CHARACTERIZATION OF MOTIFS REGULATING EMBRYONIC & SPERMATOGENIC GENE EXPRESSION

调控胚胎的基序的特征

• 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
• 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

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.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 我们的实验室有兴趣识别在胚胎发生和精子发生等关键事件期间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，这导致了这样的假设：具有相似表达模式的直系同源基因受进化上保守的机制控制。新型转录因子结合位点的计算预测是一项艰巨的任务，很大程度上是因为它们的尺寸很小。然而，有几种方法可用于发现具有高功能潜力的位点，包括基序发现算法（隐马尔可夫模型）、统计采样方法（吉布斯采样）和与某种类型的基序发现方法相结合的序列比较方法（系统发育足迹）。 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转录机制的调节，我们正在人类和模式生物（包括鱼类和啮齿动物）基因上游的基因组区域中寻找基序。为了评估候选基序的功能，我们使用电泳迁移率变动测定来测试它们特异性结合从小鼠、鳐鱼和角鲨中纯化的核蛋白的能力。我们已经成功地利用来自人类、小鼠、大鼠、角鲨、小鳐鱼、斑马鱼和河豚的可用基因组序列和基因表达信息来识别选定数量基因上游的序列保守区域。我们继续在此基础上进行构建并验证我们发现的主题。