Identifying chromosomal regions associated with glucocorticoid-regulated gene transcription

鉴定与糖皮质激素调节基因转录相关的染色体区域

• 批准号: 9468952
• 负责人: Delsy Martinez
• 金额: $ 3.84万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2019-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9468952
• 关键词: A549; Affect; Binding; Binding Proteins; Binding Sites; CCCTC-binding factor; Cell Nucleus; Cells; ChIP-seq; Characteristics; Chromatin Loop; Collaborations; Complex; DNA; Dexamethasone; Disease; Elements; Enhancers; Etiology; Gene Expression Regulation; Gene Targeting; Genes; Genetic Transcription; Genome; Genomic Segment; Genomics; Glucocorticoid Receptor; Glucocorticoids; Histones; Learning; Ligands; Ligation; Link; Mutagenesis; Mutation; Nuclear; Outcome; Play; Positioning Attribute; Property; RNA; Response Elements; Role; Sampling; Specificity; Structure; Testing; Time; Transcription Initiation Site; Transcriptional Regulation; Work; chromatin modification; cohesin; experimental study; glucocorticoid receptor alpha; in vivo; innovation; insight; interest; lung Carcinoma; promoter; structural genomics; therapeutic development; transcription factor; transcriptome sequencing

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.

项目总结 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 各方面仍不得而知。基因组在空间上被组织成进一步由兆数据库组成的隔间 称为拓扑结合结构域(TADS)的结构，具有类似的染色质修饰和 组蛋白痕迹。TAD的边界由粘附素复合体和CCCTC结合因子来划分 (CTCF)。据推测，反应元件，转录因子通常与之结合的DNA片段 增加或减少基因转录，在TAD范围内与基因启动子相互作用。脱氧核糖核酸 在线性基因组上，反应元件可以相距很远，但染色质环会使这些元件接近 核内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。事实证明，很难 识别响应元件及其同源启动子，从而确定后生动物之间的关系 转录调控和基因组排列还没有定义。 这个项目的第一个目标是确定功能反应元件及其同源调控 推动者(目标1)。我将利用糖皮质激素受体(GR)的特性，这是一种转录调节因子 其基因组结合和调节活性需要糖皮质激素配体预先结合的因子。 糖皮质激素受体反应元件(GRE)是DNA片段，在体内具有调节作用 但目前还不知道哪个GR结合位点是GRE，以及它针对的是哪个特定基因。然后我会评估 相对于已确认的糖皮质激素反应元件(GRE)的染色质环的形成和位置 启动子对，以及环简并测试(目标2)。最后，我将研究TAD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GRE及其目标基因的方案。这项工作将为我们提供 对基因调控和TAD调控结构有深入的了解。