Deciphering the contribution of enhancer transcription to enhancer function

破译增强子转录对增强子功能的贡献

• 批准号: 10533734
• 负责人: Carlos Guzman
• 金额: $ 3.41万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-01 至 2023-09-22
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10533734
• 关键词: 3-Dimensional; ATAC-seq; Area; Binding; Binding Sites; Biological Assay; Biology; CRISPR interference; Cell Nucleus; Chromatin; Coupled; DNA Sequence; Data; Disease; Elements; Enhancers; Environment; Event; Fellowship; Funding; Gene Activation; Genes; Genetic Enhancer Element; Genetic Transcription; Genome; Genomics; Goals; Health; Histone Acetylation; Individual National Research Service Award; Inflammatory; Knock-out; Learning; Link; Macrophage; Maps; Measurement; Measures; Mediating; Messenger RNA; Modeling; Molecular; Molecular Biology; Molecular Biology Techniques; Mus; Mutation; Nucleosomes; Plasmids; Postdoctoral Fellow; Proteins; RNA; RNA Polymerase II; Ramp; Regulator Genes; Regulatory Element; Reporter; Research; Research Design; Resolution; Role; Scientist; Signal Pathway; Signal Transduction; Site; Stimulus; Structure; Techniques; Testing; Textbooks; Time; Training; Transcript; Transcription Initiation; Transcription Initiation Site; Transcriptional Activation; Transcriptional Regulation; Universities; Untranslated RNA; Work; genetic variant; in vivo; next generation sequencing; novel; pre-doctoral; programs; promoter; recruit; response; skills; three dimensional structure; transcription factor; transmission process

PROJECT SUMMARY/ABSTRACT The applicant is requesting two years of support from a Ruth L. Kirschstein National Research Service Award for Individual Predoctoral Fellowship to Promote Diversity in Health-Related Research (F31-Diversity) to examine the relationship between enhancer transcription and enhancer function. Enhancers have been shown to initiate short, non-coding transcripts in quantities rivaling promoters, yet their role on enhancer function remains controversial. My preliminary data suggests that enhancers and promoters synchronize their activity to form co- regulated domains. This result is surprising given that previous studies using total RNA measurements have indicated that enhancer eRNAs ramp up before their associated mRNAs, suggesting that enhancers get activated first and that this activation then gets transmitted to the associated promoters. Co-regulated domains explain several of the mechanisms that the textbook model of enhancer function fails to. These include that enhancer sequences are indistinguishable from promoters, that they are bound and initiate transcription by RNA polymerase II, that enhancers and promoters form hubs in the nucleus, that enhancers act in an additive or synergistic manner, and the redundancies observed when knocking out single enhancers in a multi-enhancer locus. The goal of this research is to test the hypothesis that enhancers may function by serving as simultaneously activated and mutually reinforcing transcription initiation sites within CRDs. This hypothesis implies that enhancer transcription would be essential for enhancer function. I will test this hypothesis in three specific aims: (1) determine the generality of enhancer-promoter co-regulatory domains across signaling responses, to uncover whether the formation of co-regulated domains are a general regulatory mechanism underlying signal response (2) determine the relationship between enhancer transcription and enhancer function outside of their native genomic environment, to examine the relationship between enhancer transcription and enhancer function outside of their native genomic context, and (3) determine the impact of silencing enhancer transcription on gene activation in vivo, to determine the influence that shutting down enhancer transcription ahs on enhancer function in its native genomic context. This training will allow me to (1) develop skills in the areas of research design, analysis and interpretation using next-generation sequencing and molecular biology techniques; (2) learn the fundamentals of molecular, chromatin, and enhancer biology; (3) successfully defend a dissertation; and (4) obtain a competitive post-doctoral fellowship with the long-term goal to become a successful, independently-funded scientist at a research-intensive university.

项目摘要/摘要 申请人要求获得露丝·柯希斯坦国家研究服务奖的两年支持 为了促进与健康相关研究的多样性（F31多样性）的各个奖学金 增强子转录和增强子功能之间的关系。增强剂已被证明启动 短而非编码的成绩单与启动子媲美，但它们在增强子功能上的作用仍然存在 有争议的。我的初步数据表明，增强子和启动子同步其活动以形成共同 受管域。鉴于先前使用总RNA测量的研究具有 表明增强剂Ernas在其相关mRNA之前升起，这表明增强剂得到 首先激活，然后将此激活传输到相关的启动子。共同调节的域 说明增强器功能教科书模型无法做到的几种机制。其中包括 增强子序列与启动子没有区别，它们是绑定的，并通过RNA启动转录 聚合酶II，增强子和启动子在细胞核中形成枢纽，增强子在添加剂或 在多增强器中淘汰单个增强剂时，协同方式和冗余 轨迹。这项研究的目的是检验以下假设，即增强子可以通过作为 同时激活和相互加强CRD中的转录起始位点。这个假设 这意味着增强子转录对于增强子功能至关重要。我将在三个中检验这一假设 具体目的：（1）确定信号跨信号范围的增强子促销共同调节域的通用性 响应，以发现共同调节域的形成是否是一般调节机制 基础信号响应（2）确定增强子转录和增强子函数之间的关系 在其本地基因组环境之外，检查增强子转录与 增强子功能在其本地基因组环境之外，（3）确定沉默增强子的影响 对体内基因激活的转录，以确定关闭增强子转录AHS的影响 在其天然基因组环境中增强子功能。这项培训将使我（1）在该领域发展技能 研究设计，分析和解释使用下一代测序和分子生物学 技术； （2）学习分子，染色质和增强蛋白生物学的基础知识； （3）成功防守 论文； （4）获得具有竞争性的博士后奖学金，其长期目标成为 一所研究密集于大学的成功，独立资助的科学家。