CTCF dependent chromatin looping dynamics

CTCF 依赖性染色质循环动力学

• 批准号: 8490149
• 负责人: Hideo Mabuchi
• 金额: $ 25.72万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-01 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8490149
• 关键词: Affinity; Antibody Diversity; Behavior; Binding; Binding Sites; Biological Process; CCCTC-binding factor; Cell Extracts; Cell Nucleus; Cells; Chromatin; Chromatin Loop; Chromosome Condensation; Chromosome Segregation; Chromosome Structures; Chromosomes; Code; DNA; DNA Binding; DNA Methylation; Development; Dimerization; Distant; Enhancers; Eukaryotic Cell; Fluorescence; Frequencies; Gene Cluster; Gene Expression; Generations; Genes; Genetic Recombination; Genetic Transcription; Genome; Globin; Goals; Histones; Homodimerization; Human; Immunoglobulins; In Vitro; Individual; Length; Measurement; Measures; Mechanics; Mediating; Methods; Mitotic Chromosome; Modeling; Modification; Molecular Conformation; Mutagenesis; Nuclear; Nucleic Acid Regulatory Sequences; Pattern; Plasmids; Play; Process; Property; Proteins; Regulation; Relative (related person); Role; Site; Spectrum Analysis; Techniques; Testing; Text; Transcriptional Activation; Vertebrates; Zinc Fingers; abstracting; chromatin protein; cohesin; cohesion; gene repression; imprint; in vivo; insight; novel; promoter; public health relevance; research study; single molecule; statistics

Enter the text here that is the new abstract information for your application. The organization of the nucleus and the regulated folding of the genome plays essential roles in regulating gene expression, chromosome segregation and chromosome structure. Long range interactions in chromatin are required for activation of gene transcription and repression of genes during the differentiation of eukaryotic cells. Long-range contacts between different chromosomal loci also regulate processes such as antibody diversity and mitotic chromosome condensation. Despite the wide range of processes that involve chromatin loops we know very little about the mechanisms that drive chromatin folding and stabilize long range interactions in the genome. This proposal is focused on developing new methods to measure the formation of looped domains dependent upon the activity of the chromatin protein CTCF. CTCF is known to be required for the stabilization of looped regions in the genome but how it generates or stabilizes looped domains is unknown. We propose to first characterize the dynamics of CTCF dependent looping using defined chromatin substrates in vitro and on chromatinized plasmids in cell extracts. Using mutagenesis and depletion we will alter the binding affinity and dimerization properties of CTCF and its interaction with the loop stabilizing protein cohesin to determine how these activities regulate the frequency of loop generation. Using the insight we gain from these in vitro experiments we will compare the dynamics of loop formation to the statistics of long range interactions at the human globin locus. By depleting CTCF and cohesin we will relate the cellular statistics of loop formation to the in vitro mechanics of loop stabilization. Our studies should provide unique and novel insight into the processes that regulate the formation of long range chromatin interactions and how they relate to essential developmental and cell biological processes.

在此处输入文本，该文本是您的应用程序的新摘要信息。 细胞核的组织和基因组的调节折叠起着至关重要的作用 调节基因表达、染色体分离和染色体结构。长的 染色质中的一系列相互作用是基因转录激活和抑制所必需的 真核细胞分化过程中的基因。异地之间的远距离接触 染色体位点还调节抗体多样性和有丝分裂染色体等过程 缩合。尽管涉及染色质环的过程很广泛，但我们非常了解 关于驱动染色质折叠和稳定长距离相互作用的机制知之甚少 基因组。该提案的重点是开发新方法来衡量 环状结构域依赖于染色质蛋白 CTCF 的活性。据了解，CTCF 基因组中环状区域的稳定需要它，但它是如何产生或 稳定环状结构域尚不清楚。我们建议首先描述 CTCF 的动态特征 使用体外确定的染色质底物和染色质质粒进行依赖环化 存在于细胞提取物中。通过诱变和耗竭，我们将改变结合亲和力并 CTCF 的二聚特性及其与环稳定蛋白粘连蛋白的相互作用 确定这些活动如何调节循环生成的频率。利用我们的洞察力 从这些体外实验中我们将比较环形成的动力学与 人类珠蛋白位点长程相互作用的统计数据。通过消耗 CTCF 和粘连蛋白 我们将把环形成的细胞统计与环的体外力学联系起来 稳定。我们的研究应该为以下过程提供独特而新颖的见解： 调节长程染色质相互作用的形成以及它们如何与必需的相关 发育和细胞生物学过程。