Postodctoral Research Fellowship in Biological Informatics FY2006

2006 财年生物信息学博士后研究奖学金

• 批准号: 0630639
• 负责人: Trevor Siggers
• 金额: --
• 依托单位: Siggers Trevor W
• 依托单位国家: 美国
• 项目类别: Fellowship
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-10-01 至 2008-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0630639&HistoricalAwards=false
• 关键词: Postodctoral; Research; Fellowship; Biological; Informatics

Project Title: "Using Protein-Binding Microarrays and Computational Methods to Investigate Affinity-dependent Mechanisms of Cis-regulatory Elements"This project is awarded under the Postdoctoral Research Fellowships in Biological Informatics Program for 2006. Transcription factors are proteins with affinities for short DNA sequences and by binding to specific occurrences of these sequences in the genome can turn genes on and off. The Fellow will conduct his research in the lab of Martha Bulyk at the Brigham and Woman's Hospital, Harvard University to develop a practical technology to measure the affinity of a protein for all possible DNA binding sequences in an unbiased manner. Protein-binding microarrays (PBM) are small glass slides to which short, double-stranded DNA molecules (~50 base pairs) are affixed in an array of tens of thousands of spots, each spot containing many copies of a single DNA sequence. Proteins are applied to the microarray and allowed to bind to the DNA in each spot. The amount of protein bound to each spot (i.e. sequence) is subsequently quantified using a fluorescently-labeled antibody applied to the microarray. Using a newly-developed, universal PBM developed in the lab, a technology will be developed to measure the absolute binding affinities of a protein to each possible 9 base pair DNA sequence in an unbiased fashion. The complete binding-affinity profiles of 40 yeast transcription factors to all possible 9 base pair sequences will be determined using the PBM technology. This large dataset will be used to investigate the accuracy of a commonly used matrix representation for describing transcription factor binding affinities, and to examine how the binding affinity of transcription factors to individual genomic sites affects the regulation of associated genes. Matrix scores will be compared with PBM-measured affinities to assess the accuracy of the scores, to examine assumptions underlying the matrix representation, and to examine possible accuracy biases for transcription factors from different protein structural classes. For the 40 yeast transcription factors, PBM-measured affinities will be analyzed for previously-identified DNA sequences that are bound upstream of ~800 genes in vivo to understand the role of binding affinities in gene regulation. The proposed research plan will provide the Fellow with valuable experience and training in studies (both computational and experimental) on control and specificity in gene regulation, which will form a foundation for his future independent career development.

项目标题：“使用蛋白质结合微阵列和计算方法研究顺式调节元素的亲和力依赖性机制”该项目是根据2006年生物学信息学计划的博士后研究奖学金授予的。转录因子是针对短DNA序列的蛋白质，是针对短DNA序列的蛋白质，并与这些序列结合了这些序列，并具有基因的特定范围，并具有基因的转化。这位研究员将在哈佛大学的米尔塔·布利克（Martha Bulyk）的实验室进行研究，以开发一种实用技术，以公正的方式测量蛋白质对所有可能的DNA结合序列的亲和力。蛋白质结合微阵列（PBM）是小型载玻片，将短，双链的DNA分子（〜50个碱基对）固定在成千上万个斑点中，每个斑点都包含许多DNA序列的副本。将蛋白质应用于微阵列，并允许在每个位置与DNA结合。随后使用应用于微阵列的荧光标记的抗体来定量与每个斑点结合的蛋白质量（即序列）。使用实验室中开发的新开发的通用PBM，将开发一项技术，以蛋白质以公正的方式测量蛋白质的绝对结合亲和力。将使用PBM技术确定40个酵母转录因子的40个酵母转录因子的完整结合亲密关系。该大数据集将用于研究常用矩阵表示以描述转录因子结合亲和力的准确性，并研究转录因子与单个基因组位点的结合亲和力如何影响相关基因的调控。将基质得分与PBM测量的亲和力进行比较，以评估评分的准确性，检查基质表示的假设，并检查来自不同蛋白质结构类别的转录因子的可能准确性偏见。对于40个酵母转录因子，将分析PBM测量的亲和力的亲和力，以前被识别的DNA序列在〜800个基因的体内结合，以了解结合亲和力在基因调节中的作用。拟议的研究计划将为研究员提供有关基因监管的控制和特异性研究（计算和实验）的宝贵经验和培训，这将为他未来的独立职业发展奠定基础。