Mapping Transcription Factors Binding Sites in the Mouse Genome

绘制小鼠基因组中转录因子结合位点的图谱

• 批准号: 8327327
• 负责人: MICHAEL P. SNYDER
• 金额: $ 65.63万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8327327
• 关键词: Attention; Binding; Binding Sites; Biochemical; Blood; CD34 gene; Cell Line; Cells; Communities; Complement; Complex; DNA Polymerase II; Data; Databases; Deposition; Elements; Erythroid; Erythroid Cells; Eukaryota; Gene Expression; Gene Targeting; Genes; Genetic Transcription; Genome; Guidelines; Hereditary Disease; Human; Human Cell Line; Human Genetics; Human Genome; In Vitro; K-562; K562 Cells; Laboratories; Life; MEL Gene; Maps; Mouse Cell Line; Mus; Myelogenous; Nucleic Acid Regulatory Sequences; Organism; Orthologous Gene; Pattern; Regulatory Element; Reporting; Research Design; Scientist; Site; Transgenic Animals; Vertebrates; analog; base; chromatin immunoprecipitation; data sharing; in vivo; interest; knockout animal; lymphoblastoid cell line; mouse genome; precursor cell; public health relevance; research study; transcription factor

DESCRIPTION (provided by applicant): Large-scale efforts are underway to systematically map transcription factors binding sites throughout the human genome. The ENCODE project has focused its initial attention on two cell lines, 1) K562 cells, a myeloid precursor cell line and 2) GM12878, a lymphoblastoid cell line, and our laboratory has mapped the binding sites of a large number of transcription factor expressed in these cells. To study their conservation and help provide functional information into these binding sites and to determine if these sites are occupied in vivo, we propose two types of studies. First, we will map the binding sites of at least 30 transcription factor orthologs that have been analyzed in the human ENCODE project in mouse MEL and CH12 cells which are analogous to K562 and GM12878 cells, respectively. Second, we will map the binding sites of Pol II and nine other factors in cells differentiated from human CD34+ cells and primary erythroid mouse cells. These studies will determine which transcription factor binding sites and gene targets are conserved in vertebrates and which are species-specific as well as determine the extent to which targets mapped in cultured cell lines reflect in vivo binding sites. The information from these studies will be deposited into public databases and is expected to be extremely valuable to the large mouse and human genetic communities. PUBLIC HEALTH RELEVANCE: The ENCODE project has produced relatively large amounts of data on transcription factor binding and RNA expression in a limited number of human cell lines. We propose to extend these results by obtaining mouse cell lines at similar states of differentiation to human cell lines. We will then duplicate the experiments that have been done in human cells, and locate control elements based on sequence conservation and similarities in factor binding between the two species. We will also determine if elements identified in vitro are occupied in cells isolated from organisms.

描述（由申请人提供）：正在进行大规模的努力来系统地绘制整个人类基因组中的转录因子结合位点。ENCODE项目最初关注两种细胞系，1）K562细胞，骨髓前体细胞系和2）GM12878，淋巴母细胞系，我们的实验室已经绘制了这些细胞中表达的大量转录因子的结合位点。为了研究它们的保守性，并帮助提供这些结合位点的功能信息，并确定这些位点是否在体内被占据，我们提出了两种类型的研究。首先，我们将绘制至少30个转录因子直系同源物的结合位点，这些转录因子直系同源物已在人ENCODE项目中在小鼠MEL和CH12细胞中进行了分析，这些细胞分别类似于K562和GM12878细胞。其次，我们将映射Pol II和其他九种因子在从人CD 34+细胞和原代红系小鼠细胞分化的细胞中的结合位点。这些研究将确定哪些转录因子结合位点和基因靶点在脊椎动物中是保守的，哪些是物种特异性的，以及确定在培养的细胞系中映射的靶点反映体内结合位点的程度。这些研究的信息将被存入公共数据库，预计对大型小鼠和人类遗传社区极具价值。 公共卫生关系：ENCODE项目已经在有限数量的人类细胞系中产生了关于转录因子结合和RNA表达的相对大量的数据。我们建议通过获得与人类细胞系分化状态相似的小鼠细胞系来扩展这些结果。然后，我们将重复在人类细胞中进行的实验，并根据序列保守性和两个物种之间因子结合的相似性定位控制元件。我们还将确定体外鉴定的元件是否在从生物体分离的细胞中被占据。