Wisconsin Center of Excellence in Genomics Science

描述(申请人提供)：人类基因组和模式生物序列的成功完成开启了生物学研究的新纪元，现在人们的注意力集中在了解基因组序列信息的表达和控制方式上。这个拟议的威斯康星州基因组科学卓越中心的重点是通过开发与DMA相互作用的蛋白质的全面表征和定量分析的新技术，促进对影响基因转录的复杂和集成调控机制的了解。这项新技术将有助于在全基因组范围内对基因转录调控在生物过程、发育、疾病以及对生理、药物或环境应激反应的潜在机制进行功能解释。染色质免疫沉淀方法的发展使得识别与感兴趣蛋白质结合的特定DMA序列成为可能。我们建议逆转这一策略，开发一种全新的技术，使用寡核苷酸捕获来提取感兴趣的DNA序列，并使用质谱学来识别和表征与特定DNA区域结合和关联的蛋白质和蛋白质复合体。这一新方法将创造一个无价的工具，用于破译调节基本生物功能的关键控制程序。拟议的跨学科和多机构基因组科学卓越中心结合了威斯康星医学院、威斯康星大学麦迪逊大学和马奎特大学的特定专业知识。为开发这一新方法，将在四个具体领域开展技术开发：(1)蛋白质与DNA的交叉连接和染色质的碎裂；(2)以DNA序列特有的方式捕获蛋白质-DNA复合体；(3)进行质谱分析，以确定和量化结合蛋白质，确定翻译后修饰，并表征蛋白质复合体的化学计量学；以及(4)信息学，开发能够对蛋白质-DNA相互作用的变化与基因表达之间的关系进行全球分析的工具。该中心将使用从三个物种(酵母、小鼠、人类)中精心选择的日益复杂的生物系统，在一个集成的全基因组分析平台中开发和测试这项技术，该平台包括高效的数据管理和分析工具。作为中心使命的一部分，我们将把我们的技术开发努力与针对学生和研究员的跨学科培训计划结合起来，旨在培养在尖端基因组技术方面经验丰富的合格科学家。数据、技术和软件将通过包括许可和商业化活动在内的多种机制广泛传播。公共卫生相关性这项全面识别和表征基因组蛋白质-DNA相互作用的新技术的发展将有助于解释基因组的核心功能--基因转录。作为CEGS的一部分开发的工具和技术将被科学界广泛使用，并将有助于破译调控整个基因组中所有基因转录水平的关键分子机制，以及这些调控机制在疾病中是如何改变的。这一知识将彻底改变我们对基因组生物学的理解，并影响基因组信息将如何用于临床医学。

DESCRIPTION (provided by applicant): The successful completion of the human genome and model organism sequences has ushered in a new era in biological research, with attention now focused on understanding the way in which genome sequence information is expressed and controlled. The focus of this proposed Wisconsin Center of Excellence in Genomics Science is to facilitate understanding of the complex and integrated regulatory mechanisms affecting gene transcription by developing novel technology for the comprehensive characterization and quantitative analysis of proteins interacting with DMA. This new technology will help provide for a genomewide functional interpretation of the underlying mechanisms by which gene transcriptional regulation is altered during biological processes, development, disease, and in response to physiological, pharmacological, or environmental stressors. The development of chromatin immunoprecipitation approaches has allowed identification of the specific DMA sequences bound by proteins of interest. We propose to reverse this strategy and develop an entirely novel technology that will use oligonucleotide capture to pull down DNA sequences ot interest, and mass spectrometry to identify and characterize the proteins and protein complexes bound and associated with particular DNA regions. This new approach will create an invaluable tool for deciphering the critical control processes regulating an essential biological function. The proposed interdisciplinary and multi-institutional Center of Excellence in Genomics Science combines specific expertise at the Medical College of Wisconsin, the University of Wisconsin Madison, and Marquette University. Technological developments in four specific areas will be pursued to develop this new approach: (1) cross-linking of proteins to DNA and fragmentation of chromatin; (2) capture of the protein-DNA complexes in a DNA sequence-specific manner; (3) mass spectrometry analysis to identify and quantify bound proteins, determine posttranslational modifications, and characterize protein complex stoichipmetry; and (4) informatics to develop tools enabling the global analysis of the relationship between changes in protein-DNA interactions and gene expression. The Center will use carefully selected biological systems of increasing complexity from three species (yeast, mouse, human) to develop and test the technology in an integrated genome-wide analysis platform that includes efficient data management and analysis tools. As part of the Center mission, we will combine our technology development efforts with an interdisciplinary training program for students and fellows designed to train qualified scientists experienced in cutting-edge genomics technology. Data, technology, and software will be widely disseminated by multiple mechanisms including licensing and commercialization activities. PUBLIC HEALTH RELEVANCE The development of this novel technology to comprehensively identify and characterize genpmic protein- DNA interactions will help in the interpretation of a core function of the genome, gene transcription. The tools and technologies developed as part of the CEGS will be broadly available to the scientific community, and will help decipher crucial molecular mechanisms regulating the transcriptional levels of all genes across the genome, and how these regulatory mechanisms are altered in disease. This knowledge will revolutionize our understanding of genome biology, and impact how genomic information will be used in clinical medicine.