Investigating the role of genome folding in transcriptional regulation

研究基因组折叠在转录调控中的作用

• 批准号: 10275415
• 负责人: Elphege-Pierre Julien Nora
• 金额: $ 40.38万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-09 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10275415
• 关键词: Address; Architecture; Binding Sites; Biochemical; Biological Assay; Cell Differentiation process; Cell Nucleus; Chromatin; Chromatin Fiber; Chromatin Loop; Chromosome Structures; Chromosomes; Communication; Complex; Coupled; DNA; Disease; Engineering; Enhancers; Etiology; Future; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Goals; Investigation; Link; Malignant Neoplasms; Modality; Molecular; Mus; Mutation; Pathway interactions; Process; Proteins; Reporter; Research; Role; Transcriptional Regulation; cohesin; developmental disease; embryonic stem cell; epigenome; epigenomics; human disease; insight; interest; novel; novel strategies; promoter; tool; transcription factor

Project Summary During transcription, enhancers need to contact gene promoters across large chromosome domains. Chromosome folding can assist enhancer-promoter communication by bringing them close together inside the nucleus. Mutations that alter genome folding underlie many human diseases, including developmental disorders and some cancers. Yet, even after decades of research, we do not understand the causal links between chromatin architecture and transcription regulation. Specifically, we do not understand why DNA looping can correlate positively, negatively, or sometimes not at all with gene activity. To move beyond correlation to causation, we need to better understand the molecular processes that couple genome folding and gene regulation. The cohesin complex has emerged as a key player in DNA looping, because it can hold two chromatin fibers together and extrude DNA loops as it translocates on DNA. Cohesin is loaded on chromatin by its co-factor NIPBL. Cohesin then translocates until it is blocked at binding sites for the CTCF transcription factor. We recently developed tools that allow controlling various aspects of cohesin loop extrusion by manipulating NIPBL and CTCF in mouse embryonic stem cells. These tools provide a novel approach to investigate the relationship between loop extrusion by cohesin and transcription. In this proposed study, we will determine how transcription and loop extrusion are molecularly coupled and elucidate the mechanisms that explain why only some genes rely on loop extrusion to function. We will also address how cohesin loop extrusion contributes to the functions of CTCF during cell differentiation. In addition, we will identify novel pathways that regulate enhancer-promoter communication by modulating loop extrusion. To achieve these goals, we will combine gene editing, epigenomic assays, biochemical assays and novel epigenome engineering modalities with high-throughput reporter assays in mouse embryonic stem cells and their differentiated derivatives. These investigations will substantially deepen our understanding of how genome folding by cohesin proteins influences gene transcription. Completion of this project will open new avenues to explore how these processes go awry in disease, a question our group is interested to investigate in the future.

项目概要 在转录过程中，增强子需要跨大染色体区域接触基因启动子。 染色体折叠可以通过使增强子-启动子在基因组内靠近在一起来帮助它们进行通讯 核。改变基因组折叠的突变是许多人类疾病的根源，包括发育障碍 和一些癌症。然而，即使经过几十年的研究，我们仍然不明白这些因素之间的因果关系。 染色质结构和转录调控。具体来说，我们不明白为什么 DNA 循环可以 与基因活性呈正相关、负相关或有时根本不相关。超越相关性 因果关系，我们需要更好地理解基因组折叠和基因耦合的分子过程 规定。粘连蛋白复合物已成为 DNA 循环中的关键角色，因为它可以容纳两个染色质 当它在 DNA 上易位时，纤维聚集在一起并挤出 DNA 环。粘连蛋白通过其辅因子负载在染色质上 NIPBL。然后粘连蛋白易位，直到它在 CTCF 转录因子的结合位点被阻断。我们最近 开发了可以通过操纵 NIPBL 和控制粘连环挤出的各个方面的工具 小鼠胚胎干细胞中的 CTCF。这些工具提供了一种研究关系的新方法 在粘连蛋白的环挤出和转录之间。在这项拟议的研究中，我们将确定转录如何 和环挤出是分子耦合的，并阐明了解释为什么只有某些基因的机制 依靠循环挤压来发挥作用。我们还将讨论粘连环挤出如何促进功能 细胞分化过程中的CTCF。此外，我们将确定调节增强子-启动子的新途径 通过调制循环挤出进行通信。为了实现这些目标，我们将结合基因编辑、表观基因组学 分析、生化分析和具有高通量报告分析的新型表观基因组工程模式 小鼠胚胎干细胞及其分化衍生物。这些调查将大幅深化 我们对粘连蛋白基因组折叠如何影响基因转录的理解。完成此 该项目将开辟新的途径来探索这些过程如何在疾病中出错，这是我们小组正在解决的一个问题 有兴趣将来研究一下。