Wisconsin Center of Excellence in Genomics Science

描述（由申请人提供）：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时代，现在的注意力集中在理解基因组序列信息的表达和控制方式上。这个威斯康星基因组学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综合表征和定量分析的新技术，促进对影响基因转录的复杂和综合调控机制的理解。这项新技术将有助于提供基因转录调控在生物过程、发育、疾病以及对生理、药理或环境应激源的反应中发生改变的潜在机制的全基因组功能解释。染色质免疫沉淀方法的发展已经允许鉴定与感兴趣的蛋白质结合的特定DMA序列。我们建议逆转这一策略并开发一种全新的技术，该技术将使用寡核苷酸捕获来提取感兴趣的DNA序列，并使用质谱来鉴定和表征与特定DNA区域结合和相关的蛋白质和蛋白质复合物。这种新方法将为破译调节基本生物功能的关键控制过程创造一个宝贵的工具。拟议中的基因组学跨学科和多机构卓越中心结合了威斯康星医学院、威斯康星大学麦迪逊分校和马奎特大学的专业知识。将在四个特定领域寻求技术发展来开发这种新方法：(1)蛋白质与DNA的交联和染色质的断裂；(2)以DNA序列特异性的方式捕获蛋白质-DNA复合物；(3)质谱分析，以鉴定和定量结合蛋白，确定翻译后修饰，并表征蛋白质复合物的化学计量；(4)信息学，开发工具，使蛋白质- dna相互作用变化与基因表达之间的关系的全局分析。该中心将使用精心挑选的三个物种（酵母、小鼠、人类）日益复杂的生物系统，在一个集成的全基因组分析平台上开发和测试该技术，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一个跨学科的培训计划结合起来，为学生和研究员设计培训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。这项新技术的发展，全面鉴定和表征基因组蛋白- DNA相互作用，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广泛地提供给科学界，并将有助于破译调节基因组中所有基因转录水平的关键分子机制，以及这些调节机制在疾病中是如何改变的。这些知识将彻底改变我们对基因组生物学的理解，并影响基因组信息在临床医学中的应用。

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.