CHARACTERIZATION OF MOTIFS REGULATING EMBRYONIC & SPERMATOGENIC GENE EXPRESSION

调控胚胎的基序的特征

基本信息

批准号：
7720063
负责人：
Antonio J. Planchart
金额：
$ 13.67万
依托单位：
MOUNT DESERT ISLAND BIOLOGICAL 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：
2008-05-01 至 2009-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7720063
关键词：
Algorithms Animal Model Binding Binding Sites Computer Retrieval of Information on Scientific Projects Database Coupled Developmental Process Electrophoretic Mobility Shift Assay Embryo Embryonic Development Event Fishes Funding Gene Expression Genes Genomics Grant Human Institution Laboratories Methodology Methods Mus Nuclear Protein Nuclear Proteins Numbers Orthologous Gene Pattern Phylogenetic Analysis Rattus Research Research Personnel Resources Rodent Sampling Shark Site Skates Skating Source Spermatogenesis Squalidae Statistical Models Takifugu Testing United States National Institutes of Health Vertebrates Zebrafish interest markov model novel size transcription factor

Algorithms Animal Model Binding Binding Sites Computer Retrieval of Information on Scientific Projects Database Coupled Developmental Process Electrophoretic Mobility Shift Assay Embryo Embryonic Development Event Fishes Funding Gene Expression Genes Genomics Grant Human Institution Laboratories Methodology Methods Mus Nuclear Protein Nuclear Proteins Numbers Orthologous Gene Pattern Phylogenetic Analysis Rattus Research Research Personnel Resources Rodent Sampling Shark Site Skates Skating Source Spermatogenesis Squalidae Statistical Models Takifugu Testing United States National Institutes of Health Vertebrates Zebrafish interest markov model novel size transcription factor

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项目摘要

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our laboratory is interested in identifying sequence motifs that regulate gene expression during critical events such as such as embryogenesis and spermatogenesis. Embryogenesis is a highly conserved developmental process in vertebrates, leading to the hypothesis that orthologous genes with similar expression patterns are controlled by evolutionarily conserved mechanisms. Computational predictions of novel transcription factor binding sites is a daunting task due in large part to their small size. However, several approaches are useful for uncovering sites with high functional potential including motif-finding algorithms (Hidden Markov Models), statistical sampling methods (Gibbs sampling) and sequence comparison methods coupled to some type of motif finding methodology (Phylogenetic footprinting). To test our hypothesis that orthologs with conserved function are regulated by conserved transcriptional mechanisms, we are searching for motifs in the genomic regions upstream of genes from humans and model organisms, including fish and rodents. In order to evaluate the function of candidate motifs, we are using the electrophoretic mobility shift assay to test them for the ability to specifically bind nuclear proteins purified from mice, skates and dogfish sharks. We have successfully used the available genomic sequence and gene-expression information from human, mouse, rat, dogfish shark, little skate, zebrafish and Fugu to identify regions of sequence conservation upstream of a select number of genes. We continue to build upon this set and validate the motifs we discover.

该副本是利用众多研究子项目之一由NIH/NCRR资助的中心赠款提供的资源。子弹和调查员（PI）可能已经从其他NIH来源获得了主要资金，因此可以在其他清晰的条目中代表。列出的机构是对于中心，这不一定是调查员的机构。我们的实验室有兴趣确定在诸如胚胎发生和精子发生等关键事件中调节基因表达的序列基序。胚胎发生是脊椎动物中高度保守的发育过程，导致假设具有相似表达模式的直系同源基因受到进化保守的机制的控制。新型转录因子结合位点的计算预测是一项艰巨的任务，这在很大程度上是由于其小规模的大小。但是，几种方法可用于发现具有高功能势能的位点，包括基序调查算法（隐藏的马尔可夫模型），统计抽样方法（GIBBS采样）和序列比较方法与某种类型的基序发现方法（系统生成足迹）结合的序列比较方法。为了检验我们的假设，即具有保守功能的直系同源物受到保守的转录机制的调节，我们正在寻找人类和模型生物（包括鱼类和啮齿动物）基因上游基因组区域中的基序。为了评估候选基序的功能，我们正在使用电泳迁移率转移测定法来测试它们，以便能够结合从小鼠，溜冰者和狗鱼鲨鱼纯化的核蛋白质。我们已经成功地使用了来自人，小鼠，大鼠，狗鱼鲨，小滑板，斑马鱼和Fugu的可用基因组序列和基因表达信息，以识别精选基因上游上游的序列保守区域。我们继续建立在这一场景的基础上，并验证我们发现的主题。