Structure of genomic DNA at single-nucleotide resolution

单核苷酸分辨率的基因组 DNA 结构

• 批准号: 6953011
• 负责人: THOMAS D TULLIUS
• 金额: $ 29万
• 依托单位: BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-09-29 至 2007-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6953011
• 关键词: DNA; binding sites; chromatin immunoprecipitation; gene expression; genetic library; genetic mapping; genetic regulation; high throughput technology; hydroxyl radical; mathematical model; nucleic acid sequence; nucleic acid structure; nucleotides

DESCRIPTION (provided by applicant): The recent completion of the human genome has provided the raw data on which to build a deep understanding of how the human organism functions. New ways to attack diseases and ensure health will result from knowledge of genome sequences. However, more than just the sequence of nucleotides is needed to understand how genetic information is retrieved and expressed. The three-dimensional structure of DNA is critical to the functions of the proteins that package the genome and regulate gene expression, yet no method exists that is capable of mapping DNA structure on a genomic scale. In this application, a new experimental technology is proposed for determining structural information for genomic DNA. This structural information will add a new dimension to the data that will be produced by the Encyclopedia of DNA Elements (ENCODE) Project. The experimental approach outlined in this application is aimed at the more than 90% of the human genome that does not code for proteins, where the information that is necessary for gene regulation resides. The method proposed here for making maps of genomic DNA structure makes use of a high-resolution chemical probe of DNA structure, the hydroxyl radical. The Specific Aims of this application are: (1) To design and implement a database of hydroxyl radical DNA cleavage patterns. High throughput methods will be used to collect large amounts of experimental hydroxyl radical DNA cleavage data. DNA libraries and ENCODE region DNA sequences will be used for these experiments. (2) To develop methods to predict the hydroxyl radical cleavage pattern of any DNA sequence. The hydroxyl radical cleavage pattern database will be used to construct a model for how the structure of DNA depends on the sequence of nucleotides. This model will be used to predict the hydroxyl radical cleavage patterns of genomic DNA, including parts of the ENCODE regions of the human genome. (3) To make structural maps of genomic DNA. Since previous work has demonstrated that the hydroxyl radical cleavage pattern provides detailed information on the shape of the surface of DNA, experimental (and predicted) hydroxyl radical cleavage patterns will be used to make maps of cis-acting factor binding sites and sequences critical to the folding of chromatin. Computational tools, including hidden Markov models, will be trained on the database of hydroxyl radical cleavage patterns in order to recognize structural patterns in genomic DNA sequences.

描述（由申请人提供）：最近完成的人类基因组提供了原始数据，可以据此深入了解人体有机体的功能。对基因组序列的了解将产生攻击疾病和确保健康的新方法。然而，要理解遗传信息是如何检索和表达的，仅仅需要核苷酸序列是不够的。 DNA 的三维结构对于包装基因组和调节基因表达的蛋白质的功能至关重要，但目前还没有能够在基因组规模上绘制 DNA 结构图的方法。在此应用中，提出了一种新的实验技术来确定基因组 DNA 的结构信息。这些结构信息将为 DNA 元素百科全书 (ENCODE) 项目生成的数据添加新的维度。本申请中概述的实验方法针对的是 90% 以上不编码蛋白质的人类基因组，其中存在基因调控所需的信息。这里提出的绘制基因组 DNA 结构图的方法利用了 DNA 结构的高分辨率化学探针，即羟基自由基。本申请的具体目标是：（1）设计并实现羟基自由基DNA切割模式的数据库。高通量方法将用于收集大量实验性羟基自由基DNA切割数据。 DNA 文库和 ENCODE 区域 DNA 序列将用于这些实验。 (2) 开发预测任何DNA序列的羟自由基裂解模式的方法。羟基自由基裂解模式数据库将用于构建 DNA 结构如何依赖于核苷酸序列的模型。该模型将用于预测基因组 DNA 的羟基自由基裂解模式，包括人类基因组的部分 ENCODE 区域。 (3)绘制基因组DNA的结构图。由于先前的工作已证明羟基自由基裂解模式提供了有关 DNA 表面形状的详细信息，因此实验（和预测的）羟基自由基裂解模式将用于绘制对染色质折叠至关重要的顺式作用因子结合位点和序列的图谱。包括隐马尔可夫模型在内的计算工具将在羟基自由基裂解模式数据库上进行训练，以识别基因组 DNA 序列中的结构模式。