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

基本信息

批准号：
7862508
负责人：
JASON D LIEB
金额：
$ 178.37万
依托单位：
UNIV OF NORTH CAROLINA CHAPEL HILL
依托单位国家：
美国
项目类别：
财政年份：
2007
资助国家：
美国
起止时间：
2007-05-04 至 2013-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7862508
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 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 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 histone modification in vivo meetings mutant programs protein function research study segregation transcription factor

项目摘要

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）：将真核基因组包装到染色质中，该蛋白质调节蛋白质的功能，这些蛋白质介导了转录活性和其他基本过程，包括重组和有丝分裂和减数分裂过程中基因组的忠实分离。该提案的目的是确定在线虫C.秀丽隐杆线虫中调节染色质结构和功能的离散元素，线虫秀丽隐杆线虫是大规模基因组研究和基因功能发现中核心重要性的模型。我们将首先使用CHLP-CHIP和相关方法来映射选定的组蛋白修饰和与染色体相关的蛋白的基因组分布，然后将这些信息与其他Modencode组的数据结合使用，以构建染色质功能的定量模型。具体来说，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素。我们分析的重点将是指定核小体定位和占用率的元素，基因表达的控制结构域，诱导X染色体的抑制作用，指导有丝分裂分离和基因组重复，控制减数分裂过程中同源配对和重新组合，并在原子核内组织染色体定位。 126策略性选择的靶标包括关键组蛋白修饰，组蛋白变体，RNA聚合酶II同工型，剂量补偿蛋白，中心分子成分，同源生成促进剂，重组标记物和核型成分组成部分。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素，并将结果与畅通无阻的秀丽隐杆线虫基因组相结合。 2。在生物学上验证鉴定的功能元素并构建染色体功能的集成的定量模型。我们将将目标1中生成的信息与有关目标生物学的现有知识进行整合，对缺乏所选靶蛋白的突变体和RNAi提取物进行CHLP-CHIP分析，使用核体外阵列来评估候选鉴定的序列基序的能力，以确定序列序列以在体内招募目标，并确定所选目标的组织特异性模型，并创建集成的模型，并建立整体模型，并整合整体。在持续的扩张和秀丽隐杆线虫研究的悠久历史的背景下，实现这些目标将为应对使用基因组序列信息来理解和预测生物学功能的挑战提供一个重要的里程碑。