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: 6878793
• 负责人: THOMAS D TULLIUS
• 金额: $ 28.17万
• 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/6878793
• 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）：人类基因组的最新完成提供了对人类有机体如何运作的深刻了解的原始数据。攻击疾病并确保健康的新方法将由基因组序列知识引起。但是，不仅需要核苷酸的序列来了解如何检索遗传信息和表达遗传信息。 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，但是不存在能够在基因组规模上绘制DNA结构的方法。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（编码）项目所产生的数据增加一个新的维度。本应用程序中概述的实验方法的目的是超过90％的人类基因组，该基因组不为蛋白质进行编码，其中基因调节所需的信息属于蛋白质。这里提出的用于制作基因组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。该应用程序的具体目的是：（1）设计和实施羟基自由基DNA裂解模式的数据库。高通量方法将用于收集大量实验羟基自由基DNA裂解数据。 DNA文库和编码区域DNA序列将用于这些实验。 （2）开发方法来预测任何DNA序列的羟基自由基裂解模式。羟基自由基裂解模式数据库将用于构建一个模型，用于DNA的结构如何取决于核苷酸的序列。该模型将用于预测基因组DNA的羟基自由基裂解模式，包括人类基因组的编码区域的一部分。 （3）制作基因组DNA的结构图。由于先前的工作表明，羟基自由基裂解模式提供了有关DNA表面形状的详细信息，实验性（和预测的）羟基自由基裂解模式将用于使顺式作用因子结合位点和序列的映射对染料蛋白的折叠至关重要。计算工具，包括隐藏的马尔可夫模型，将在羟基自由基裂解模式的数据库上进行训练，以识别基因组DNA序列中的结构模式。