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Deciphering the regulatory principles governing enhancer specificity

解读增强剂特异性的监管原则

基本信息

批准号：
10319729
负责人：
Emma Kirsten Farley
金额：
$ 16.49万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-02-01 至 2022-05-31
项目状态：
已结题

项目摘要

Abstract Enhancers are the genomic elements that encode the instructions for when and where genes are expressed during development. The majority of mutations leading to disease are thought to reside in enhancers. However, we do not understand which changes in enhancer sequence are inert sequence variations between individuals or populations and which impact gene regulation and cellular integrity. These fundamental questions remain unsolved, because we cannot relate enhancer sequence to gene expression and phenotype. This gap in our knowledge is stalling our ability to interpret genomic data and understand development, cellular integrity, and diseases. Enhancer sequences provide a scaffold for transcription factors to bind to, by recognizing specific signatures in the DNA. The physical constraints that govern how these proteins interact with enhancer DNA could lead to a set of grammatical constraints that can be used to understand the relationship between enhancer sequence and tissue specific gene expression. I propose the development of a toolkit of methodologies and approaches to decipher the grammatical constraints on tissue specific enhancer activity. I will use highly parallel functional reporter assays, high-throughput genotype to phenotype studies along with biochemical assays, synthetic biology, and loss of function strategies. These experiments will be carried out in the chordate Ciona intestinalis, as it is a unique system in which millions of enhancer variants can be assayed for function in all cells of a developing embryo. Work in Ciona will be complemented with experiments in chick, mouse and tissue culture to directly inform vertebrate development and pinpoint mutations causing disease. Determining the ‘genetic code’ that relates the coding sequences of genes into protein has provided detailed insight into a major component of our genome. Once we have a similar code to decipher the instructions for when and where these genes are expressed, we will have powerful tools to understand how the genome encodes the instructions for building and maintaining life.

抽象的增强子是基因组元件，编码基因何时何地的指令在开发过程中表达。大多数导致疾病的突变被认为存在于增强剂。然而，我们不明白增强子序列中哪些变化是惰性序列个体或群体之间的差异会影响基因调控和细胞完整性。这些基本问题仍未解决，因为我们无法将增强子序列与基因联系起来表达和表型。我们知识上的差距阻碍了我们解释基因组数据的能力并了解发育、细胞完整性和疾病。增强子序列提供了一个支架通过识别 DNA 中的特定特征来结合转录因子。物理限制控制这些蛋白质如何与增强子 DNA 相互作用可能会导致一组语法可用于理解增强子序列和组织之间关系的约束特定的基因表达。我建议开发一个方法论和方法工具包破译组织特异性增强子活性的语法限制。我将使用高度并行功能报告分析、高通量基因型到表型研究以及生化分析、合成生物学和功能丧失策略。这些实验将在脊索动物海鞘，因为它是一个独特的系统，其中可以产生数百万个增强子变体检测发育中胚胎的所有细胞的功能。 Ciona 的工作将得到补充在小鸡、小鼠和组织培养中进行实验，直接了解脊椎动物的发育并精确定位突变导致疾病。确定与基因编码序列相关的“遗传密码” 对蛋白质的研究为我们基因组的主要组成部分提供了详细的见解。一旦我们有一个类似的代码来破译这些基因何时何地表达的指令，我们将有理解基因组如何编码构建和维护指令的强大工具生活。