SGER: High-throughput Determination of Position Weight Matrices

SGER：位置权重矩阵的高通量确定

• 批准号: 0406496
• 负责人: Gregory Wray
• 金额: $ 6.53万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-03-15 至 2005-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0406496&HistoricalAwards=false
• 关键词: SGER; throughput; Determination; Position; Weight

Transcription factors regulate gene expression by binding in a sequence-specific manner to double-stranded DNA and modulating the initiation of new transcripts. The unique binding specificities of transcription factors are critical components of their ability to regulate gene expression. Yet determining binding specificity is time-consuming and detailed information is available for only a fraction of transcription factors, even in well-studied organisms. The goal of this project is to develop and validate a rapid, simple, high-throughput assay to determine the full spectrum of binding specificities (or position weight matrix) for any transcription factor. The approach uses a microarray containing thousands of different dsDNA hairpin probes to assay relative binding of all permutations of seven base pairs. This method will be tested by comparing results to those obtained using existing, more laborious methods, and then refined, calibrated, and optimized for general use. This high-throughput method should be applicable to understanding the binding specificity of almost any protein:DNA interaction. It is expected that this approach will offer several distinct advantages over existing methods for determining position weight matrices: speed, simplicity, and comprehensive sampling of all potential binding sites. Successful validation of this method should benefit basic research on mechanisms of gene expression by providing detailed information about the binding specificities of many different transcription factors. Other aspects of basic research will also benefit, including automated annotation of genome sequences and evolutionary analyses of gene networks.

转录因子通过以序列特异性方式与双链 DNA 结合并调节新转录本的起始来调节基因表达。 转录因子独特的结合特异性是其调节基因表达能力的关键组成部分。 然而，确定结合特异性非常耗时，而且即使在经过充分研究的生物体中，也只能获得一小部分转录因子的详细信息。 该项目的目标是开发和验证一种快速、简单、高通量的检测方法，以确定任何转录因子的全谱结合特异性（或位置权重矩阵）。 该方法使用包含数千个不同 dsDNA 发夹探针的微阵列来测定七个碱基对的所有排列的相对结合。 该方法将通过与使用现有的、更费力的方法获得的结果进行比较来进行测试，然后针对一般用途进行改进、校准和优化。 这种高通量方法应该适用于了解几乎所有蛋白质：DNA 相互作用的结合特异性。 预计这种方法将比现有的确定位置权重矩阵的方法提供几个明显的优势：速度、简单性和所有潜在结合位点的全面采样。 该方法的成功验证应通过提供有关许多不同转录因子的结合特异性的详细信息，有利于基因表达机制的基础研究。基础研究的其他方面也将受益，包括基因组序列的自动注释和基因网络的进化分析。