Esrrb function in the extraembryonic ectoderm is required for proper primordial germ cell specification [microarray]

Estrogen related receptor beta (Esrrb) is an orphan nuclear receptor that is required for self-renewal and pluripotency in mouse embryonic stem (ES) cells. However, in the early post-implantation mouse embryo, Esrrb is specifically expressed in the extraembryonic ectoderm (ExE) and plays a crucial role in trophoblast development. In this study, to better understand the function of Esrrb in trophoblast lineage cells, we performed microarray analysis of Esrrb-null mutant versus wild-type mouse embryos. To further characterize the regulatory targets of Esrrb, we treated trophoblast stem (TS) cells with either Esrrb inhibitor DES or vehicle and compared their global gene expression profile via RNA-seq analysis. In addition, to ask whether these target genes are directly regulated by Esrrb, we performed Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis of TS cells using anti-Esrrb antibody. Extraembryonic ectoderm from WT and Esrrb mutant mice were pooled into 3 biological replicates each, and gene expression differences were assessed with Affymetrix microarray雌激素相关受体β（Estrogen related receptor beta，Esrrb）是一类孤儿核受体，对小鼠胚胎干（ES）细胞的自我更新与多能性维持不可或缺。然而在小鼠植入后早期胚胎中，Esrrb仅特异性表达于胚外外胚层（ExE），并在滋养层发育过程中发挥关键调控作用。本研究为深入解析Esrrb在滋养层谱系细胞中的功能，对Esrrb敲除突变胚胎与野生型小鼠胚胎开展了微阵列分析。为进一步刻画Esrrb的下游调控靶标，我们使用Esrrb抑制剂DES与溶剂对照分别处理滋养层干（TS）细胞，并通过RNA测序（RNA-seq）分析比对二者的全局基因表达谱。此外，为明确这些靶基因是否受Esrrb直接调控，我们采用抗Esrrb抗体对TS细胞进行了染色质免疫共沉淀测序（Chromatin immunoprecipitation-sequencing，ChIP-seq）分析。我们将野生型与Esrrb突变小鼠的胚外外胚层分别收集为3个生物学重复样本，并通过Affymetrix微阵列平台评估两组间的基因表达差异。