Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development [RNA-seq]

H3K9me3-dependent heterochromatin is considered as one of the major barriers for cell fate changes, and must be reprogrammed during fertilization to reactivate highly specialized paternal and maternal genome to establish totipotency. However, the molecular details are lacked for early embryos due to the limited materials. Here we map the genome-wide distribution of H3K9me3 modification in the early embryo as well as in the cell fate determined embryonic tissues after implantation. We find that H3K9me3 exhibits distinct dynamic features in promoters and retro-transposons. Both maternal and paternal genome undergo large scale of H3K9me3 reestablishment after fertilization, and the imbalance of maternal H3K9me3 signal over paternal last until the blastocyst stage. The rebuilding of H3K9me3 on LTR retro-transposons maintains its repression state after the global DNA demethylation, and we further discover that Chaf1a is essential for the establishment of H3K9me3 on LTRs and the loss function of Chaf1a leads to embryo development failure. Finally, we find that lineage specific H3K9me3 is established after lineage commitment in post-implantation embryos. Thus, our data demonstrate that H3K9me3-dependent heterochromatin undergoes dramatic reprogramming during early embryo development and the establishment of H3K9me3 on LTRs is essential for proper embryo development. We mapped the H3K9me3 modifications on embryos from zygote to 8.5 day stage (with separated ICM and TE, Epi and Exe). The mouse metaphase II (MII) oocytes, sperm, as well as mouse embryonic stem cells (mESCs) and mouse trophoblast stem cells (mTSCs) were also analyzed. In the ChIP-seq analysis on pre-implantation embryos, 500 cells were used for per reaction and two or three replicates were performed for each stage. This series contains the RNA-seq data on embryos from embryos from zygote to 6.5 day stage (with separated ICM and TE, Epi and Exe) including morula stage with siRNA.依赖于组蛋白H3赖氨酸9三甲基化（H3K9me3）的异染色质被视为阻碍细胞命运转变的主要屏障之一，在受精过程中必须经历重编程，以激活高度特化的父本与母本基因组，进而建立全能性。但由于早期胚胎样本稀缺，其相关分子机制细节仍未被充分阐明。本研究绘制了早期胚胎以及着床后细胞命运定型的胚胎组织中H3K9me3修饰的全基因组分布图谱。研究发现，H3K9me3在启动子区域与逆转录转座子（retro-transposons）中呈现出截然不同的动态变化特征。受精后，父本与母本基因组均发生了大规模的H3K9me3重建立过程，且母本H3K9me3信号相较于父本的失衡状态会持续至囊胚期。在全局DNA去甲基化后，长末端重复序列逆转录转座子（LTR retro-transposons）上的H3K9me3重建维持了其转录沉默状态；我们进一步发现，Chaf1a对于LTR区域的H3K9me3建立至关重要，而Chaf1a功能缺失会导致胚胎发育失败。最后，我们观察到着床后胚胎的谱系特异性H3K9me3修饰是在谱系定型后建立的。综上，本研究数据表明，依赖于H3K9me3的异染色质在早期胚胎发育过程中经历了剧烈的重编程，而LTR区域的H3K9me3建立对于正常胚胎发育不可或缺。本研究绘制了从受精卵到8.5天阶段胚胎的H3K9me3修饰图谱（涵盖分离得到的内细胞团（ICM）、滋养外胚层（TE）、上胚层（Epi）与胚外组织（Exe）样本）。此外还分析了小鼠第二次减数分裂中期（MII）卵母细胞、精子，以及小鼠胚胎干细胞（mESCs）与小鼠滋养层干细胞（mTSCs）。在针对着床前胚胎的染色质免疫共沉淀测序（ChIP-seq）分析中，每个反应使用500个细胞，每个阶段设置2至3次生物学重复。本数据集包含从受精卵到6.5天阶段胚胎的RNA测序（RNA-seq）数据（涵盖分离得到的ICM、TE、Epi与Exe样本，以及转染小干扰RNA（siRNA）的桑葚胚样本）