Computational & Functional Annotation of the Zebrafish Genome Regulatory Toolbox

计算型

基本信息

批准号：
8330288
负责人：
Nadav Ahituv
金额：
$ 38.48万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-29 至 2014-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8330288
关键词：
Animal Model Automobile Driving Binding Sites Biological Biological Assay Candidate Disease Gene Cataloging Catalogs Clinical Code Communities Complex Comprehension Computational Technique Computer Simulation Coupled DNA Data Development Developmental Gene Developmental Process Disease Elements Embryo Enhancers Evolution Fertilization Functional RNA Gene Expression Gene Expression Regulation Generations Genes Genetic Genome Genomics Hour Human Human Development Human Genome In Situ Hybridization Individual Internet Knock-out Knowledge Lampreys Location Modeling Molecular Morphologic artifacts Mutation Nucleic Acid Regulatory Sequences Nucleotides Open Reading Frames Organism Orthologous Gene Pathway interactions Pattern Phylogenetic Analysis Plague Preclinical Drug Evaluation Property Regulation Regulator Genes Regulatory Element Reporter Genes Research Resources Scanning Shark Specificity Testing Time Tissues Transgenes Transgenic Organisms Validation Work Zebrafish base computerized tools cost drug candidate gene discovery genome sequencing genome-wide high throughput screening human disease improved in vivo interest knock-down mutant novel promoter research study small molecule teleost fish tool transcription factor vertebrate genome zebrafish genome

项目摘要

Computational & Functional Annotation of the Zebrafish Genome Regulatory Toolbox Zebrafish with its growing arsenal of tools that allow the generation of transgenics, gene knockdowns and knockouts, and mutant resources coupled with its high-throughput and cost efficiency is quickly becoming the major animal model for drug screens and gene related studies. However, as with other vertebrate genomes, the majority of the zebrafish genome (97%) is made up of non-genic sequences whose functional necessity remains largely unknown. One vital function that is clearly embedded in these regions is gene regulation, instructing genes when and where to turn on or off. However, unlike genes where we know their genomic location, their code, and the consequences of nucleotide changes within them, in gene regulatory sequences we don't have that knowledge. This knowledge is extremely vital, with a wide variety of clinical and molecular data supporting these sequences to be an important driver for development, evolution, diversity, and disease. In this proposal, we will combine advanced computational tools with high-throughput zebrafish functional studies to annotate this noncoding terrain. Using and refining multiple vertebrate genome alignments we have generated an unprecedented set of 166,693 zebrafish conserved noncoding elements (CNEs), with at least 8,805 regions having a direct ortholog in the human genome. Preliminary studies for a portion of these sequences using a zebrafish transgenic enhancer assay, find 41% of these sequences to function as enhancers at 24 to 48 hours post fertilization. Taking advantage of this transgenic assay we aim to screen 200 sequences a year for enhancer activity. These sequences will be selected from our large CNE set, sequences whose enhancer activity and tissue-timepoint specificity will be predicted using sophisticated computational tools, and community requested sequences. This characterization will not only allow the functional annotation of these sequences, but will also generate a novel and extremely important toolkit of gene regulatory elements that can drive expression of any gene of interest at precise locations and precise developmental time points. In addition, we will also use the annotated regulatory landscape to discover novel genes with potential important developmental function. This will be carried out by analyzing the expression patterns and functional consequences due to knockdown of less characterized genes that lie in rich regulatory regions, a common sign for the existence of important developmental gene regulators. Additional computational techniques will be used to discover genes under tight regulation in novel tissue contexts, as well as pathways which are currently not studied in the context we find them enriched in. All the data generated in this proposal, both computational and functional, will be made available to the community through a dedicated web browser (http://zebrafish.stanford.edu/) as well as integration into ZFIN, Ensembl, and the UCSC genome browser. Combined, our work will advance zebrafish as the major animal model for annotating and characterizing the noncoding portion of the vertebrate genome.

斑马鱼基因组调节工具箱的计算和功能注释斑马鱼的工具越来越多，可以产生转基因，基因敲低和淘汰赛和突变资源以及其高通量和成本效率的努力正在迅速成为药物筛查和基因相关研究的主要动物模型。但是，与其他脊椎动物基因组一样斑马鱼基因组的大多数（97％）由非基因序列组成，其功能必要性仍然是未知的。这些区域中明显嵌入的一种重要功能是基因调节，指导基因何时何地打开或关闭。但是，与我们知道其基因组的基因不同在基因调节序列中，位置，代码以及核苷酸的后果发生变化我们没有那种知识。这些知识至关重要，有多种临床和分子支持这些序列的数据是发展，进化，多样性和疾病的重要驱动力。在此提案中，我们将将高级计算工具与高通量斑马鱼功能相结合研究以注释这一非编码地形。使用和完善多个脊椎动物基因组比对我们有产生了前所未有的166,693个斑马鱼保守的非编码元素（CNES），至少具有至少 8,805个地区在人类基因组中具有直接直系同源物。这些部分的初步研究使用斑马鱼转基因增强剂测定法序列，找到其中41％的序列以功能为受精后24至48小时的增强剂。利用这种转基因测定，我们旨在筛选200 每年进行增强活性的序列。这些序列将从我们的大型CNE集序列中选择将使用复杂的计算来预测其增强器活性和组织时间特异性工具和社区要求的序列。这种表征不仅将允许功能注释在这些序列中，但还将生成一个基因调节元件的新颖且极为重要的工具包这可以在精确位置和精确的发育时间点上驱动任何感兴趣的基因的表达。在此外，我们还将使用带注释的调节景观来发现具有潜在重要重要性的新基因发展功能。这将通过分析表达模式和功能来执行后果是由于在丰富的调节区域中击倒较低的基因而引起的，这是一个常见的迹象为了存在重要的发展基因调节剂。将使用其他计算技术在新的组织环境中发现基因，以及目前尚未发现的途径在上下文中进行了研究，我们发现它们丰富了。功能性，将通过专用的Web浏览器提供给社区（http://zebrafish.stanford.edu/）以及集成到Zfin，Ensembl和UCSC基因组浏览器中。结合在一起，我们的工作将推动斑马鱼作为注释和表征的主要动物模型脊椎动物基因组的非编码部分。

项目成果

期刊论文数量（2）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option.

DOI：
10.1371/journal.pgen.1003728
发表时间：
2013-08
期刊：
PLoS genetics
影响因子：
4.5
作者：
Wenger AM;Clarke SL;Notwell JH;Chung T;Tuteja G;Guturu H;Schaar BT;Bejerano G
通讯作者：
Bejerano G

A tetra-gonal polymorph of bis-[hydro-tris-(pyrazol-1-yl)borato]iron(II).

双-[氢-三-(吡唑-1-基)硼酸]铁(II)的四方多晶型物。