Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape

We have performed deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This revealed thousands of novel non-annotated genes as well as alternative promoters for ~10% of reference genes expressed in oocytes, a large fraction of which coincide with transposable elements of the MaLR and ERVK families. We defined the oocyte DNA methylation landscape as composed of large-scale hyper- and hypo-methylated domains. Correlation with our transcriptome assembly revealed that transcription correlates accurately with DNA methylation and potentially account for ~85-90% of the DNA methylome. RNA-Seq in mouse oocytes at different stages of folliculogenesis本研究针对小鼠卵子发生（oogenesis）的不同阶段开展了深度RNA测序（RNA-Seq）与从头转录组组装（de novo transcriptome assembly）工作。研究共发现数千个未被注释的新基因，同时在卵母细胞中表达的参考基因中，鉴定出约10%的基因存在可变启动子；其中很大一部分可变启动子与MaLR和ERVK家族的转座因子（transposable elements）相重合。本研究将卵母细胞的DNA甲基化景观定义为由大规模高甲基化与低甲基化结构域构成。与本研究转录组组装结果的相关性分析显示，转录过程与DNA甲基化状态精准相关，且该关联可解释约85%~90%的DNA甲基化组构成。此外，本研究还完成了针对卵泡发生（folliculogenesis）不同阶段的小鼠卵母细胞的RNA测序工作。