A High-Resolution Enhancer Atlas of the Developing Forebrain

前脑发育的高分辨率增强器图谱

基本信息

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
项目类别：
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

项目摘要

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取决于基因表达的动态但精确的空间和时间控制。尽管公众正在努力在基因组规模上积极绘制基因表达模式，但驱动这些精致模式的转录增强子序列仍然不清楚。比较基因组方法越来越能够对假定的远距离作用增强子的位置进行相对可靠的预测，但由于缺乏高质量的实验数据集，尚未对它们的确切组织特异性有更深入的了解。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基因测定结合起来，并鉴定了 100 多个远距离作用增强子序列，这些序列可重复地驱动发育中前脑的体内表达，并且在许多情况下位于已知所需基因附近用于大脑发育。在这里，我们建议利用这种独特的增强子集合来生成发育中前脑的第一代高分辨率顺式调控图谱。这一目标将通过对迄今为止发现的所有前脑增强子进行详细的组织学和神经解剖学分析来实现。然后，我们将在前脑内驱动相同模式的元件进行分类，并通过计算定义它们的共同转录因子结合位点和其他序列特征，并使用该前脑顺式调控代码生成全基因组增强子目录。这种预测的有效性将通过在转基因小鼠中测试 200 个这些元素来确定。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生成的增强子将通过现有的门户网站向社区提供，使研究人员能够访问这些数据a）了解前脑基因的调节，b）识别用于人类遗传疾病调控突变筛选的候选区域，c) 检索用于各种下游实验应用的组织特异性试剂，d) 下载用于计算或实验调控研究的数据集。公共健康相关性了解基因如何控制人脑发育的努力主要集中在基因在发育过程中何时何地活跃，但很大程度上忽略了控制这些活动的基因开关（“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谱，以帮助预测整个人类基因组中额外的前脑增强子，从而为科学界提供“大脑增强子图谱”。这些研究可能会对定义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产生影响。