Enhance human ENCODE by function comparisons to mouse

通过与小鼠的功能比较来增强人类 ENCODE

• 批准号: 7940960
• 负责人: ROSS C HARDISON
• 金额: $ 75万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-26 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7940960
• 关键词: Adopted; BFU-E; Base Sequence; Binding; Binding Sites; Biochemical; Biochemical Markers; Biological Assay; Biological Process; Cell Line; Cell model; Cells; Chromatin Structure; Chromosomes; Classification; Collaborations; Complement; Complex; Correlative Study; DNA; DNA Sequence; DNA-Protein Interaction; Data; Deoxyribonucleases; Development; Developmental Biology; Diabetes Mellitus; Disease; Disease susceptibility; Elements; Enhancers; Erythroblasts; Erythropoiesis; Event; Evolution; Frequencies; Future; GATA1 gene; Gene Expression; Genes; Genetic; Genome; Goals; Harvest; Heart Diseases; Human; Human Cell Line; Human Genome; Human Genome Project; Indium; Individual; Institution; Investigation; Lead; Light; Location; Lymphocyte; Lymphoid; Machine Learning; Malignant Neoplasms; Mammals; Maps; Molecular; Molecular Conformation; Molecular Evolution; Molecular Genetics; Mouse Cell Line; Mus; Muscle Cells; Myelogenous; National Human Genome Research Institute; Nuclear; Persons; Phase; Phylogenetic Analysis; Predisposition; Prevention; Problem Solving; Process; Quality Control; Request for Applications; Research; Research Personnel; Sequence Analysis; Site; Sorting - Cell Movement; Staging; Stimulus; System; Technology; Time Study; Transcript; Transcription Initiation Site; Transcriptional Regulation; Variant; Work; base; cell type; comparative; data mining; effective therapy; embryonic stem cell; genome sequencing; genome-wide; high standard; histone modification; human GATA1 protein; human data; human disease; improved; insight; mouse genome; novel; pathogen; promoter; public health relevance; response; restoration; transcription factor

DESCRIPTION (provided by applicant): Our goal is to discover and use relationships between mouse and human regulatory genomes to advance the ENCODE Project in its effort to map all functional elements in the human genome. Our comparative approach aims to uncover principles and solve problems that are proving difficult by studying the human genome alone. ENCODE is vigorously mapping hundreds of function-associated biochemical markers in selected cell lines, resulting already in tens of millions of reproducible biochemical features. Some observed protein:DNA interactions find and refine known transcriptional enhancers, promoters, silencers, together with associated chromatin structure, as was anticipated. But substantial questions arise as to how many of the myriad biochemical events are functional, what those functions are, which gene or genes are meaningful targets, etc. To highlight and sort functionally important biochemical marks from others, we will systematically identify the molecular events retained by both mouse and human since they diverged. We will then analyze how conservation of biochemical features relates to conservation of DNA sequence and conservation of regulated gene expression. By using the mouse, we can leverage decades of molecular genetics and manipulated mouse genomes that do not exist in any other mammal. In Aim 1 we execute genome-wide assays for biochemical signatures of functional DNA sequences in a few specific mouse cell types. By using well-studied mouse lines and cell states, we can interpret results in light of previously validated elements and in light of ENCODE human results. We will use ENCODE standards for high throughput, sequence-based assays to determine gene expression, DNase hypersensitive sites, histone modifications and selected transcription factor occupancy in seven mouse cell types. The eight selected features are the most informative ones for function, and thus most useful for comparison with human data. In Aim 2, we apply a genome-wide implementation of chromosome conformation capture to map the interactions between transcription factor binding sites and their responsive genes in two cell types. These results will be compared to those from an ENCODE developmental project. Comparative analysis in Aim 3 will insure that the impact of the data we produce will go beyond the individual mouse cell systems per se. To do this we have organized a collaboration of investigators at multiple institutions, in which each group is expert in one or more critical aspects. Our data, made public and accessible via ENCODE, will fuel and accelerate many future studies after the 2-yr stimulus both in and beyond ENCODE. This responds to NHGRI request for applications on "Enhancement of the value of the human ENCODE Project by conducting a parallel effort on the mouse genome." The proposed work will improve the maps of biologically functional DNA sequences in humans, which in turn will help explain how variants in human genome sequences could be associated with human diseases, leading to candidates for novel avenues for effective therapy and prevention. PUBLIC HEALTH RELEVANCE: Every person differs in his or her response to pathogens and in the likelihood that they will suffer from complex diseases such as cancer, heart disease or diabetes. Individual susceptibility to disease is determined in part by genetics, and we can map with high precision the locations of DNA variants associated with disease susceptibility. In order to understand how these variants contribute to disease susceptibility, we need to identify the biological functions of all DNA sequences; the proposed work will help us map these functional DNA sequences.

描述（由申请人提供）：我们的目标是发现并利用小鼠和人类调控基因组之间的关系来推进 ENCODE 项目，努力绘制人类基因组中的所有功能元件。我们的比较方法旨在揭示原理并解决仅通过研究人类基因组很难解决的问题。 ENCODE 正在大力绘制选定细胞系中数百个功能相关生化标记的图谱，已产生数千万个可重复的生化特征。正如预期的那样，一些观察到的蛋白质：DNA 相互作用发现并完善了已知的转录增强子、启动子、沉默子以及相关的染色质结构。但是，大量的生化事件中有多少是有功能的，这些功能是什么，哪些基因是有意义的靶标，等等。为了突出和分类其他功能上重要的生化标记，我们将系统地识别小鼠和人类自分化以来保留的分子事件。然后我们将分析生化特征的保守性与 DNA 序列的保守性和受调控基因表达的保守性之间的关系。通过使用小鼠，我们可以利用数十年的分子遗传学并操纵任何其他哺乳动物中不存在的小鼠基因组。在目标 1 中，我们对几种特定小鼠细胞类型中功能性 DNA 序列的生化特征进行了全基因组测定。通过使用经过充分研究的小鼠系和细胞状态，我们可以根据先前验证的元素和 ENCODE 人类结果来解释结果。我们将使用 ENCODE 标准进行高通量、基于序列的测定，以确定七种小鼠细胞类型中的基因表达、DNase 超敏位点、组蛋白修饰和选定的转录因子占据。所选择的八个特征是功能信息最丰富的特征，因此对于与人类数据进行比较最有用。在目标 2 中，我们应用染色体构象捕获的全基因组实施来绘制两种细胞类型中转录因子结合位点及其响应基因之间的相互作用。这些结果将与 ENCODE 开发项目的结果进行比较。目标 3 中的比较分析将确保我们产生的数据的影响将超越单个小鼠细胞系统本身。为此，我们组织了多个机构的研究人员进行合作，每个小组都是一个或多个关键方面的专家。我们的数据通过 ENCODE 公开和访问，将在 ENCODE 内外的两年刺激之后推动和加速许多未来的研究。这响应了 NHGRI 的“通过对小鼠基因组进行并行工作来增强人类 ENCODE 项目的价值”的申请请求。拟议的工作将改善人类生物功能DNA序列的图谱，这反过来将有助于解释人类基因组序列的变异如何与人类疾病相关，从而找到有效治疗和预防的新途径。 公共卫生相关性：每个人对病原体的反应以及罹患癌症、心脏病或糖尿病等复杂疾病的可能性都不同。个体对疾病的易感性部分是由遗传学决定的，我们可以高精度地绘制与疾病易感性相关的 DNA 变异的位置。为了了解这些变异如何导致疾病易感性，我们需要确定所有 DNA 序列的生物学功能；拟议的工作将帮助我们绘制这些功能性 DNA 序列。