CAREER: Phenotypic and developmental effects of enhancer variation on cichlid craniofacial evolution

基因是由它们的调控元件精确地开启和关闭的。该项目研究了基因调控的改变如何在动物发育中产生变化，特别是在面部骨骼中。这项工作将通过基因组分析确定调控元件，量化胚胎发育过程中改变的基因调控如何改变面部形状，并使用显微镜评估DNA突变对调控功能的影响。鉴于（1）85%的致病突变会影响基因调控，（2）基因调控的变化被预测为进化多样性的主要来源，这项工作将为DNA变化如何在动物发育和人类疾病中产生自然变异提供见解。教育活动将改善本科生和K-12学生在STEM学科保留的关键因素。这将通过以下方式实现：（1）对本科生进行辅导;（2）为中学课堂创建基于探究的活动，这些活动将在当地学校实施，并分发给全国的教育工作者。理解顺式调节中遗传变异的功能影响是我们理解表型多样性产生的主要差距。本项目的研究目标是分析非编码基因调控增强子在慈鲷鱼颅面进化背景下的表型功能，慈鲷鱼是适应性辐射的教科书范例。具体目标是（1）利用四种互补的基因组策略来全面鉴定具有遗传变异的候选增强子，（2）使用CRISPR-Cas9量化调节增强子活性的表型和转录效应，以及（3）经验性地评估遗传变异对增强子活性的影响。随着对增强子在体内的活性，转录调控和对表型的影响方面的功能效应的关注，这项工作将解决基因型-表型关系的知识的主要差距。这些数据将为那些设计基因调控语法模型的人提供经验信息，为显着加速非编码DNA中因果遗传变异的发现和系统记录提供框架，并为进化发育生物学的核心理论提供实验证据（Evo-Devo）。该项目由内部监督办公室发展系统组共同资助，该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Genes are precisely turned on and off by their regulatory elements. This project examines how altered gene regulation can generate changes in animal development, specifically in the facial skeleton. This work will identify regulatory elements through genome analysis, quantify how altered gene regulation during embryonic development changes facial shape, and assess the effects of DNA mutations on regulatory function using microscopy. Given that (1) 85% of disease-causing mutations affect gene regulation and (2) changes to gene regulation are predicted to be a major source of evolutionary diversity, this work will provide insights into how DNA changes can produce both natural variation in animal development and disease in humans. Educational activities will improve factors key in retention of undergraduate and K-12 students in STEM disciplines. This will be accomplished through (1) mentorship of undergraduates and (2) creation of inquiry-based activities for the middle school classroom that will be implemented in local schools and distributed to educators nationally. Understanding the functional impact of genetic variation in cis-regulation is a major gap in our understanding of the generation of phenotypic diversity. The research objective of this project is to analyze the phenotypic function of non-coding, gene regulatory enhancers within the context of craniofacial evolution in cichlid fishes, a textbook example of an adaptive radiation. The specific aims are to (1) utilize four complementary genomic strategies to comprehensively identify candidate enhancers with genetic variation, (2) quantify phenotypic and transcriptional effects of modulating enhancer activity using CRISPR-Cas9, and (3) empirically assess the effect of genetic variation on enhancer activity. With a focus on the functional effect of enhancers in vivo in terms of activity, transcriptional regulation, and effect on phenotype, this work will address a major gap in knowledge of the genotype-phenotype relationship. These data will provide empirical information for those designing models of the grammar of gene regulation, a framework to significantly accelerate the discovery and systematic documentation of causal genetic variations in non-coding DNA, and experimental evidence for a central theory of Evolutionary Developmental Biology (Evo-Devo).This project is jointly funded by the Developmental Systems Cluster of IOS, and by the Established Program to Stimulate Competitive Research (EPSCoR)This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.