A Novel Approach to Decoding Vertebrate Gene Regulation

解码脊椎动物基因调控的新方法

• 批准号: 8724822
• 负责人: Samantha Jean Riesenfeld
• 金额: $ 1.84万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2014-09-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8724822
• 关键词: Novel; Approach; Decoding; Vertebrate; Gene

DESCRIPTION (provided by applicant): While the 2% of our genome that encodes proteins has been successfully annotated and characterized, deciphering the regulatory code embedded in the remaining 98% remains a challenge. Improving our understanding of the regulatory code is essential for determining the cell-type-specific regulatory circuits that govern organogenesis and contribute to disease. Developmental regulatory networks in the sea urchin have been comprehensively described. In vertebrates, however, most studies of regulatory variation have taken a top-down approach, computationally predicting regulatory elements or experimentally characterizing binding sites of individual transcription factors. Although many known regulatory regions are large and complex, preliminary in vivo functional studies indicate that DNA sequences as short as six base pairs (bp) drive precise expression of a reporter gene to specific tissues, and that a two-nucleotide substitution leads to a change in the domain of the expression. The proposed project will pioneer a novel bottom-up approach to decipher the vertebrate regulatory code by characterizing the regulatory potential of all 6-base pair (bp) sequences. These short motifs will be tested for enhancer activity using zebra fish transgenesis during development. The first specific aim of the project is to computationally design a collection of reporter constructs that covers all 6-mers compactly and enables efficient functional characterization of 6-mer enhancers. This is a challenging computational problem, and the algorithms designed and implemented at this stage will be a powerful resource for the efficient design of oligomers for future enhancer experiments and many other biological assays. The second aim is to compute and analyze the genomic distributions of experimentally validated enhancers and use the results to interpret expression data. Finally, the third aim is to develop and test models for the interaction of multiple regulatory 6-mers. Particular attention will be devoted to additive effects of combinations of enhancers and the identification of potential silencers. By building and functionally translating a regulatory language from scratch, this project complements top-down efforts to understand the regulatory code. This project will have an enormous impact on numerous biological fields, from developmental and evolutionary biology to genome annotation. Various clinical applications will also benefit from this project, such as reprogramming strategies for stem-cell-based regenerative therapies. In addition, it will pave the way for gene therapy by genetically engineering regulatory elements that drive compounds to specific tissues at different time points.

描述（由申请人提供）：虽然我们编码蛋白质的2%基因组已成功注释和表征，但破译嵌入其余98%中的调控代码仍然是一个挑战。提高我们对调控密码的理解对于确定控制器官发生和导致疾病的细胞类型特异性调控回路至关重要。海胆的发育调控网络已经得到了全面的描述。然而，在脊椎动物中，大多数调控变异的研究都采取了自上而下的方法，通过计算预测调控元件或通过实验表征单个转录因子的结合位点。虽然许多已知的调控区是大而复杂的，但初步的体内功能研究表明，短至六个碱基对（bp）的DNA序列驱动报告基因精确表达到特定组织，并且两个核苷酸的取代导致表达结构域的变化。拟议的项目将开创一种新的自下而上的方法来破译脊椎动物的监管代码，通过表征所有6个碱基对（bp）序列的监管潜力。这些短基序将在发育期间使用斑马鱼转基因测试增强子活性。该项目的第一个具体目标是通过计算设计一系列报告构建体，这些构建体覆盖所有6-mer复合体，并能够有效地表征6-mer增强子的功能。这是一个具有挑战性的计算问题，在这个阶段设计和实现的算法将是一个强大的资源，为未来的增强子实验和许多其他生物测定的低聚物的有效设计。第二个目标是计算和分析实验验证的增强子的基因组分布，并使用结果来解释表达数据。最后，第三个目标是开发和测试模型的相互作用的多个监管6聚体。特别注意将致力于添加剂的增强剂和潜在的沉默剂的识别组合的效果。通过从头开始构建和功能性翻译监管语言，该项目补充了自上而下的理解监管代码的努力。该项目将对许多生物学领域产生巨大影响，从发育和进化生物学到基因组注释。各种临床应用也将受益于该项目，例如基于干细胞的再生疗法的重编程策略。此外，它将通过基因工程调控元件为基因治疗铺平道路，这些调控元件在不同的时间点将化合物驱动到特定的组织。