Mapping Transcription Factors Binding Sites in the Mouse Genome

描述(由申请人提供)：大规模的努力正在进行中，以系统地绘制整个人类基因组中转录因子结合位点的图谱。ENCODE项目最初关注的是两个细胞系，1)髓系前体细胞K562细胞和2)淋巴母细胞系GM12878，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，帮助提供这些结合位点的功能信息，并确定这些结合位点是否在体内被占据，我们提出了两种类型的研究。首先，我们将在小鼠MEL和CH12细胞中分别定位至少30个在人类ENCODE项目中分析过的转录因子同源基因的结合位点，这两个细胞分别类似于K562和GM12878细胞。其次，我们将在人CD34+细胞和原代红系小鼠细胞分化的细胞中定位POL II和其他九种因子的结合位点。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，哪些是物种特有的，以及在培养的细胞系中定位的靶点在多大程度上反映了体内的结合位点。来自这些研究的信息将被存入公共数据库，预计将对大型老鼠和人类基因界具有极其宝贵的价值。 与公共卫生相关：ENCODE项目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株具有相似分化状态的小鼠细胞株来扩展这些结果。然后，我们将复制在人类细胞中所做的实验，并根据两个物种之间的序列保守性和因子结合的相似性来定位控制元件。我们还将确定体外鉴定的元素是否存在于从生物体分离的细胞中。

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.