Systematic Analysis of Drosophila transcription factor binding specificities

果蝇转录因子结合特异性的系统分析

基本信息

批准号：
7878863
负责人：
Michael H Brodsky
金额：
$ 62.04万
依托单位：
UNIV OF MASSACHUSETTS MED SCH WORCESTER
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：
2008-09-08 至 2011-12-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7878863
关键词：
Animal Model Binding Binding Sites Cataloging Catalogs Chromosome Mapping Cis-Acting Sequence Collaborations Communities Complement Complex DNA Binding DNA Binding Domain DNA Sequence Data Data Set Data Sources Databases Development Disease Drosophila genus Drosophila melanogaster Elements Evolution Family Family member Frequencies Funding Gene Expression Genes Genetic Transcription Genome Genome Mappings Genomics Goals Helix-Turn-Helix Motifs Homo Human Hybrids Illinois Indium Lead Maps Modeling Mutation Normal Cell Nucleic Acid Regulatory Sequences Online Systems Organism Proteins Research Research Personnel Specificity System Technology Trans-Activators Universities Variant bZIP Domain chromatin immunoprecipitation computerized tools genome-wide homeodomain improved interest public health relevance rapid technique research study success tool transcription factor web based interface web-accessible

项目摘要

DESCRIPTION (provided by applicant): The full annotation of an organism's genome requires the systematic identification of cis-regulatory sequences and the trans-acting factors that bind them. For all organisms, a significant remaining impediment to this goal is the limited number of transcription factors (TFs) with well-characterized DNA-binding specificities. We have developed a bacterial one-hybrid system that provides a rapid method to characterize the DNA-binding specificities of TFs. Using this technology, we have determined the specificity of 15% (108/~750) of all of the predicted sequence-specific transcription factors in Drosophila melanogaster. This catalog of specificities includes proteins representing 12 different types of DNA-binding domains and all 84 independent homeodomain family members. To complement this dataset we have developed computational tools that map the genomic distribution of TF binding site frequencies and use this information to identify putative cis-regulatory modules (CRMs) for any combination of TFs in our dataset. A web-based interface allows users to perform genome-wide searches for CRMs or to display binding site frequencies for TFs or combinations of TFs as tracks within the popular Gbrowse interface. We now propose to characterize the DNA-binding specificity of all remaining D. melanogaster TFs, including all monomeric and homo-oligomeric TFs as well as all functional heterodimeric combinations from the basic leucine zipper and basic helix-loop-helix families. We will also refine our computational tools to improve their ability to distinguish CRMs within the genome and we will integrate other data sources (e.g. ChIP-chip datasets) to enhance the ability to predict CRMs. This effort will culminate in the development of web-accessible database and search tools that will allow the scientific community to computationally identify putative CRMs that are regulated by any combination of factors of interest. An outgrowth of our analysis will be genome-wide annotations of CRMs for subsets of factors that function in known transcriptional regulatory networks. To date, a complete description of TF specificities has not been obtained in any organism. Combined with improved computational tools and the extensive and growing body of experimental studies on D. melanogaster transcription, a catalog of TF specificities will allow the systematic annotation of CRMs throughout its genome. Once developed, these databases and tools should be directly applicable to the annotation of CRMs in other organisms, including humans. PUBLIC HEALTH RELEVANCE: Although the genome project has extensively mapped which DNA sequences in humans and other organisms encode genes, mapping the regulatory regions that turn genes on and off has proven to be much more difficult. We will use newly developed experimental and computational tools to systematically map these control elements in an entire genome. This new genome "map" will help researchers understand how these elements function in normal cells and how mutations in these elements can lead to disease.

描述（由申请人提供）：对生物体基因组的完整注释需要系统地识别顺式调节序列和结合它们的跨性因素。对于所有生物体，对此目标的剩余障碍是具有良好表征的DNA结合特异性的转录因子（TF）数量有限。我们已经开发了一种细菌的单杂交系统，该系统提供了一种快速的方法来表征TF的DNA结合特异性。使用这项技术，我们确定了果蝇中所有预测的序列特异性转录因子的15％（108/〜750）的特异性。这种特异性目录包括代表12种不同类型的DNA结合域和所有84个独立同源域家庭成员的蛋白质。为了补充该数据集，我们开发了计算工具来映射TF绑定位点频率的基因组分布，并使用此信息来识别假定的顺式调节模块（CRMS），以在我们的数据集中使用TFS的任何组合。基于Web的接口允许用户对CRMS进行全基因组的搜索或显示TFS或TFS组合的绑定站点频率作为流行的GBROWSE接口中的轨道。现在，我们建议表征所有其余的D. melanogaster TF的DNA结合特异性，包括所有单体和同性恋者TF，以及来自基本亮氨酸拉链和碱性螺旋螺旋 - 环螺旋螺旋的所有功能性异二聚体组合。我们还将完善我们的计算工具，以提高其区分基因组中CRM的能力，并将其他数据源（例如CHIP-CHIP数据集）整合起来，以增强预测CRM的能力。这项工作将最终达到可访问的数据库和搜索工具的开发，这些工具将使科学界能够在计算上识别由任何感兴趣因素组合所调节的推定CRM。我们分析的产物将是CRM的全基因组注释，用于在已知的转录调节网络中起作用的因素。迄今为止，尚未在任何生物体中获得对TF特异性的完整描述。结合改进的计算工具以及对D. melanogaster转录的广泛和不断增长的实验研究，TF特异性的目录将使CRM在其整个基因组中进行系统的注释。一旦开发，这些数据库和工具应直接适用于包括人类在内的其他生物体中CRM的注释。公共卫生相关性：尽管基因组项目已广泛绘制了人类和其他生物体中的DNA序列编码基因，但事实证明，映射开机和关闭基因的调节区域已被证明要困难得多。我们将使用新开发的实验和计算工具在整个基因组中系统地绘制这些控制元素。这个新的基因组“地图”将帮助研究人员了解这些元素在正常细胞中的作用以及这些元素中的突变如何导致疾病。

项目成果

期刊论文数量（3）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.

DOI：
10.1093/nar/gkq858
发表时间：
2011-01
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Zhu LJ;Christensen RG;Kazemian M;Hull CJ;Enuameh MS;Basciotta MD;Brasefield JA;Zhu C;Asriyan Y;Lapointe DS;Sinha S;Wolfe SA;Brodsky MH
通讯作者：
Brodsky MH