CAREER Deciphering how enhancers encode tissue-specificity and phenotypes

破译增强子如何编码组织特异性和表型

• 批准号: 2239957
• 负责人: Emma Farley
• 金额: $ 140万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-12-15 至 2027-11-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2239957&HistoricalAwards=false
• 关键词: CAREER; Deciphering; how; enhancers; encode

Our genome is 3 billion letters of DNA which encode the tools (proteins) and instructions for making every single cell within our body. These instructions for building us are embedded within genomic sequences called enhancers, which act as switches to turn on the production of proteins in particular cell types at particular times, allowing a fertilized egg to develop into a complex organism. Changes in the enhancer sequence can alter where proteins are made, causing dramatic effects, such as extra toes, loss of fins, or even novel functions that allow an organism to exist in a new environment. Indeed, changes within enhancers underlie the majority of differences between individuals and contribute to the diversity of species on our planet. Yet these elements are poorly understood. This research will develop cutting-edge approaches to test millions of versions of enhancers for function to understand how changes in the enhancer sequence can alter when and where proteins are made. These findings will help uncover how genomes encode the instructions for making us and how changes within enhancers can lead to changes in the function and structure of an organism. Middle school students from a Title I school will contribute to this research by conducting experiments in the classroom and on the university campus. Supporting underprivileged students from a young age and giving them access to research and higher education experiences is essential to help students see college as an attainable goal, engage in science, and strive for educational goals. Enhancers are genomic elements that control the timing and location of gene expression; as such, enhancers ensure the successful development and integrity of an organism. Although we can identify putative enhancers in genomes with relative ease, we have little understanding of how the underlying sequence encodes gene expression. This lack of knowledge is a major problem as sequence changes within enhancers are thought to underlie the majority of phenotypic diversity. The goal of this proposal is to develop a deep understanding of how enhancers encode tissue-specific expression patterns, how transcription factors interact specifically with enhancer sequences, and the mechanisms by which enhancer variants alter phenotypes. To achieve these goals, this research will use a creative combination of high-throughput enhancer assays in developing vertebrate embryos (chick), binding assays, and transgenic approaches in mice. These assays will be implemented in the context of limb development as this is an ideal system in which to study how enhancers encode tissue-specific expression patterns and how changes in these patterns impact organismal integrity. These studies will uncover overarching principles governing the relationship between enhancer sequence and tissue-specific expression and provide a mechanistic understanding of how sequence changes within enhancers alter phenotypes. The broader impacts will involve middle school students from a Title I school contributing to this research by conducting experiments in the classroom and on the university campus.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.

我们的基因组由30亿个DNA字母组成，它们编码了制造我们体内每一个细胞的工具（蛋白质）和指令。这些构建我们的指令嵌入在被称为增强子的基因组序列中，这些增强子就像开关一样，在特定时间开启特定细胞类型的蛋白质生产，从而使受精卵发育成复杂的生物体。增强子序列的改变可以改变蛋白质的合成位置，从而产生巨大的影响，比如多出脚趾，失去鳍，甚至是允许生物体在新环境中生存的新功能。事实上，增强子内部的变化是个体之间大多数差异的基础，并有助于我们星球上物种的多样性。然而，人们对这些因素知之甚少。这项研究将开发尖端的方法来测试数以百万计的增强子版本的功能，以了解增强子序列的变化如何改变蛋白质的产生时间和地点。这些发现将有助于揭示基因组如何编码制造我们的指令，以及增强子内部的变化如何导致生物体功能和结构的变化。来自Title I学校的中学生将通过在教室和大学校园进行实验来为这项研究做出贡献。从小就支持贫困学生，让他们有机会进行研究和接受高等教育，这对于帮助学生将大学视为一个可实现的目标、从事科学研究并为教育目标而奋斗至关重要。增强子是控制基因表达时间和位置的基因组元件；因此，增强剂确保了生物体的成功发育和完整性。虽然我们可以相对容易地识别基因组中假定的增强子，但我们对潜在序列如何编码基因表达知之甚少。这种知识的缺乏是一个主要问题，因为增强子内部的序列变化被认为是大多数表型多样性的基础。本提案的目标是深入了解增强子如何编码组织特异性表达模式，转录因子如何与增强子序列特异性相互作用，以及增强子变体改变表型的机制。为了实现这些目标，本研究将使用一种创造性的组合，在发育中的脊椎动物胚胎（小鸡）中进行高通量增强子测定，在小鼠中进行结合测定和转基因方法。这些试验将在肢体发育的背景下实施，因为这是研究增强子如何编码组织特异性表达模式以及这些模式的变化如何影响组织完整性的理想系统。这些研究将揭示控制增强子序列和组织特异性表达之间关系的总体原则，并提供增强子内部序列变化如何改变表型的机制理解。更广泛的影响将涉及来自第一标题学校的中学生，通过在教室和大学校园进行实验，为这项研究做出贡献。该奖项反映了美国国家科学基金会的法定使命，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。

项目成果

Affinity-optimizing enhancer variants disrupt development.

• DOI: 10.1038/s41586-023-06922-8
• 发表时间: 2024-02
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Lim, Fabian;Solvason, Joe J.;Ryan, Genevieve E.;Le, Sophia H.;Jindal, Granton A.;Steffen, Paige;Jandu, Simran K.;Farley, Emma K.
• 通讯作者: Farley, Emma K.