Comparative analysis of the 4D encoding of regulatory networks in stem cells

描述（由申请人提供）：虽然人体中的所有细胞共享相同的基因组，但不同的细胞类型具有由复杂的基因调控网络控制的特征基因表达模式。了解基因组中这些发育程序的编码以及它们如何产生分化细胞类型的不同转录组是功能基因组学的主要目标，也是现代生物医学研究的主要研究主题之一。现在有充分的证据表明，数千种基因表达的严格时空调控是由称为增强子的调控元件控制的，增强子可以通过远程环相互作用在远离同源启动子的地方找到。随着多种高通量测定方法的发展，以确定蛋白质- dna相互作用、基因表达水平和远程相互作用，我们正处于复杂综合研究的尖端，我们可以使用这些测定方法的组合来询问有关蛋白质- dna相互作用和增强子-启动子相互作用如何在全基因组范围内解释高分辨率分化时间过程中细胞状态变化的基本问题。我们建议开发几种新的实验和计算方法，以提高蛋白质- dna相互作用以及远程相互作用的分辨率，适用性和有效性，以了解它们在祖细胞向分化细胞类型分化过程中控制基因表达的作用。一旦开发出来，这些方法将广泛应用于功能基因组学的各种研究。为了证明这些方法的力量，我们将应用它们来研究现有的人类、小鼠、马和狗干细胞向心肌细胞和神经元的分化，以了解这些远程相互作用的作用、保存和动力学。该结果将极大地扩展我们对哺乳动物同源细胞分化中远程相互作用的进化和作用的理解，以及特定的远程相互作用是否对干细胞有效分化为完全分化的细胞类型至关重要。

DESCRIPTION (provided by applicant): While all of the cells in a human body share the same genome, different cell types have characteristic gene expression patterns that are controlled by elaborate gene regulatory networks. Understanding the encoding of these developmental programs in the genome and how they give rise to the diverse transcriptomes of differentiated cell types is the primary goal of functional genomics and one of the driving research themes of modern biomedical research in general. There is now ample evidence that the tight spatio-temporal regulation of the expression of thousands of genes is controlled by regulatory elements called enhancers that can be found far away from their cognate promoters via long-range looping interactions. With the development a multiple high-throughput assays to determine protein-DNA interactions, gene expression levels, and long- range interactions, we are on the cusp of sophisticated integrative studies where we can use combinations of these assays to ask fundamental questions about how protein-DNA interactions and enhancer-promoter interactions genome-wide account for changes in cell state across high-resolution differentiation time courses. We propose to develop several new experimental and computational methods to increase the resolution, applicability, and validation of protein-DNA interactions as well as long-range interactions to understand their role in controlling gene expression during differentiation from progenitor cells to differentiated cell types. Once developed, these methods will be widely applicable across a variety of studies in functional genomics. To demonstrate the power of these methods, we will apply them to study the differentiation of existing human, mouse, horse and dog stem cells into cardiomyocytes and neurons in order to understand the role, conservation and dynamics of these long-range interactions. The results will greatly expand our understanding of both the evolution and role of long-range interactions in homologous cell differentiation in mammals and whether particular long-range interactions are critical for the efficient differentiation of stem cells into fully- differentiated cell types.