DNA methylation analysis and expression profiling during murine embryogenesis and in embryos deficient for DNMT3A or DNMT3B

We quantified the targets and kinetics of DNA methylation acquisition in mouse embryos, and determined the contribution of the de novo methyltransferases DNMT3A and DNMT3B to this process. We provide single-base maps of cytosine methylation by RRBS from the blastocysts to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity, and performed RNA-Seq in embryos lacking DNMT3B activity. We sequenced RRBS libraries prepared from genomic DNA isolated from embryos at consecutive stages of development between E3.5 and E11.5,and adult differentiated cells (sperm, liver). We performed RRBS on blastocysts at E3.5/E4.5, dissected epiblasts at E5.5/E6.5/E7/5, whole embryos at E8.5/E10.5 and limbs at E11.5. RRBS experiments in Dnmt3a-/- and Dnmt3b-/- embryos were performed in biological duplicates on individual embryos. We sequenced RNA-Seq libraries prepared from total RNAs of three WT and Dnmt3b-/- littermate embryos collected at E8.5.我们定量解析了小鼠胚胎中DNA甲基化获取的靶点与动力学特性，并明确了从头DNA甲基转移酶（de novo methyltransferase）DNMT3A与DNMT3B在该过程中的功能贡献。本数据集提供了通过简化代表性亚硫酸氢盐测序（Reduced Representation Bisulfite Sequencing, RRBS）得到的胞嘧啶甲基化单碱基图谱，样本涵盖从囊胚到着床后阶段的胚胎，以及缺失DNMT3A或DNMT3B活性的胚胎；同时我们对缺失DNMT3B活性的胚胎开展了RNA测序（RNA-Seq）实验。 我们对采集自胚胎发育第3.5天至第11.5天连续发育阶段的胚胎，以及成年分化细胞（精子、肝脏）的基因组DNA构建的RRBS文库进行了测序。实验样本包括：E3.5/E4.5时期的囊胚、E5.5/E6.5/E7/5时期的分离上胚层、E8.5/E10.5时期的完整胚胎，以及E11.5时期的肢体。 针对Dnmt3a⁻/⁻与Dnmt3b⁻/⁻胚胎的RRBS实验，以单个胚胎为材料完成了生物学重复。我们对采集自E8.5时期的3只野生型（Wild Type, WT）与3只Dnmt3b⁻/⁻同窝胚胎的总RNA构建的RNA-Seq文库完成了测序。