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

项目摘要/摘要 我的研究重点是精确理解活细胞和人类疾病中RNA的调节。 在确定改变RNA的因素和元素时，绘制发生调控的位置是至关重要的 表情。进一步提高基因组分辨率和RNA表达的时空分辨率 一直是分子和疾病机制方面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，以增强子RNA(ERNA)为指导。Erna转录是一种新的机制，它 RNA是由增强子序列本身而不是其目标基因合成的。埃尔娜有 扩展了之前对如何构建增强剂并允许映射的重要了解 在更高分辨率的增强子内的子区域。基于ERNA的增强剂地图将引导我们获得更多 高效地发现与疾病基因失调有关的基因组元素，并具体剖析 突变引起的遗传变异或突变这将对人类的主要疾病产生广泛的影响，我的 具体的重点是免疫代谢疾病和ENA起始部位增强子变异的影响。 第二个焦点是导致差异RNA运输、加工、 和腐烂。无膜细胞器，如应激颗粒，被认为是一种新的机制。 通过相分离和隔离控制基因表达。我将探讨这样一个想法，即空间 区划赋予了时间基因表达的特异性。特别是，我将剖析其中的特殊性 应激颗粒中RNA加工在免疫细胞激活和耗竭中的高时间分辨率和 探索它们与疾病相关基因的失调之间的联系。这将导致小说的发现 治疗靶点为相分离过程中的特异性因素。 为了解决这些问题，我的团队利用了高通量RNA测序方法的力量，并且 进一步调整它们。我们开发了新的RNA测序方法，如精密连续测序， 染色质连续测序、末端位移测序和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)尾巴 修饰和RNA封存。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相结合 以具有成本效益的方式进行高空间和时间分辨率的分区。这些创新将 增强了精炼遗传图谱的能力，提高了分析RNA的时空分辨率 表情。我们的任务是发现RNA寿命的关键机制和检查点，重点是 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 在进一步合作努力中绘制地图，以推进人类疾病的精准医学。

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.