Promoter Regulation in Response to Environmental Stress

 描述（由申请人提供）：真核基因的调控涉及数百种蛋白质。它们如何在组成基因组的数千个基因中共同工作尚不清楚。为了全面了解所有基因是如何调控的，我们需要知道所有相关蛋白质的精确空间组织，结构和占用水平。我们已经开发了一种全基因组检测方法，称为ChIP-exo，以测量基因组调控的这些方面，现在建议开发一种更高通量的检测方法，并将其应用于数百种基因组结合蛋白的作图（目的1）。从这一点上，我们期望获得一个全面的了解染色质的结构组织和它的调节。 有关基因组结合事件的结构信息被编织到探测特定DNA接触点的核酸外切酶终止位点的复杂图案中。这些模式及其与其他蛋白质产生的模式的关系通常需要大量的生物信息学分析，这通常是典型的湿台科学家无法达到的。问题的根源在于命令行操作、脚本和适当的脚本应用程序的陡峭学习曲线，以及保持数据分析的组织性。这在生物发现中造成了一个固有的缓慢的试错过程。因此，为了缓解将ChIP-exo数据提取到生物发现中的瓶颈，这对目标1至关重要，我们将开发一个专用的和专门的生物信息学管道，旨在进行快速，简单和有效的ChIP-exo分析。结合事件之间的关系将提供新的见解转录复合体的组装和调控。 目标1的目标是收集200个酵母潜在基因组结合蛋白及其相互作用伴侣或复合物在多种细胞状态（生长条件，细胞周期）下的ChIP-exo数据。测试结果包括基因组位置和亚复合体组织的精确近bp图谱，具有最小的假阳性和假阴性。我们设想实现一个快照的详细空间组织基因组结合蛋白在启动子。 目标2的目标是创建一个用户友好，快速导航的平台，使用我们建立的管道在ChIP-exo和相关数据上执行脚本。ChIP-exo数据集的公共使用效用将通过专用平台得到增强。

 DESCRIPTION (provided by applicant): The regulation of eukaryotic genes involves many hundreds of proteins. How they work together at the many thousands of genes that comprise a genome is not known. In order to obtain a comprehensive understanding of how all genes are regulated, we need to know the precise spatial organization, structure, and occupancy levels of all involved proteins. We have developed a genome-wide assay, called ChIP-exo, to measure these aspects of genome regulation, and now propose to develop a higher-throughput version of the assay, and apply it to the mapping of hundreds of genome-binding proteins (aim 1). From this we expect to gain a comprehensive understanding of the structural organization of chromatin and its regulation. The structural information about genomic binding events is woven into the complex patterning of exonuclease stop sites that probe specific DNA contact points. These patterns and their relationships with patterns generated by other proteins often require substantial bioinformatic analyses, which is often out of reach of typical wet-bench scientists. The root of the problem lies at steep learning curve for command-line operations, scripting and proper script application, and keeping data analyses organized. This creates an inherently slow trial-and-error process in biological discovery. Therefore, to alleviate the bottleneck in distillig ChIP-exo data into biological discovery which is so essential to aim 1, we will develop a dedicated and specialized bioinformatic pipeline designed to conduct rapid, easy, and efficient ChIP-exo analyses. Relationships among binding events will provide new insights into transcription complex assembly and regulation. The goal of aim 1 will be to collect ChIP-exo data on 200 yeast potential genome-binding proteins, and their interacting partners or complexes, under multiple cellular states (growth conditions, cell cycle). Tangible outcomes include a precise near-bp map of genomic locations and sub-complex organization, with minimal false positives and negatives. We envision achieving a snapshot of the detailed spatial organization genome- binding proteins at promoters. The goal of aim 2 will be to create a user-friendly, quickly-navigable, platform to execute scripts on ChIP-exo and related data, using our established pipeline. Public use utility of the ChIP-exo datasets will be enhanced with a dedicated platform.