Identification of DNA Elements Governing Chromatin Function in C elegans

秀丽隐杆线虫中控制染色质功能的 DNA 元件的鉴定

• 批准号: 7417620
• 负责人: JASON D LIEB
• 金额: $ 180.72万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-04 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7417620
• 关键词: Algorithms; Aliquot; Antibodies; Antibody Specificity; Archives; Be++ element; Behavior; Beryllium; Binding; Biological Process; Biology; C. elegans genome; Caenorhabditis elegans; Cell Extracts; Cell Nucleus; Centromere; Chromatin; Chromatin Modeling; Chromatin Structure; Chromosome Pairing; Chromosome Positioning; Chromosomes; Class; DNA; DNA Polymerase II; Data; Databases; Detection; Development; Dosage Compensation (Genetics); Elements; Epigenetic Process; Gene Expression; General Transcription Factors; Genetic Recombination; Genetic Transcription; Genome; Genomics; Germ Cells; Goals; Histone H2B; Histones; Homologous Gene; Immunoblotting; Immunofluorescence Immunologic; Intestines; Knowledge; Location; Maps; Measures; Mediating; Meiosis; Meiotic Recombination; Methods; Micrococcal Nuclease; Mitosis; Mitotic; Modeling; Modification; Molecular Profiling; Muscle; Nematoda; Nerve; Nuclear Envelope; Nuclear Matrix; Nuclear Pore; Nucleosomes; Pattern; Positioning Attribute; Process; Protein Isoforms; Protein Microchips; Proteins; RNA; RNA Interference; RNA Polymerase II; Recording of previous events; Recruitment Activity; Replication Origin; Repression; Research; Research Personnel; Resolution; Shipping; Ships; Sorting - Cell Movement; Specific qualifier value; Structure; Subcutaneous Tissue; Testing; Tissues; Transcription Initiation; Validation; Variant; X Chromosome; base; chromatin protein; design; gene function; genome sequencing; in vivo; mutant; programs; protein function; research study; segregation; transcription factor

DESCRIPTION (provided by applicant): Eukaryotic genomes are packaged into chromatin, which regulates the function of proteins that mediate transcriptional activity and other essential processes, including recombination and the faithful segregation of the genome during mitosis and meiosis. The goal of this proposal is to identify discrete elements that regulate chromatin structure and function in the nematode C. elegans, a model metazoan of central importance in large-scale genomic research and gene function discovery. We will first use ChlP-chip and related methods to map the genomic distributions of selected histone modifications and chromosome-associated proteins, and then use that information, in combination with data from other modENCODE groups, to build quantitative models of chromatin function. Specifically, we will: 1. Identify and technically validate functional elements that control chromatin and chromosome behavior. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. An efficient pipeline design will facilitate identification and validation of the different classes of functional elements associated with these targets and will integrate the results with the well-annotated C. elegans genome. 2. Biologically validate identified functional elements and build integrated, quantitative models of chromosome function. We will integrate information generated in Aim 1 with existing knowledge on the biology of the targets, perform ChlP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions. Achieving these goals in the context of the ongoing expansion and rich history of C. elegans research will provide an important milestone in meeting the challenge of using genome sequence information to understand and predict biological functions.

描述（由申请人提供）：真核基因组包装在染色质中，染色质调节介导转录活性和其他基本过程的蛋白质的功能，包括有丝分裂和减数分裂期间基因组的重组和忠实分离。这个计划的目标是确定在线虫C中调节染色质结构和功能的离散元件。elegans，一种在大规模基因组研究和基因功能发现中具有重要意义的模式后生动物。我们将首先使用ChIP芯片和相关方法来绘制选定的组蛋白修饰和染色体相关蛋白的基因组分布，然后使用该信息，结合其他modENCODE组的数据，建立染色质功能的定量模型。具体而言，我们将： 1.识别和技术验证控制染色质和染色体行为的功能元件。 我们分析的重点将是指定核小体定位和占用，控制基因表达的结构域，诱导X染色体的抑制，引导有丝分裂分离和基因组复制，在减数分裂过程中管理同源配对和重组，并组织细胞核内的染色体定位的元素。126个战略选择的目标包括关键组蛋白修饰，组蛋白变体，RNA聚合酶II亚型，剂量补偿蛋白，着丝粒成分，同源配对促进剂，重组标记和核包膜成分。一个有效的管道设计将有助于识别和验证与这些目标相关的不同类别的功能元件，并将结果与注释良好的C。线虫基因组 2.生物学验证已识别的功能元件，并建立染色体功能的综合定量模型。 我们将整合目标1中产生的信息与目标生物学的现有知识，对缺乏选定目标蛋白的突变体和RNAi提取物进行ChIP芯片分析，使用染色体外阵列评估候选识别序列基序在体内招募目标的能力，识别选定目标的组织特异性模式，并创建转录和全染色体功能的综合定量模型。 实现这些目标的背景下，不断扩大和丰富的历史，C。线虫的研究将是一个重要的里程碑，有助于利用基因组序列信息了解和预测生物功能。