Characterizing a mechanism of enhancer-promoter interaction in vivo

表征体内增强子-启动子相互作用的机制

• 批准号: 10680165
• 负责人: Grace Cabot Bower
• 金额: $ 4.35万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-30 至 2026-09-29
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10680165
• 关键词: 3-Dimensional; Address; Affect; Architecture; Area; Automobile Driving; Base Pairing; Binding; Bioinformatics; Biological Assay; Cell Nucleus; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Colon Carcinoma; Communication; Complex; Congenital Disorders; DNA; DNA Sequence; DNA Structure; Data; Data Set; Development; Developmental Gene; Disease; Distal; Elements; Embryo; Enhancers; Environment; Fluorescent in Situ Hybridization; Gene Activation; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Gene Transfer Techniques; Genes; Genetic Enhancer Element; Genomics; Goals; Homeobox; Investigation; Knock-out; Limb structure; Link; Malignant Neoplasms; Mediating; Mentors; Methods; Modeling; Multiomic Data; Mus; Mutagenesis; Mutagens; Mutation; Nuclear; Other Genetics; Pathogenesis; Pathology; Play; Property; Protein Family; Regulatory Element; Reporter; Research; Resolution; Role; System; Technical Expertise; Techniques; Testing; Training; Transgenes; Transplantation; Untranslated RNA; Visualization; Work; career development; chromosome conformation capture; craniofacial disorder; design; developmental genetics; genomic locus; homeodomain; in vivo; insight; novel; promoter; remote control; response; superresolution microscopy; tool; transcription factor

PROJECT SUMMARY/ABSTRACT Enhancers are short DNA sequences that regulate complex patterns of gene expression during development. Misregulation of enhancer activity is associated with a wide range of pathologies, from congenital disorders to cancer. However, many properties of enhancers are not well understood, particularly how enhancers act over long genomic distances. While some enhancers are located proximally to their target genes, others are located distally, activating gene expression over thousands or even millions of base pairs of genomic distance. Most in vivo techniques that assess enhancer activity make use of a transgene system that places the enhancer directly upstream of a reporter. While transgenesis is a powerful tool, it cannot assess the role of genomic distance in enhancer activity. To address this, our group developed a novel in vivo mouse enhancer reporter assay to characterize the distal activity of enhancers. Using this method, we identified a novel cis-regulatory sequence, the RC element, that is necessary and sufficient for distal enhancer activity. The overall goal of this proposal is to characterize this newly identified RC element and dissect its role in mediating distal enhancer activity. To address this goal, this proposal outlines a plan to visualize the impact of the RC element on enhancer-promoter interaction (Aim 1) and to determine what factors are critical regulators of RC element function (Aim 2). For the former, both fluorescence in situ hybridization and chromosome capture based techniques will be employed to carefully analyze enhancer-promoter co-localization and overall nuclear organization in the presence and absence of the RC element. For the latter, mutagenesis of the RC element will be used to identify critical motifs. In parallel, knockout of candidate transcription factor regulators will be used to evaluate their importance in RC element-dependent enhancer activity. Findings resulting from this proposal will help elucidate a novel mechanism coordinating enhancer activity, adding to our overall understanding of gene regulation. My sponsor (Dr. Evgeny Kvon) and co-sponsor (Dr. Ken Cho) are experts in the field of developmental genetics, and, with their guidance, I have designed a training plan to help guide my transition to independent research. My plan focuses on developing my abilities in five key areas: technical skills, scientific communication, mentoring, and career development.

项目总结/摘要 增强子是在发育过程中调节基因表达的复杂模式的短DNA序列。 增强子活性的失调与广泛的病理学相关，从先天性疾病到 癌然而，增强子的许多性质还不清楚，特别是增强子如何作用于 长的基因组距离。虽然一些增强子位于其靶基因的近端，但其他增强子位于其靶基因的近端。 在基因组距离的数千甚至数百万个碱基对上激活基因表达。最 评估增强子活性的体内技术利用转基因系统， 一个记者的上游。虽然转基因是一个强大的工具，但它不能评估基因组距离在基因组中的作用。 增强子活性为了解决这个问题，我们的小组开发了一种新的体内小鼠增强子报告基因测定， 表征增强子的远端活性。利用这种方法，我们鉴定了一个新的顺式调控序列， RC元件，其对于远端增强子活性是必需且充分的。本提案的总体目标是 来表征这个新鉴定的RC元件并剖析其在介导远端增强子活性中的作用。到 为了实现这一目标，该提案概述了一个计划，以可视化RC元素对增强子-启动子的影响 相互作用（目标1），并确定哪些因素是RC元件功能的关键调节器（目标2）。为 前者，荧光原位杂交和基于染色体捕获的技术都将用于 仔细分析增强子-启动子共定位和存在下的总体核组织， 没有RC元素。对于后者，RC元件的诱变将用于鉴定关键基序。 同时，敲除候选转录因子调节子将用于评估它们在RC中的重要性。 元件依赖性增强子活性。这项建议的结果将有助于阐明一部小说 协调增强子活性的机制，增加了我们对基因调控的整体理解。我的担保人 (Dr. Evgeny Kvon）和共同赞助人（Ken Cho博士）是发育遗传学领域的专家， 在他们的指导下，我设计了一个培训计划来帮助指导我向独立研究的过渡。我的计划 重点发展我在五个关键领域的能力：技术技能，科学沟通，指导， 职业发展。