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: 8516079
• 负责人: Samantha Jean Riesenfeld
• 金额: $ 5.77万
• 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 2014-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8516079
• 关键词: Address; Algorithms; Attention; Base Pairing; Binding Sites; Bioinformatics; Biological; Biological Assay; Biological Process; Biology; ChIP-seq; Code; Collection; Complement; Complex; Computational Technique; DNA Sequence; Data; Development; Developmental Biology; Developmental Gene; Disease; Enhancers; Future; Gene Expression; Gene Expression Regulation; Gene Transfer Techniques; Genes; Genetic Engineering; Genome; Genomics; Goals; Human; Human Genome; Individual; Knowledge; Laboratories; Language; Lead; Learning; Length; Measures; Methodology; Modeling; Nucleic Acid Regulatory Sequences; Nucleotides; Open Reading Frames; Organ; Organogenesis; Pattern; Phenotype; Proteins; Regulator Genes; Regulatory Element; Regulatory Pathway; Reporter; Reporter Genes; Resources; Sea Urchins; Staging; Testing; Time; Tissues; Translating; Variant; Vertebrates; Work; Zebrafish; base; candidate validation; cell type; clinical application; combinatorial; design; design and construction; gene therapy; genome annotation; genome-wide analysis; improved; in vivo; novel; novel strategies; regenerative therapy; research study; response; stem cells; synthetic biology; therapeutic development; transcription factor

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）：虽然我们基因组中编码蛋白质的2%已经被成功地注释和表征，但破译嵌入其余98%的调控代码仍然是一个挑战。提高我们对调控代码的理解对于确定控制器官发生和促进疾病的细胞类型特异性调控回路至关重要。海胆发育调控网络已被全面描述。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。尽管许多已知的调控区域大而复杂，但初步的体内功能研究表明，短至6个碱基对（bp）的DNA序列可以驱动报告基因在特定组织中的精确表达，并且两个核苷酸的替换会导致表达区域的变化。该项目将开创一种新的自下而上的方法，通过描述所有6碱基对（bp）序列的调控潜力来破译脊椎动物的调控代码。这些短基序将在斑马鱼的发育过程中通过转基因来测试增强子的活性。该项目的第一个具体目标是通过计算设计一个报告结构集合，该集合紧凑地覆盖了所有6-聚合体，并能够有效地表征6-聚合体增强子的功能。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为未来增强子实验和许多其他生物分析的高效设计低聚物提供强大的资源。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多个调节6-mers相互作用的模型。将特别注意增强剂组合的加性效应和确定潜在的消声剂。通过从头开始构建和功能翻译监管语言，该项目补充了自顶向下理解监管代码的努力。这个项目将对许多生物学领域产生巨大的影响，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这个项目，如干细胞再生疗法的重编程策略。此外，它将为基因治疗铺平道路，通过基因工程调控元件，在不同的时间点将化合物驱动到特定的组织。