Mechanisms of enhancer activation in early development

描述(申请人提供)：基因组信息的解释涉及细胞历史和细胞外环境的整合，这最终发生在染色质水平，并由功能多样化的顺式调节元件介导，如增强子、启动子、沉默和绝缘体。其中，作为整合转录因子(TF)结合平台的增强子在指导细胞类型特异性基因表达方面起着核心作用。增强剂有一些共同的染色质特征，如核酸酶超敏和富集组蛋白修饰的侧翼核小体H3K4me1和H3K27ac。这些简单染色质特征的表观基因组图谱已经彻底改变了我们以全基因组、特定细胞类型和独立于保守区的方式识别增强子元件的能力。这些研究揭示了不同细胞类型中增强剂利用的意想不到的复杂性和动力学。例如，关键的谱系特异性基因座的特征通常是存在由高水平的转录因子、通用辅活化子和H3K27ac定义的同时活跃的增强子，并对扰动表现出异常的敏感性。这些簇状增强子排列被称为超级增强剂。虽然目前围绕哺乳动物增强子生物学有相当大的兴奋，但一些基本的增强子特性仍未被研究。例如，虽然无数的研究利用了组蛋白修饰来绘制增强子图谱，但对这些标记在增强子区域的功能意义却知之甚少。在这项拟议的研究中，我们将使用一个定义良好且健壮的早期细胞命运决定模型，我们将其命名为“胚胎干细胞(ESC)到外胚样细胞(EpiLC)的转变”，以研究H3K4me1在从头选择新的激活增强剂中的功能。同样，尽管超级增强子可能对控制细胞命运和疾病状态至关重要，但我们不知道它们是如何发挥作用的，以及是否通过聚集多个同时具有活性的增强子来出现新的调控现象。我们将使用ESC到EpiLC的转换模型来剖析一个动态调节的超级增强子的解剖和三维结构。我们将讨论其单个元件之间是否存在串扰，这可能解释超级增强子元件的一些不寻常行为。拟议的研究将为多能性和发育基因调控的基本机制提供见解。

DESCRIPTION (provided by applicant): Interpretation of genomic information involves integration of cellular history and extracellular environment, which ultimately occurs at the level of chromatin and is mediated by the functionally diversified cis-regulatory elements, such as enhancers, promoters, silencers and insulators. Among those, enhancers, which function as integrated transcription factor (TF) binding platforms, play a central role in directing cell type-specific gene expression. Enhancers share certain common chromatin features, such as nuclease hypersensitivity and enrichment of flanking nucleosomes for histone modifications H3K4me1 and H3K27ac. Epigenomic mapping of these simple chromatin features has revolutionized our ability to recognize enhancer elements in a genome-wide, cell type-specific and conservation independent manner. These studies revealed unexpected complexity and dynamics of enhancer utilization in different cell types. For example, key lineage-specific loci ar often characterized by the presence of simultaneously active enhancers defined by high levels of TFs, general coactivators and H3K27ac, and showing unusual sensitivity to perturbations. These clustered enhancer arrangements have been termed super-enhancers. While there is currently a considerable excitement around mammalian enhancer biology, some fundamental enhancer properties remain unexamined. For example, while a myriad of studies utilized histone modifications in enhancer mapping, there is very little insight into a functional significance of these marks at enhancer regions. In the proposed research we will use a well- defined and robust model of early cell fate decision, which we termed "embryonic stem cell (ESC) to epiblast-like cell (EpiLC) transition", to study function of H3K4me1 in de novo selection of new enhancers for activation. Similarly, although super-enhancers may be critical for controlling cell fate and disease states, we do not understand how they function and whether new regulatory phenomena emerge through clustering multiple, simultaneously active enhancers. We will use the ESC to EpiLC transition model to dissect anatomy and three dimensional architecture of a dynamically regulated super-enhancer. We will address whether cross-talk between its individual elements exists, which could account for some of the unusual behaviors of super-enhancer elements. Proposed research will provide insights into basic mechanisms of pluripotency and developmental gene regulation.