Wisconsin Center of Excellence in Genomics Science

威斯康星州基因组科学卓越中心

• 批准号: 8402866
• 负责人: MICHAEL OLIVIER
• 金额: $ 244.35万
• 依托单位: MEDICAL COLLEGE OF WISCONSIN
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-12 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8402866
• 关键词: Affect; Animal Model; Area; Attention; Base Pairing; Binding; Binding Proteins; Bioinformatics; Biological; Biological Process; Biology; Cellular biology; Chemistry; Chromatin; Clinical Medicine; Communities; Complex; Computer software; DNA; DNA Fragmentation; DNA Methylation; DNA Sequence; DNA-Protein Interaction; Data; Data Analyses; Data Set; Databases; Development; Disease; Dissociation; Doctor of Philosophy; Electron Transport; Fungal Genome; Gene Expression; Genes; Genetic; Genetic Engineering; Genetic Transcription; Genome; Genomics; Health; Histones; Human; Human Genome; Imagery; Individual; Informatics; Institution; Instruction; Insulin-Like Growth-Factor-Binding Proteins; Knock-out; Knockout Mice; Knowledge; Laboratories; Licensing; Life; Ligands; Link; Liver; Mass Spectrum Analysis; Mathematics; Mediating; Mentors; Methodology; Methylation; Minority; Mission; Modeling; Modification; Molecular; Molecular Biology; Mus; Nature; Nucleotides; Oligonucleotides; Outcome; Physiological; Pilot Projects; Polymerase; Post-Translational Protein Processing; Principal Investigator; Process; Protein Analysis; Protein Binding; Proteins; Protocols documentation; Publishing; Qualifying; RNA; Reagent; Regulator Genes; Reporting; Research; Research Personnel; Resources; Science; Scientist; Sequence-Specific DNA Binding Protein; Stress; Students; Technology; Testing; Training; Training Programs; Transcriptional Regulation; Underrepresented Minority; Universities; Wisconsin; Yeasts; arm; base; biological research; biological systems; career; chromatin immunoprecipitation; commercialization; computer science; crosslink; data integration; data management; design; environmental stressor; experience; genome database; genome sequencing; genome-wide; genome-wide analysis; hepatocyte nuclear factor; interest; knowledge base; link protein; mammalian genome; medical schools; mouse genome; new technology; novel strategies; programs; protein complex; research study; response; stoichiometry; technology development; tool; transcription factor; undergraduate student; web site

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.

描述（由申请人提供）：人类基因组和模式生物体序列的成功完成开创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表达和控制的方式上。这个拟议的威斯康星州卓越中心的基因组学科学的重点是促进理解的复杂和综合的调控机制，影响基因转录，通过开发新的技术，全面表征和定量分析与DMA相互作用的蛋白质。这项新技术将有助于提供一个全基因组的功能解释的基础机制，基因转录调控在生物过程中改变，发展，疾病，并在响应生理，药理学，或环境压力。染色质免疫沉淀方法的发展已经允许识别由感兴趣的蛋白质结合的特异性DNA序列。我们建议扭转这一策略，并开发一种全新的技术，将使用寡核苷酸捕获拉下感兴趣的DNA序列，和质谱鉴定和表征的蛋白质和蛋白质复合物结合和特定的DNA区域。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。拟议中的跨学科和多机构基因组科学卓越中心结合了威斯康星州医学院、威斯康星州麦迪逊大学和马奎特大学的具体专业知识。将在四个具体领域进行技术开发以开发这种新方法：（1）蛋白质与DNA的交联和染色质的断裂;（2）以DNA序列特异性方式捕获蛋白质-DNA复合物;（3）质谱分析以鉴定和定量结合的蛋白质，确定翻译后修饰，并表征蛋白质复合物的化学计量;和（4）信息学，以开发能够对蛋白质-DNA相互作用的变化与基因表达之间的关系进行全局分析的工具。该中心将使用从三个物种（酵母、小鼠和人类）中精心挑选的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，我们将联合收割机的技术开发工作与跨学科的培训计划，为学生和研究员，旨在培养合格的科学家在尖端基因组学技术经验。数据、技术和软件将通过多种机制广泛传播，包括许可和商业化活动。 公共卫生相关性开发这种新技术来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，即基因转录。作为CEGS的一部分开发的工具和技术将广泛提供给科学界，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，以及这些调控机制如何在疾病中改变。这些知识将彻底改变我们对基因组生物学的理解，并影响基因组信息如何用于临床医学。