Epigenetic control of the stem cell gene regulatory network

胚胎干细胞(ESCs)来源于囊胚期胚胎的内细胞团，是一种功能强大的 细胞分化的体外模型和再生治疗的潜在细胞来源。更好的 了解控制分化的因素对于有力地指导胚胎干细胞产生成熟是必要的。 用于治疗的细胞类型。此外，体内分化的扰动会导致早期的缺陷 胚胎和失败的怀孕。我们正致力于阐明esc基因的组成和连接。 监管网络，以便更好地控制ESC分化，更完整地了解ESC 早期发展。虽然ESC GRN转录因子由三类调控因子组成， 表观遗传调节器和RNA--只有前两类的功能在一定程度上被理解。我们 最近发现了ESC表观基因组的一个结构特征--RNA/DNA杂交体(RDHs)在细胞中的关键作用 命运。我们发现，RDHs是维持ESCs-细胞分化潜能所必需的，但减少了 RDHs的分化保真度较低，分化曲线不对称。我们最近发现RDHs 在ESC GRN中发挥关键作用，这可能是这些表型的原因。RDH的枯竭导致 数以千计的基因调控不当。有趣的是，对于这些基因中的一小部分，我们发现RDHs 调控两个关键的表观遗传调控因子PRC2和Tip60-P400的结合。然而，大多数基因 受RDH监管的人既不是这些因素的直接目标，也不是间接目标，这引发了还有什么其他因素的问题 GRN的组成部分由RDH调制。在这里，我们建议使用表观基因组图谱和系统 全面阐明RDHs在GRN中的作用的水平方法。此外，我们还将利用一部小说 新的Rdh结合因子的鉴定方法。最后，我们将使用单细胞分析技术来 阐明RDH是如何逐个细胞地调节细胞命运的。这些研究将提供多种新的见解 研究RNAs在ESC GRN中的功能。此外，这些研究将加强我们对如何 细胞在胚胎干细胞分化过程中获得特定的命运。

Embryonic stem cells (ESCs) derived from the inner cell mass of blastocyst stage embryos are a powerful in vitro model for cellular differentiation and a potential source of cells for regenerative therapies. A better understanding of the factors controlling differentiation is necessary to robustly direct ESCs to produce mature cell types for therapeutic purposes. In addition, perturbations in differentiation in vivo lead to defects in early embryos and failed pregnancies. We are focusing on elucidating the components and wiring of the ESC gene regulatory network, in order to better control ESC differentiation and gain a more complete understanding of early development. Although three classes of regulatory factors comprise the ESC GRN—transcription factors, epigenetic regulators, and RNAs—the functions of only the first two classes are understood to a degree. We recently uncovered a key role for a structural feature of the ESC epigenome, RNA/DNA hybrids (RDHs), in cell fate. We found that RDHs are necessary to maintain the differentiation potential of ESCs—cells with reduced RDHs showed poor differentiation fidelity and a skewed differentiation profile. We recently found that RDHs play a key role in the ESC GRN, which likely accounts for these phenotypes. Depletion of RDHs leads to misregulation of thousands of genes. Interestingly, for a small fraction of these genes, we found that RDHs regulate the binding of two key epigenetic regulatory factors, PRC2 and Tip60-p400. However, most genes regulated by RDHs are neither direct nor indirect targets of these factors, raising the question of what other components of the GRN are modulated by RDHs. Here we propose to use epigenomic profiling and systems level approaches to comprehensively elucidate the roles of RDHs in the GRN. In addition, we will utilize a novel method for identification of new RDH-binding factors. Finally, we will use single cell profiling techniques to elucidate how RDHs regulate cell fate on a cell-by-cell basis. These studies will provide multiple new insights into how RNAs function within the ESC GRN. In addition, these studies will enhance our understanding of how cells acquire specific fates during ESC differentiation.