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High Resolution Functional Maps of Enhancer RNA and Subcellular RNA Granules in Human Immune Cells

人类免疫细胞中增强子 RNA 和亚细胞 RNA 颗粒的高分辨率功能图谱

基本信息

批准号：
10623195
负责人：
Hojoong Kwak
金额：
$ 40.39万
依托单位：
CORNELL UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-08-01 至 2026-05-31
项目状态：
未结题

项目摘要

Project Abstract/Summary My research focuses on the precise understanding of the regulation of RNA in living cells and human diseases. Mapping where the regulations take place is critical in identifying factors and elements that alter RNA expression. Further enhancing the genomic resolution and the spatiotemporal resolution of RNA expression have been a strong driver of leading discoveries in molecular and disease mechanisms. My first focus is to define the high-resolution maps of the transcriptional enhancers in peripheral blood immune cells, using enhancer RNA (eRNA) as the guide. eRNA transcription is a novel mechanism of which the RNA is synthesized from enhancer sequences themselves other than their target genes. eRNA has expanded the previous understanding of how enhancers are constructed and allowed mapping important subregions within the enhancers in higher resolution. eRNA based maps of enhancers will guide us to more efficiently discover genomic elements linked to the dysregulation of disease genes, and specifically dissect causal genetic variations or mutations. This will have a widespread impact on major human diseases, and my specific focus is on immunometabolic diseases and the impact of enhancer variations at the eRNA start sites. The second focus is on the subcellular compartments that leads to differential RNA trafficking, processing, and decay. Membraneless organelles, such as stress granules, are suggested to be the novel mechanism of gene expression control through phase separation and sequestration. I will explore the idea that spatial compartmentalization confers specificity of temporal gene expression. In particular, I will dissect the specificity of RNA processing in stress granules in high temporal resolution in immune cell activation and exhaustion and explore their linkage to the dysregulation of disease associated genes. This will lead to the discovery of novel therapeutic targets on the specificity factors during the phase separation process. To address these, my group harnesses the power of high throughput RNA sequencing methods, and further tailor them. We developed novel RNA sequencing methods such as Precision Run-On sequencing, Chromatin Run-On sequencing, Tail End Displacement sequencing, and RNA granule sequencing. These methods elucidate multiple aspects of RNA mechanism in high throughput: nascent transcription, poly(A) tail modification, and RNA sequestration. We will continue to improve and develop novel RNA analysis strategies to dissect eRNA transcription, RNA modifications, and combining these methods with subcellular compartmentalization in high spatial and temporal resolution in cost efficient manners. These innovations will lead to enhancements in refining genetic maps and higher spatiotemporal resolution in analyzing RNA expression. Our mission is to discover critical mechanisms and checkpoints of RNA lifespan, focusing on eRNA and RNA granules. This will provide foundations to apply the ideas and methods of high-resolution RNA mapping in further collaborative efforts for advancing the precision medicine of human disease.

项目摘要/总结我的研究重点是精确了解活细胞中 RNA 的调控和人类疾病。绘制法规发生地点对于识别改变 RNA 的因素和元素至关重要表达。进一步增强RNA表达的基因组分辨率和时空分辨率一直是分子和疾病机制领域领先发现的强大推动力。我的第一个重点是定义外周血中转录增强子的高分辨率图谱免疫细胞，使用增强子RNA（eRNA）作为指导。 eRNA转录是一种新机制 RNA是由增强子序列本身而不是其靶基因合成的。 eRNA 有扩展了之前对增强子如何构建的理解并允许映射重要增强器内的分区域具有更高分辨率。基于 eRNA 的增强子图谱将指导我们更多有效地发现与疾病基因失调相关的基因组元件，并有针对性地剖析因果遗传变异或突变。这将对人类重大疾病产生广泛影响，我具体重点是免疫代谢疾病和 eRNA 起始位点增强子变异的影响。第二个重点是亚细胞区室，它导致不同的 RNA 运输、加工、和腐烂。无膜细胞器，如应激颗粒，被认为是新的机制通过相分离和隔离来控制基因表达。我将探讨空间的想法区室化赋予了时间基因表达的特异性。特别是，我将剖析特殊性免疫细胞激活和耗竭过程中应激颗粒中高时间分辨率 RNA 加工的研究探索它们与疾病相关基因失调的联系。这将导致新奇的发现治疗目标是相分离过程中的特异性因素。为了解决这些问题，我的团队利用高通量 RNA 测序方法的力量，并且进一步定制它们。我们开发了新型 RNA 测序方法，例如 Precision Run-On 测序、染色质连续测序、尾端置换测序和 RNA 颗粒测序。这些方法阐明高通量 RNA 机制的多个方面：新生转录、poly(A) 尾修饰和 RNA 隔离。我们将继续改进和开发新的RNA分析策略剖析 eRNA 转录、RNA 修饰，并将这些方法与亚细胞以具有成本效益的方式进行高空间和时间分辨率的划分。这些创新将改进遗传图谱并提高 RNA 分析时空分辨率表达。我们的使命是发现 RNA 寿命的关键机制和检查点，重点关注 eRNA 和 RNA 颗粒。这将为应用高分辨率RNA的思想和方法提供基础规划进一步的合作努力，以推进人类疾病的精准医学。