Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, China.
Mol Biol Evol. 2023 Aug 3;40(8). doi: 10.1093/molbev/msad172.
The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.
DNA 甲基化在无脊椎动物中的作用尚未得到充分描述，环节动物门的关键数据也缺失。我们通过对深海多毛类动物（深海喷口和渗漏处的优势种）进行全基因组范围内的 DNA 甲基化首次调查，填补了这一知识空白：Escarpia echinospica、Ridgeia piscesae 和 Paralvinella palmiformis。这些动物的高质量基因组组装后，从 Oxford Nanopore 测序中推断出 DNA 甲基化的调用。这些蠕虫的基因组编码了 DNA 甲基化代谢的所有关键酶，并具有类似于其他无脊椎动物的镶嵌甲基组。这些多毛类动物的转录组数据支持以下假说：基因体甲基化增强了管家基因的表达，启动子甲基化作为一种沉默机制，而不是 DNA 甲基化抑制转座元件活性的假说。负责维持极端静水压力下体内平衡的基因的保守表观遗传特征表明，DNA 甲基化在这些蠕虫中发挥着重要的适应性作用。
