Dynamic antagonism between key repressive pathways maintains the placental epigenome (RNA-seq). Dynamic antagonism between key repressive pathways maintains the placental epigenome (RNA-seq)

DNA and Histone-3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb Repressive Complexes regulate the CpG-rich promoters of developmental genes. In contrast to this general framework, the extraembryonic lineages display noncanonical, globally intermediate DNA methylation levels that includes disruption of local Polycomb domains. To better understand this unusual landscape’s molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse Trophoblast Stem Cells (TSCs). We find that the extraembryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized appearance, our data point to a highly controlled equilibrium between counteracting repressors within extraembryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation. Overall design: Gene expression profiling of trophoblast stem cells in normal conditions and treated with DNMT1 or EZH2 inhibitor.

DNA甲基化与组蛋白H3赖氨酸27甲基化（Histone-3 Lysine 27 methylation）通常作为抑制性表观修饰，在不同的基因组区室中行使调控功能。在哺乳动物体内，绝大多数基因组区域维持DNA甲基化状态，而多梳抑制复合体（Polycomb Repressive Complexes）负责调控发育基因的CpG富集型启动子。与这一普遍的表观调控框架形成鲜明对比的是，胚外谱系呈现出非经典的、整体呈中等水平的DNA甲基化模式，同时伴随局部多梳结构域的紊乱。
为深入解析这一异常表观基因组特征的分子特性，我们通过遗传与化学手段，对小鼠滋养层干细胞（Trophoblast Stem Cells, TSCs）中的主要表观遗传通路进行了扰动实验。研究结果显示，胚外表观组反映了持续且动态的从头甲基转移酶募集过程，这一过程持续受到多梳复合体的拮抗，从而维持中等水平、局部紊乱的甲基化状态。尽管该表观组外观呈现无序状态，我们的数据表明，胚外细胞内相互拮抗的两类抑制因子之间存在高度受控的动态平衡，这一平衡似乎可以无限期维持，且不具备表观遗传调控胚胎形式中常见的双稳态特征。
整体实验设计：对正常培养条件下以及经DNA甲基转移酶1（DNMT1）或zeste同源增强子2（EZH2）抑制剂处理的滋养层干细胞开展基因表达谱分析。