Role of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes [RRBS]

With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during pre-implantation development. Recent studies have suggested that Tet3-mediated oxidation of 5-methylcytosine (5mC) and DNA replication-dependent dilution both contribute to global paternal DNA demethylation, but demethylation of the maternal genome occurs via replication. Here we present genome-scale DNA methylation maps for both the paternal and maternal genomes of Tet3-depleted and/or DNA replication-inhibited zygotes. In both genomes, we found that inhibition of DNA replication blocks DNA demethylation independently from Tet3 function, and that Tet3 facilitates DNA demethylation by coupling with DNA replication. For both, our data indicate that replication-dependent dilution is the major contributor to demethylation, but Tet3 plays an important role, particularly at certain loci. Our study therefore both defines the respective functions of Tet3 and DNA replication in paternal DNA demethylation and reveals an unexpected contribution of Tet3 to demethylation of the maternal genome. In this data set, we include RRBS data of manually isolated paternal and maternal pronuclei from both WT and Tet3 CKO zygotes with or without aphidicolin treatment

除印记基因（imprinted genes）与特定重复序列外，DNA甲基化（DNA methylation）会在植入前发育（pre-implantation development）过程中发生全局性消除。近期研究表明，Tet3介导的5-甲基胞嘧啶（5-methylcytosine，5mC）氧化与依赖DNA复制（DNA replication）的稀释过程共同介导全局性父本DNA去甲基化（DNA demethylation），而母本基因组的去甲基化仅依赖DNA复制完成。本研究提供了Tet3缺陷型（Tet3-depleted）和/或DNA复制抑制型（DNA replication-inhibited）受精卵（zygotes）的父本与母本基因组的全基因组规模DNA甲基化图谱。在两类基因组中，我们均发现DNA复制抑制可独立于Tet3功能阻断DNA去甲基化，且Tet3可通过与DNA复制耦合促进DNA去甲基化。对于两类基因组而言，我们的数据显示依赖DNA复制的稀释仍是去甲基化的主要途径，但Tet3也发挥了重要作用，尤其是在特定基因座（loci）处。因此，本研究既明确了Tet3与DNA复制在父本DNA去甲基化中的各自功能，也揭示了Tet3对母本基因组去甲基化的意外贡献。本数据集包含经或未经阿非迪霉素（aphidicolin）处理的野生型（WT）与Tet3条件性敲除（Tet3 CKO）受精卵的手工分离父本与母本原核（pronuclei）的简化代表性亚硫酸氢盐测序（RRBS）数据。