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: 7462575
• 负责人: THOMAS D TULLIUS
• 金额: $ 50万
• 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 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7462575
• 关键词: Address; Algorithms; Base Sequence; Biological Process; Collection; DNA; DNA Databases; DNA Sequence; DNA Structure; Data; Data Set; Databases; Deposition; Development; Genome; Genomics; Goals; Housing; Human; Human Genome; Hydroxyl Radical; Indium; Informatics; Investigation; Lead; Maps; Measures; Medicine; Methodology; Methods; Nucleotides; Pattern; Phase; Pilot Projects; Production; Protocols documentation; Research; Resolution; Resources; Scheme; Shapes; Structure; Work; base; pressure; research study; verification and validation

This application describes a project that aims to answer the question, do some parts of the human genome function by virtue of their structure, and not directly by their nucleotide sequence? To address this question a structural map of the 30 Mb of the ENCODE regions of human genomic DNA, at single-nucleotide resolution, has been produced, based on hydroxyl radical cleavage patterns of DNA. A freely available database, ORChID (OH Radical Cleavage Intensity Database), was constructed to house hydroxyl radical cleavage data. An algorithm was developed to predict the hydroxyl radical cleavage pattern of any DNA sequence to high accuracy. This algorithm was applied to the ENCODE regions of the human genome, and the resulting data were deposited in the UCSC genome browser. This dataset of DNA structural data can be searched for structural patterns in genomic DNA that may be associated with biological function. The first objective of this project is to develop high-throughput methods for collecting hydroxyl radical cleavage data, to enhance the predictive power of the ORChID database. The second objective is to locate structural features in human genomic DNA that are under selective evolutionary pressure, but for which the exact nucleotide sequence is not under selection. Experimental data production and informatics pipelines, data verification and validation protocols, and plans for data deposition are detailed in the application.

该应用程序描述了一个旨在回答问题的项目，是通过其结构而不是直接通过其核苷酸序列来回答人类基因组功能的某些部分？为了解决这个问题，基于DNA的羟基自由基裂解模式，已经生成了人类基因组DNA的30 Mb的结构图。构建了一个免费可用的数据库兰花（OH根部裂解强度数据库），用于容纳羟基自由基裂解数据。开发了一种算法来预测任何DNA序列的羟基自由基裂解模式，以高精度。该算法应用于人基因组的编码区域，所得数据沉积在UCSC基因组浏览器中。可以在基因组DNA中搜索DNA结构数据的数据集，这些模式可能与生物学功能相关。该项目的第一个目的是开发用于收集羟基自由基裂解数据的高通量方法，以增强兰花数据库的预测能力。第二个目标是在选择性进化压力下定位人类基因组DNA中的结构特征，但确切的核苷酸序列不在选择中。应用程序中详细介绍了实验数据生成和信息管道，数据验证和验证协议以及数据沉积计划。