Genome-wide map of active promoters in the mouse cells

描述（由申请人提供）： 哺乳动物基因的时间和组织特异性表达依赖于转录调控蛋白与顺式元件如启动子、增强子和绝缘子之间复杂的相互作用。先前的大规模努力已经为大多数哺乳动物基因产生了一个极好的转录起始位点目录，但是控制特定细胞类型中每个启动子激活的机制在很大程度上仍然未知。为了更好地理解组织和细胞类型特异性基因表达的调控机制，重要的是表征每个启动子在特定细胞类型中的活性，并确定每个基因的顺式调控元件，包括增强子和绝缘子。在这里，我们建议使用实验室小鼠作为模型系统，并进行全基因组分析的活性启动子，增强子和绝缘子元件在一个小组的胚胎和成人组织与医学相关。具体而言，我们将（1）在一组代表性的胚胎和成体组织中鉴定小鼠基因组中的活性启动子;（2）在相同的胚胎和成体组织中鉴定小鼠基因组中的潜在增强子和绝缘子元件;（3）鉴定和表征小鼠基因组中的组织特异性启动子和增强子;以及（4）验证选定的一组鉴定的启动子和增强子的功能。这项拟议中的研究如果完成，将导致整个小鼠基因组的启动子，潜在的增强子和绝缘子的全面图谱。该资源将为分析小鼠细胞中的基因调控网络提供基础，并指导小鼠基因组的功能注释。这些结果也将有助于理解顺式调控序列的进化，当与人类ENCODE项目进展时提供的类似结果进行比较时。实验室小鼠是了解人类生物学和人类疾病分子基础的重要模型系统。作为人类基因组的参考，小鼠基因组序列在基因注释中被证明是非常有价值的。实验室小鼠作为模型系统的效用目前受到缺乏对控制小鼠细胞中常见和种属特异性基因表达程序的基因调控机制的理解的限制。在这个项目中，我们建议定义一组基因组序列称为顺式调控元件在小鼠基因组中。这些调控DNA由启动子、增强子、绝缘子和其他调控序列组成。作为理解哺乳动物细胞基因调控机制的关键一步，我们将绘制小鼠基因组中启动子、增强子和绝缘子的全面图谱。我们将使用一种新开发的高通量实验策略来鉴定这些序列，这些序列参与小鼠胚胎干细胞、胚胎成纤维细胞以及一组胚胎和成人组织中的基因激活。我们将鉴定组织特异性启动子和增强子，并描述控制特定组织中基因表达程序的调控机制。该研究的完成有望提高我们对哺乳动物细胞中基因调控机制的认识，并为理解人类的相同过程提供参考。

DESCRIPTION (provided by applicant): Temporal and tissue-specific gene expression in mammals depends on complex interactions between transcriptional regulatory proteins and cis-elements such as promoter, enhancers and insulators. Previous large-scale efforts have produced an excellent catalog of transcriptional start sites for most mammalian genes but the mechanisms that control the activation of each promoter in specific cell types remains largely unknown. To better understand the regulatory mechanisms of tissue- and cell type-specific gene expression, it is important to characterize the activities of each promoter in specific cell types, and identify the cis-regulatory elements including enhancers and insulators for each gene. Here, we propose to use the laboratory mouse as a model system and conduct genome-wide analysis of active promoters, enhancers and insulator elements in a panel of embryonic and adult tissues with medical relevance. Specifically, we will (1) identify the active promoters in the mouse genome in a representative set of embryonic and adult tissues; (2) identify potential enhancers and insulator elements in the mouse genome in the same embryonic and adult tissues; (3) identify and characterize tissue-specific promoters and enhancers in the mouse genome; and (4) validate the function of a select set of identified promoters and enhancers. The proposed study, if completed, will result in a comprehensive map of promoters, potential enhancers and insulators throughout the mouse genome. The resource will provide a foundation for analyzing the gene regulatory networks in the mouse cells, and guide the functional annotation of the mouse genome. The results will also help understand the evolution of cis-regulatory sequences, when compared to similar results to be made available as the human ENCODE project progresses. The laboratory mouse represents an important model system for understanding human biology and the molecular basis of human diseases. As a reference to the human genome, the mouse genome sequence has proved extremely valuable in gene annotation. The utility of the laboratory mouse as a model system is currently limited by the lack of understanding of gene regulatory mechanisms that control both common and species-specific gene expression programs in mouse cells. In this project, we propose to define the set of genomic sequences known as cis-regulatory elements in the mouse genome. These regulatory DNA consists of promoters, enhancers, insulators and other regulatory sequences. As a key step towards understanding the gene regulatory mechanisms in mammalian cells, we will produce a comprehensive map of promoters, enhancers and insulators in the mouse genome. We will use a newly developed, high throughput experimental strategy to identify these sequences that are engaged in gene activation in the mouse embryonic stem cells, embryonic fibroblasts, and a panel of embryonic and adult tissues. We will identify tissue specific promoters and enhancers, and characterize the regulatory mechanisms that control the gene expression programs in the specific tissues. Completion of the proposed research is expected to improve our knowledge of the gene regulatory mechanisms in mammalian cells, and provide a reference for understanding the same process in human beings.