A High-Resolution Enhancer Atlas of the Developing Forebrain

前脑发育的高分辨率增强器图谱

• 批准号: 7694253
• 负责人: Len Alexander Pennacchio
• 金额: $ 55.11万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-30 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7694253
• 关键词: Adult; Atlases; Automobile Driving; Binding Sites; Biological Assay; Brain; Brain Diseases; Cataloging; Catalogs; Characteristics; Code; Collection; Communities; Computing Methodologies; Coupled; DNA; DNA Sequence; Data; Data Set; Databases; Deposition; Development; Distant; Elements; Embryo; Enhancers; Functional RNA; Funding; Gene Expression; Generations; Genes; Genetic; Genome; Genomics; Goals; Hereditary Disease; Histology; Human; Human Development; Human Genetics; Human Genome; Indium; Internet; Laboratories; Link; Location; Maps; Methods; Mus; Mutation; Mutation Detection; National Human Genome Research Institute; Nucleic Acid Regulatory Sequences; Paraffin; Pattern; Property; Prosencephalon; Reagent; Regulation; Regulatory Element; Reporter; Research Personnel; Resolution; Resources; Role; Specificity; Specimen; Testing; Tissues; Training; Transcriptional Regulation; Transgenic Mice; Vocabulary; base; beta-Galactosidase; comparative; computerized tools; developmental disease; genome sequencing; genome-wide; improved; in vivo; markov model; programs; public health relevance; transcription factor; vertebrate genome; web site

DESCRIPTION (provided by applicant): Development of the mammalian forebrain critically depends on the dynamic but precise spatial and temporal control of gene expression. While ongoing public efforts are actively mapping gene expression patterns on a genomic scale, the transcriptional enhancer sequences that drive these exquisite patterns remain poorly defined. Comparative genomic methods increasingly enable relatively confident predictions of the location of putative distant-acting enhancers, but a deeper understanding of their exact tissue-specificities has yet to emerge due to the lack of high-quality collections of experimental datasets. In preliminary studies, we have coupled comparative genomics to a high-throughput mouse transgenic reporter assay and identified more than 100 distant-acting enhancer sequences that reproducibly drive in vivo expression in the developing forebrain and are in many cases located near genes known to be required for brain development. Here we propose to exploit this unique enhancer collection to produce a first-generation high-resolution cis-regulatory atlas of the developing forebrain. This goal will be achieved through detailed histological and neuroanatomical analysis of all forebrain enhancers identified so far. We will then bin elements that drive identical patterns within the forebrain and computationally define their common transcription factor binding sites and other sequence features and use this forebrain cis-regulatory code to generate genome-wide enhancer catalogues. The validity of such predictions will be determined through the testing of 200 of these elements in transgenic mice. High-resolution data and annotations from the initial atlas as well as enhancers generated through our predictions will be made available to the community through an existing web portal, allowing researchers to access this data to a) understand the regulation of forebrain genes, b) identify candidate regions for regulatory mutation screens in human genetic disorders, c) retrieve tissue-specific reagents for a variety of downstream experimental applications, d) download data sets for computational or experimental regulatory studies. PUBLIC HEALTH RELEVANCE Efforts to understand how genes control the development of the human brain have focused on when and where genes are active during development, but have largely ignored the role of genetic switches ("enhancers") that control these very activities. Here we propose to map the precise activity of several hundred enhancers in the brain to aid in predicting additional forebrain enhancer in the entire human genome and thereby provide the scientific community with a "brain enhancer atlas". These studies are likely to have implications in defining the role of these switches for normal brain function and how they go awry in human brain diseases.

描述(由申请人提供)：哺乳动物前脑的发育关键依赖于对基因表达的动态但精确的空间和时间控制。虽然正在进行的公众努力正在积极地在基因组规模上绘制基因表达模式，但驱动这些精致模式的转录增强子序列仍然定义不清。比较基因组学方法越来越多地能够相对自信地预测假定的远程作用增强剂的位置，但由于缺乏高质量的实验数据集，对其确切的组织特异性的更深层次的了解尚未出现。在初步研究中，我们将比较基因组学与高通量小鼠转基因报告分析相结合，并确定了100多个可重复驱动发育中前脑体内表达的远程作用增强子序列，在许多情况下，它们位于已知大脑发育所需的基因附近。在这里，我们建议利用这一独特的增强子集合来制作第一代高分辨率顺式调控图谱，以了解发育中的前脑。这一目标将通过对迄今已确定的所有前脑增强剂进行详细的组织学和神经解剖学分析来实现。然后，我们将结合在前脑中驱动相同模式的元件，通过计算定义它们共同的转录因子结合位点和其他序列特征，并使用这个前脑顺式调节代码来生成全基因组增强子目录。这些预测的有效性将通过在转基因小鼠身上测试其中200种元素来确定。来自初始图谱的高分辨率数据和注释以及通过我们的预测产生的增强剂将通过现有的门户网站提供给社区，使研究人员能够访问这些数据，以a)了解前脑基因的调节，b)确定人类遗传疾病中调节突变筛选的候选区域，c)为各种下游实验应用检索组织特异性试剂，d)下载用于计算或实验调节研究的数据集。为了了解基因如何控制人脑的发育，与公共卫生相关的努力侧重于基因在发育过程中何时何地活跃，但在很大程度上忽视了控制这些活动的遗传开关(“增强子”)的作用。在这里，我们建议绘制大脑中数百个增强子的精确活动图，以帮助预测整个人类基因组中更多的前脑增强子，从而为科学界提供“脑增强剂图谱”。这些研究可能会对确定这些开关对正常大脑功能的作用以及它们在人类大脑疾病中如何出错具有一定的意义。