Systematic Analysis of Drosophila transcription factor binding specificities

果蝇转录因子结合特异性的系统分析

• 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
• 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

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）：生物体基因组的完整注释需要系统地鉴定顺式调控序列和结合它们的反式作用因子。对于所有生物体来说，实现这一目标的一个重大障碍是具有充分表征的 DNA 结合特异性的转录因子 (TF) 的数量有限。我们开发了一种细菌单杂交系统，该系统提供了一种快速方法来表征 TF 的 DNA 结合特异性。利用这项技术，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。该特异性目录包括代表 12 种不同类型 DNA 结合结构域和所有 84 个独立同源结构域家族成员的蛋白质。为了补充这个数据集，我们开发了计算工具来绘制 TF 结合位点频率的基因组分布，并使用这些信息来识别数据集中任意 TF 组合的假定顺式调控模块 (CRM)。基于网络的界面允许用户对 CRM 进行全基因组搜索，或在流行的 Gbrowse 界面中将 TF 或 TF 组合的结合位点频率显示为轨迹。 我们现在建议表征所有剩余的黑腹果蝇 TF 的 DNA 结合特异性，包括所有单体和同源寡聚 TF 以及来自基本亮氨酸拉链和基本螺旋-环-螺旋家族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内 CRM 的能力，并且我们将整合其他数据源（例如 ChIP 芯片数据集）以增强预测 CRM 的能力。这项工作将最终开发出可通过网络访问的数据库和搜索工具，使科学界能够通过计算识别受任何感兴趣因素组合调节的假定 CRM。我们分析的结果将是对已知转录调控网络中起作用的因子子集的 CRM 进行全基因组注释。 迄今为止，尚未在任何生物体中获得 TF 特异性的完整描述。结合改进的计算工具和广泛且不断增长的黑腹果蝇转录实验研究，TF 特异性目录将允许对整个基因组中的 CRM 进行系统注释。一旦开发完成，这些数据库和工具应该可以直接应用于其他生物体（包括人类）的 CRM 注释。公共卫生相关性：尽管基因组计划已经广泛绘制了人类和其他生物体编码基因的 DNA 序列图谱，但事实证明绘制打开和关闭基因的调控区域要困难得多。我们将使用新开发的实验和计算工具来系统地绘制整个基因组中的这些控制元件。这个新的基因组“图谱”将帮助研究人员了解这些元件在正常细胞中如何发挥作用，以及这些元件的突变如何导致疾病。

项目成果

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