Analysis of combinatorial cis-regulation in synthetic and genomic promoters

项目摘要 当基因移动到新的染色体位置时，它们通常在 不同的层次。我们将利用这些染色体位置效应来研究不同之处 染色体位置影响顺式调节序列(CRS)的活性。我们建议 衡量大型且多样化的CRS集合的活动在发生变化时是如何变化的 移至不同的染色体位置(目标1)。为了大规模收集这些数据，我们将引入 一种新的大规模平行报告基因分析方法(MPRA)。我们的目标是解决几个问题。 1.如何解释不同染色体之间调节潜力的差异 位置？当CRS的活动因其移动到新位置而发生更改时， 这些变化是由于新的染色质状态、附近增强子的活性，还是两者兼而有之？ 2.CRS和基因组位置的调控作用何时独立，何时独立 他们以复杂的方式互动？交互作用取决于CRS的属性和 特殊的染色质景观？ 我们还建议用一项研究来补充我们对基因表达水平的调查 基因组位置如何影响基因表达动态(目标2)。通过测量细胞- 不同CRS在不同染色体位置产生的mRNA到细胞的模式，我们将 揭示染色体环境如何改变表达的动态。成功者 完成本提案的目标将导致对数量和分子的理解 CRS和染色质环境对基因表达的联合调控。一目了然 了解CRS在基因组中的功能将有助于识别和解释疾病- 导致影响顺式调控的基因变异。

Project Summary When genes move to new chromosomal locations they are often expressed at drastically different levels. We will use these chromosome position effects to investigate how different chromosomal locations affect the activity of cis-regulatory sequences (CRS). We propose to measure how the activities of a large and diverse collection of CRS change when they are moved to different chromosomal locations (Aim 1). To collect this data at scale we will introduce a new massively parallel reporter gene assay (MPRA). We aim to address several questions. 1. What accounts for the differences in regulatory potential between chromosome positions? When the activity of a CRS changes because it moves to a new location, are the changes due to the new chromatin state, the activity of nearby enhancers, or both? 2. When are the regulatory effects of CRS and genome position independent and when do they interact in complex ways? Do interactions depend on the properties of CRS and the specific chromatin landscape? We also propose to complement our investigation of gene expression levels with a study of how genome position influences gene expression dynamics (Aim 2). By measuring the cell- to-cell patterns of mRNA generated by different CRS at different chromosome locations, we will uncover how chromosome environments alter the dynamics of expression. The successful completion of the aims of this proposal will result in a quantitative and molecular understanding of the combinatorial regulation of gene expression by CRS and chromatin environment. A clear understanding of how CRS function in the genome will help identify and interpret disease- causing genetic variants that affect cis-regulation.