation at the DNA/RNA level.
The results revealed that high temperature stress significantly affected not only the DNA methylation and transcriptome levels of S. intermedius (P < 0.05), but also growth. MethylRAD-seq analysis revealed 12,129 CG differential methylation sites and 966 CWG differential methylation sites, and identified a total of 189 differentially CG methylated genes and 148 differentially CWG methylated genes. Based on KEGG enrichment analysis, differentially expressed genes (DEGs) are mostly enriched in energy and cell division, immune, and neurological damage pathways. Further RNA-seq analysis identified a total of 1968 DEGs, of which 813 genes were upregulated and 1155 genes were downregulated. Based on the joint MethylRAD-seq and RNA-seq analysis, metabolic processes such as glycosaminoglycan degradation, oxidative phosphorylation, apoptosis, glutathione metabolism, thermogenesis, and lysosomes are regulated by DNA methylation.
High temperature affected the DNA methylation and expression levels of genes such as MOAP-1, GGT1 and RDH8, which in turn affects the metabolism of HPSE, Cox, glutathione, and retinol, thereby suppressing the immune, energy metabolism, and antioxidant functions of the organism and finally manifesting as stunted growth. In summary, the observations in the present study improve our understanding of the molecular mechanism of the response to high temperature stress in sea urchin.
DNA 甲基化通过影响基因表达在生命过程中发挥重要作用，但目前尚不清楚 DNA 甲基化是如何控制的，以及它如何在高温胁迫条件下调节基因转录。通过 MethylRAD-seq 和 RNA-seq 分析，研究了 DNA 甲基化变异与中间刺参（Strongylocentrotus intermedius）对热应激的基因表达变化之间的潜在联系。我们筛选了 DNA 甲基化驱动基因，以全面阐明其在 DNA/RNA 水平上对高温适应的调控机制。
结果表明，高温胁迫不仅显著影响了中间刺参的 DNA 甲基化和转录组水平（P<0.05），还影响了生长。MethylRAD-seq 分析显示，有 12129 个 CG 差异甲基化位点和 966 个 CWG 差异甲基化位点，共鉴定出 189 个差异 CG 甲基化基因和 148 个差异 CWG 甲基化基因。基于 KEGG 富集分析，差异表达基因（DEGs）主要富集在能量和细胞分裂、免疫和神经损伤途径中。进一步的 RNA-seq 分析共鉴定出 1968 个 DEGs，其中 813 个基因上调，1155 个基因下调。基于 MethylRAD-seq 和 RNA-seq 的联合分析，DNA 甲基化调节了糖胺聚糖降解、氧化磷酸化、细胞凋亡、谷胱甘肽代谢、产热和溶酶体等代谢过程。
高温影响了 MOAP-1、GGT1 和 RDH8 等基因的 DNA 甲基化和表达水平，进而影响了 HPSE、Cox、谷胱甘肽和视黄醇的代谢，从而抑制了机体的免疫、能量代谢和抗氧化功能，最终表现为生长迟缓。综上所述，本研究的观察结果提高了我们对海胆应对高温胁迫分子机制的理解。
