Epigenetic control of the stem cell gene regulatory network

干细胞基因调控网络的表观遗传控制

• 批准号: 10394283
• 负责人: THOMAS G FAZZIO
• 金额: $ 37.47万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-08-15 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10394283
• 关键词: Adult; Alleles; Architecture; Binding; Bioinformatics; Cell Fate Control; Cell model; Cells; Complex; Congenital Abnormality; DNA; DNA Binding; DNA Methylation; DNA Methylation Regulation; Data; Data Set; Defect; Development; Embryo; Endoderm; Epigenetic Process; Eukaryota; Gene Expression Regulation; Genes; Genomic Instability; Grant; Hybrids; Immunoglobulin Class Switching; Immunoglobulin Switch Recombination; Impairment; Individual; Inner Cell Mass; Knock-out; Lead; Light; Location; Maintenance; Maps; Mass Spectrum Analysis; Measures; Mesoderm; Methods; Modeling; Nucleosomes; Outcome; Pathway interactions; Phenotype; Play; Population; Pregnancy; Process; Proteins; RNA; RNA analysis; RNA purification; Regulation; Role; Site; Source; Stem cell pluripotency; Structure; System; Techniques; Testing; Therapeutic; Transcription Initiation; Tweens; Variant; base; blastocyst; cell fate specification; cell transformation; cell type; crosslink; embryonic stem cell; epigenome; epigenomics; gene regulatory network; genetic regulatory protein; genome-wide; histone modification; hybrid gene; in vitro Model; in vivo; insight; multidisciplinary; novel; overexpression; pluripotency; pregnancy failure; prevent; recruit; regenerative cell; regenerative therapy; role model; self-renewal; single-cell RNA sequencing; stem cell differentiation; stem cell genes; stem cell proliferation; transcription factor; transcription regulatory network; transcription termination

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.

源自囊胚期胚胎内细胞团的胚胎干细胞 (ESC) 具有强大的 细胞分化的体外模型和再生疗法的潜在细胞来源。更好的 了解控制分化的因素对于强有力地指导 ESC 产生成熟的细胞是必要的。 用于治疗目的的细胞类型。此外，体内分化的扰动会导致早期细胞的缺陷。 胚胎和妊娠失败。我们致力于阐明 ESC 基因的组成和接线 调控网络，以便更好地控制ESC分化并获得更全面的了解 早期发展。尽管 ESC GRN 包含三类调节因子——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了解。我们 最近发现了 ESC 表观基因组结构特征 RNA/DNA 杂合体 (RDH) 在细胞中的关键作用 命运。我们发现 RDH 对于维持 ESC 的分化潜力是必需的，ESC 是细胞的分化潜能降低的细胞。 RDH 表现出较差的分化保真度和倾斜的分化特征。我们最近发现 RDH 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 数千个基因的失调。有趣的是，对于这些基因的一小部分，我们发现 RDH 调节两个关键表观遗传调控因子 PRC2 和 Tip60-p400 的结合。然而，大多数基因 受 RDH 监管的机构既不是这些因素的直接目标，也不是间接目标，这就提出了一个问题：还有哪些其他因素？ GRN 的组成部分由 RDH 调制。在这里，我们建议使用表观基因组分析和系统 水平方法全面阐明 RDH 在 GRN 中的作用。此外，我们还将利用小说 鉴定新 RDH 结合因子的方法。最后，我们将使用单细胞分析技术来 阐明 RDH 如何逐个细胞地调节细胞命运。这些研究将提供多种新见解 研究 RNA 如何在 ESC GRN 内发挥作用。此外，这些研究将加深我们对如何 细胞在 ESC 分化过程中获得特定的命运。