Mechanisms of enhancer activation in early development

描述（由申请人提供）：基因组信息的解释涉及细胞历史和细胞外环境的整合，最终发生在染色质水平，并由功能多样化的顺式调控元件介导，如增强子、启动子、沉默子和绝缘子。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中起着核心作用。增强子具有某些共同的染色质特征，如核酸酶超敏和组蛋白修饰H3K4me1和H3K27ac的侧核小体富集。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、细胞类型特异性和保守独立的方式识别增强子元件的能力。这些研究揭示了增强子在不同细胞类型中利用的出乎意料的复杂性和动态性。例如，关键的谱系特异性位点通常以同时存在活性增强子为特征，这些增强子由高水平的tf、一般共激活子和H3K27ac定义，并且对扰动表现出异常的敏感性。这些聚集的增强子排列被称为超级增强子。虽然目前对哺乳动物增强子生物学有相当大的兴趣，但一些基本的增强子特性仍未得到研究。例如，虽然无数的研究利用组蛋白修饰在增强子作图中，但很少有关于这些标记在增强子区域的功能意义的见解。在拟议的研究中，我们将使用一个定义良好且稳健的早期细胞命运决定模型，我们将其称为“胚胎干细胞（ESC）向上皮细胞样细胞（EpiLC）转变”，以研究H3K4me1在重新选择新的激活增强子中的功能。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，但我们不了解它们是如何起作用的，也不了解是否通过聚集多个同时活跃的增强子出现了新的调节现象。我们将使用ESC到EpiLC过渡模型来解剖一个动态调节的超级增强子的解剖和三维结构。我们将讨论其各个元素之间是否存在串扰，这可能解释超级增强子元素的一些不寻常行为。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.