Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation.
Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation.
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环境诱导夏眠期间海参全基因组 DNA 甲基化特征
DOI：
10.3390/genes11091020
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发表时间：
2020-08-31
期刊：
影响因子：
3.5
通讯作者：
Chen M
中科院分区：
文献类型：
--
作者：
Yang Y;Zheng Y;Sun L;Chen M
生物体对严重的环境变化的反应是进入低代谢状态，最大限度地降低代谢率，暂停发育和繁殖，并在关键的生态变化中生存下来。一旦环境条件有利，他们就会恢复积极的生活方式。海洋无脊椎动物生活在水生环境中，终生适应环境变化。海参和海绵是最近才知道的两种海洋生物，它们会对温度变化作出反应。海参已成为研究海洋无脊椎动物环境诱导夏眠的理想模式生物。DNA甲基化是最广泛被认为是表观遗传标记，已被报道有助于水生生物响应环境胁迫的表型可塑性。多数甲基化相关酶，包括DNA甲基转移酶、甲基化CpG结合域蛋白和DNA去甲基化酶，在夏眠期间表达上调。我们对非夏眠期和深夏眠期海参肠道进行了高分辨率全基因组亚硫酸氢盐测序。还在不同的基因组特征和整个转录单位中进行了进一步的DNA甲基化谱分析。在转录单位扫描过程中，观察到内部外显子甲基化水平的不同升高，内含子/外显子边界清晰。最低的甲基化水平发生在第一个外显子，其次是最后一个外显子和内部外显子。在夏眠组的内含子和mRNA区域内观察到非CpG甲基化（CHG和CHH）的显著增加。共有1393个基因在高甲基化DMR（差异甲基化区域）内注释，749个基因在低甲基化DMR内注释。差异甲基化基因在mRNA监测途径、代谢途径和RNA转运中富集。其中24个高甲基化基因和15个低甲基化基因为逆转录病毒相关Pol转座子多聚蛋白（RPPT）基因。本研究为进一步了解环境诱导的水生生物代谢低下的表观遗传控制提供了依据。
Organisms respond to severe environmental changes by entering into hypometabolic states, minimizing their metabolic rates, suspending development and reproduction, and surviving critical ecological changes. They come back to an active lifestyle once the environmental conditions are conducive. Marine invertebrates live in the aquatic environment and adapt to environmental changes in their whole life. Sea cucumbers and sponges are only two recently known types of marine organisms that aestivate in response to temperature change. Sea cucumber has become an excellent model organism for studies of environmentally-induced aestivation by marine invertebrates. DNA methylation, the most widely considered epigenetic marks, has been reported to contribute to phenotypic plasticity in response to environmental stress in aquatic organisms. Most of methylation-related enzymes, including DNA methyltransferases, Methyl-CpG binding domain proteins, and DNA demethylases, were up-regulated during aestivation. We conducted high-resolution whole-genome bisulfite sequencing of the intestine from sea cucumber at non-aestivation and deep-aestivation stages. Further DNA methylation profile analysis was also conducted across the distinct genomic features and entire transcriptional units. A different elevation in methylation level at internal exons was observed with clear demarcation of intron/exon boundaries during transcriptional unit scanning. The lowest methylation level occurs in the first exons, followed by the last exons and the internal exons. A significant increase in non-CpG methylation (CHG and CHH) was observed within the intron and mRNA regions in aestivation groups. A total of 1393 genes were annotated within hypermethylated DMRs (differentially methylated regions), and 749 genes were annotated within hypomethylated DMRs. Differentially methylated genes were enriched in the mRNA surveillance pathway, metabolic pathway, and RNA transport. Then, 24 hypermethylated genes and 15 hypomethylated genes were Retrovirus-related Pol polyprotein from transposon (RPPT) genes. This study provides further understanding of epigenetic control on environmental induced hypometabolism in aquatic organisms.
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影响因子：
12.3
作者：
Akalin A;Kormaksson M;Li S;Garrett-Bakelman FE;Figueroa ME;Melnick A;Mason CE
通讯作者：
Mason CE
影响因子：
64.5
作者：
Goldberg, Aaron D.;Allis, C. David;Bernstein, Emily
通讯作者：
Bernstein, Emily
影响因子：
4.6
作者：
Hao Y;Cui Y;Gu X
通讯作者：
Gu X
海参基因组为皂苷生物合成和夏眠调节提供了见解
影响因子：
33.5
作者：
Li Y;Wang R;Xun X;Wang J;Bao L;Thimmappa R;Ding J;Jiang J;Zhang L;Li T;Lv J;Mu C;Hu X;Zhang L;Liu J;Li Y;Yao L;Jiao W;Wang Y;Lian S;Zhao Z;Zhan Y;Huang X;Liao H;Wang J;Sun H;Mi X;Xia Y;Xing Q;Lu W;Osbourn A;Zhou Z;Chang Y;Bao Z;Wang S
通讯作者：
Wang S
影响因子：
0.7
作者：
Morin, Pier, Jr.;Storey, Kenneth B.
通讯作者：
Storey, Kenneth B.