Identifying chromosomal regions associated with glucocorticoid-regulated gene transcription

项目摘要 基因组在细胞核中的排列方式在基因调控中起着重要作用，但有几个 方面仍然未知。基因组在空间上被组织成进一步由巨噬细胞组成的隔室 称为拓扑关联结构域（TADs）的结构，具有相似的染色质修饰， 组蛋白标记。细胞边界由粘着蛋白复合物和CCCTC结合因子划分 （CTCF）。据推测，反应元件，即转录因子通常结合的DNA片段， 增加或减少基因转录，与基因启动子相互作用的范围内的一个基因。DNA 在线性基因组上，反应元件可以相距很远，但染色质环使这些元件接近 在细胞核中进行基因转录的基因启动子。我的目标是研究基因之间的关系 转录和两个更高级的基因组结构，染色质环和TADs。已经证明难以 鉴定应答元件及其同源启动子，从而鉴定后生动物之间的关系， 转录调控和基因组排列尚未定义。 本项目的第一个目标是确定功能反应元件及其同源调控 启动子（目标1）。我将利用糖皮质激素受体（GR）的特性， 其基因组结合和调节活性需要先与糖皮质激素配体结合的因子。 糖皮质激素受体反应元件（GR）是在体内赋予调节作用的DNA片段 但不知道哪个GR结合位点是GRE以及它靶向哪个特定基因。然后我会评估 染色质环相对于经验证的糖皮质激素反应元件（GRE）的形成和位置- 启动子对，并测试环简并性（Aim 2）。最后，我将研究边界是否限制了 循环和GRE动作（目标3）。 这项提案将是第一个正确识别GRES及其靶基因的提案。这项工作将为我们提供 对基因调控和转录调控结构有深入的了解。

PROJECT SUMMARY The way the genome is arranged in the nucleus plays an important role in gene regulation but several aspects remain unknown. Genomes are spatially organized into compartments further made up of megabase structures called topologically associating domains (TADs) that have similar chromatin modifications and histone marks. TAD boundaries are demarcated by the Cohesin complex and the CCCTC binding factor (CTCF). It is presumed that response elements, segments of DNA where transcription factors typically bind to increase or decrease gene transcription, interact with promoters of genes within the scope of a TAD. DNA response elements can be far apart on a linear genome but chromatin loops bring these elements in proximity of gene promoters for gene transcription in the nucleus. I aim to investigate the relationship between gene transcription and two higher-order genome structures, chromatin loops and TADs. It has proven difficult to identify response elements and their cognate promoters thus the relationship between metazoan transcriptional regulation and genomic arrangements has not been defined. The first objective of this project is to identify functional response elements and their cognate regulated promoters (Aim 1). I will exploit the properties of the glucocorticoid receptor (GR), a transcriptional regulatory factor whose genomic binding and regulatory activities require prior binding by glucocorticoid ligands. Glucocorticoid receptor response elements (GREs) are segments of DNA that confer a regulatory action in vivo but it is not known which GR binding site is a GRE and which specific gene it targets. I will then assess the formation and positions of chromatin loops relative to validated glucocorticoid response element (GRE) – promoter pairs, and test for loop degeneracy (Aim 2). Finally, I shall examine whether TAD boundaries limit looping and GRE action (Aim 3). This proposal will be the first to properly identify GREs and their target genes. This work will provide us with insight regarding gene regulation and TAD regulatory structure.