Epigenetic control of the stem cell gene regulatory network

胚胎干细胞（Embryonic stem cells，ESCs）来源于胚泡期胚胎的内细胞团，是一种强大的干细胞。 细胞分化的体外模型和用于再生疗法的细胞的潜在来源。更好的 了解控制分化的因素对于强有力地指导ESCs产生成熟的 用于治疗目的的细胞类型。此外，体内分化中的扰动导致早期分化缺陷。 胚胎和失败的怀孕。我们的重点是阐明ESC基因的组成和布线 调控网络，以便更好地控制ESC分化，并获得更完整的了解 早期发展。尽管三类调节因子构成了ESC GRN转录因子， 表观遗传调节因子和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表观基因组的结构特征，RNA/DNA杂交体（RDH），在细胞中的关键作用， 命运我们发现，RDH是维持胚胎干细胞分化潜能所必需的， RDHs表现出较差的分化保真度和偏斜的分化特征。我们最近发现， 在ESC GRN中发挥关键作用，这可能解释了这些表型。RDH的耗尽导致 成千上万个基因的错误调控。有趣的是，对于这些基因中的一小部分，我们发现RDH 调节两个关键的表观遗传调节因子PRC 2和Tip 60-p400的结合。然而，大多数基因 由RDH监管的人既不是这些因素的直接目标，也不是这些因素的间接目标，这就提出了一个问题， GRN的分量由RDH调制。在这里，我们建议使用表观基因组分析和系统 水平的方法，以全面阐明的RDHs在GRN的作用。此外，我们将利用一本小说 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， 阐明RDH如何在细胞基础上调节细胞命运。这些研究将提供多个新的见解 RNA如何在ESC GRN中发挥作用。此外，这些研究将提高我们的理解， 细胞在ESC分化期间获得特定的命运。

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.