Silencing of developmental genes by H3K27me3 and DNA methylation reflects the discrepant plasticity of embryonic and extraembryonic lineages
Silencing of developmental genes by H3K27me3 and DNA methylation reflects the discrepant plasticity of embryonic and extraembryonic lineages
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H3K27me3 和 DNA 甲基化对发育基因的沉默反映了胚胎和胚胎外谱系的可塑性差异
DOI：
10.1038/s41422-018-0010-1
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发表时间：
2018
期刊：
影响因子：
44.1
通讯作者：
Naihe Jing
中科院分区：
文献类型：
--
作者：
Xianfa Yang;Boqiang Hu;Yu Hou;Yunbo Qiao;Ran Wang;Yingying Chen;Yun Qian;Su Feng;Jun Chen;Chang Liu;Guangdun Peng;Fuchou Tang;Naihe Jing
哺乳动物胚胎发生中最重要的课题之一是多细胞谱系的产生。简言之，一个单细胞全能合子在囊胚期发育成内细胞团（ICM）和滋养外胚层（TE）。然后，ICM进一步产生上胚层细胞并最终形成多个体细胞谱系，而TE发育为胚外外胚层（ExE）细胞并最终形成胎盘组织。哺乳动物胚胎发育的高度有序的程序是由表观遗传机制时空调控的。以前的工作表明，ICM和TE仍然在很大程度上表观遗传上无法区分，1，2即使存在显着的转录差异。最近，我们揭示了小鼠E7中关键发育相关基因（DRG）的空间特异性转录组。0原肠胚，我们还注意到，这些DRG沉默的原肠胚区域具有不同的发育潜力。3然而，是否有任何差异的表观遗传机制的区域特异性分布的DRG在植入后胚胎和这些表观遗传差异如何有助于区域化的发展潜力在小鼠胚胎中仍然不清楚。在这里，我们集中在两个主要的表观遗传沉默机制，H3 K27 me3和DNA甲基化（DNAme），在小鼠植入后胚胎（图1a和补充信息，图S1A和B），这已经很好地表征了植入前胚胎。1，2在三个连续的阶段将胚胎解剖成ExE和外胚层（Epi），包括最后一个均匀的外胚层阶段（E6. 5）、初始区域化阶段（E7. 0)和三胚层形成阶段（E7. 5)4（图1a和补充信息，图S1B）。根据区域化发展倾向，E7. 0和E7。将5个上胚层进一步解剖成前（A）、后（P）和前中胚层（AM，对于E7）。仅5）部分用于高保真表观遗传分析，其可以通过区域特异性标志物表达来指示（补充信息，图S1C和D）。考虑到植入后早期胚胎的细胞数量有限，使用适用于104个细胞5的改良染色质免疫沉淀法来分析H3K27me3的修饰模式，并使用还原代表性亚硫酸氢盐测序6来分析DNA甲基化组。每份样本生成两份具有高重现性的生物学重复样本（补充信息，图S1E、F和表S1）。从E6开始，我们观察到植入后阶段DNAme的弱动力学。5到E7 5阶段（图1 B）。值得注意的是，ExE细胞具有较低的DNAme水平比胚内细胞。同时，在植入后胚胎的发育过程中鉴定了H3 K27 me3的普遍重塑（图1 B和补充信息，图S2 A）。聚类分析显示，在植入前和植入后胚胎之间存在H3K27me3和DNAme的显著差异（补充信息，图S2B和C）。有趣的是，H3 K27 me3和DNAme的基因组分布在多个基因组区域表现出负相关，例如CpG岛（CGI）和脑池内A颗粒（IAP）区域（图1 B）。引人注目的是，大多数植入后胚胎的从头H3K27me3发生在调控基因组区域，如CGIs。此外，H3K27me3的弱动力学可以在重复区域，如内源性逆转录病毒K区（ERVKs）鉴定。同时，在调控区和重复元件处观察到DNAme的增加。那个...
Dear Editor, One of the most important topics in mammalian embryogenesis is the generation of multiple cell lineages. Briefly, one single-cell totipotent zygote develops into the inner cell mass (ICM) and trophectoderm (TE) at the blastocyst stage. Afterwards, the ICM further generates the epiblast cells and finally forms multiple somatic cell lineages, while the TE develops into extraembryonic ectoderm (ExE) cells and eventually forms the placental tissue. The highly ordered programming of mammalian embryo development is spatial-temporally regulated by epigenetic mechanisms. Previous work has revealed that the ICM and TE remain largely epigenetically indistinguishable, 1, 2 even though there exist significant transcriptional distinctions. Recently we revealed the spatial-specific transcriptome of key development-related genes (DRGs) in mouse E7. 0 gastrula, and we also noticed that these DRG-silenced gastrula regions possess distinct developmental potencies. 3 However, whether there are any distinctions of epigenetic mechanisms underlying the region-specific distribution of DRGs in post implantation embryos and how these epigenetic distinctions contribute to the regionalized developmental potential in mouse embryos remain unclear. Here, we focused on two major epigenetic silencing mechanisms, H3K27me3 and DNA methylation (DNAme), in mouse post implantation embryos (Fig. 1 a and Supplementary information, Figure S1A and B), which have been well characterized in preimplantation embryos. 1, 2 The embryos were dissected into ExE and epiblast (Epi) at three consecutive stages, encompassing the last homogeneous epiblast stage (E6. 5), the initial regionalized stage (E7. 0) and the three germ-layer formation stage (E7. 5) 4 (Fig. 1 a and Supplementary information, Figure S1B). According to the regionalized developmental propensity, the E7. 0 and E7. 5 epiblasts were further dissected into anterior (A), posterior (P), and anterior mesoderm (AM, for E7. 5 only) parts for high-fidelity epigenetic profiling, which can be indicated by region-specific marker expression (Supplementary information, Figure S1C and D). Given the limited cell number of early post implantation embryos, modified chromatin immunoprecipitation adapted for 104 cells 5 was utilized to profile the modification pattern of H3K27me3 and reduced representation bisulfite sequencing 6 was used to profile DNA methylome. Two biological replicates with high reproducibility (Supplementary information, Figure S1E, F and Table S1) were generated for each sample. We observed weak dynamics of DNAme at post implantation stage from E6. 5 to E7. 5 stage (Fig. 1 b). Noticeably, the ExE cells possessed lower DNAme level than the intraembryonic cells. Meanwhile, pervasive remodeling of H3K27me3 was identified during the development of the post implantation embryo (Fig. 1 b and Supplementary information, Figure S2A). Clustering analysis revealed that significant distinctions of H3K27me3 and DNAme exist between pre and post implantation embryos (Supplementary information, Figure S2B and C). Interestingly, genomic distributions of H3K27me3 and DNAme exhibited negative correlation at multiple genomic regions, such as CpG islands (CGIs) and intracisternal A-particle (IAP) regions (Fig. 1 b). Strikingly, most de novo H3K27me3 of post implantation embryos occurred at the regulatory genomic regions, such as CGIs. Moreover, weak dynamics of H3K27me3 can be identified at the repetitive regions, such as endogenous retrovirus K regions (ERVKs). Meanwhile, the increment of DNAme was observed at both the regulatory regions and repetitive elements. The …