a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates.
b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH.
Epigenetics. 2017 Sep;12(9):811-824. doi: 10.1080/15592294.2017.1359382. Epub 2017 Nov 24.
The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are 2 waves of global DNA demethylation and re-methylation: the first occurs before gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions. While many studies have described the dynamics of methylome changes during early zebrafish development, the factors involved in establishing the DNA methylation landscape in zebrafish embryos have not been identified. We test the hypothesis that the zebrafish ortholog of H2A.Z (H2afv) restricts DNA methylation during development. We find that, in control embryos, bulk genome methylation decreases after gastrulation, with a nadir at the bud stage, and peaks during mid-somitogenesis; by 24 hours post -fertilization, total DNA methylation levels return to those detected in gastrula. Early zebrafish embryos depleted of H2afv have significantly more bulk DNA methylation during somitogenesis, suggesting that H2afv limits methylation during this stage of development. H2afv deficient embryos are small, with multisystemic abnormalities. Genetic interaction experiments demonstrate that these phenotypes are suppressed by depletion of DNA methyltransferase 1 (Dnmt1). This work demonstrates that H2afv is essential for global DNA methylation reprogramming during early vertebrate development and that embryonic development requires crosstalk between H2afv and Dnmt1.
DNA 甲基组在脊椎动物发育的不同阶段重新形成模式。在斑马鱼中，存在两次全基因组 DNA 去甲基化和再甲基化：第一次发生在原肠胚形成之前，此时亲代甲基组被改变为合子模式，第二次发生在胚胎体轴形成后，在器官特化期间。组蛋白变体 H2A.Z 和 DNA 甲基化区域的占据通常呈负相关，并且有人提出 H2A.Z 限制了高度甲基化区域的边界。虽然许多研究描述了早期斑马鱼发育过程中甲基组变化的动态，但尚未确定在斑马鱼胚胎中建立 DNA 甲基化景观的相关因素。我们检验了以下假设：即 H2A.Z（H2afv）的斑马鱼同源物在发育过程中限制 DNA 甲基化。我们发现，在对照胚胎中，原肠胚形成后整个基因组的甲基化程度降低，在芽期达到最低点，在体节形成中期达到峰值；受精后 24 小时，总 DNA 甲基化水平恢复到原肠胚期的水平。H2afv 耗竭的早期斑马鱼胚胎在体节形成期间具有显著更多的整体 DNA 甲基化，这表明 H2afv 限制了该发育阶段的甲基化。H2afv 缺陷胚胎较小，具有多系统异常。遗传相互作用实验表明，这些表型被 DNA 甲基转移酶 1（Dnmt1）耗竭所抑制。这项工作表明，H2afv 是早期脊椎动物发育过程中全基因组 DNA 甲基化重编程所必需的，并且胚胎发育需要 H2afv 和 Dnmt1 之间的相互作用。
