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RNA在活细胞和人类疾病中的调节。 绘制调控发生的位置对于识别改变RNA的因子和元件至关重要 表情进一步提高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的主要发现的强大驱动力。 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转录是一种新的机制， RNA由增强子序列本身而不是其靶基因合成。eRNA具有 扩展了以前对增强子如何构建的理解，并允许映射重要的 增强子内的子区域以更高的分辨率。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，并特异性地剖析 因果性遗传变异或突变。这将对人类重大疾病产生广泛影响， 特别关注免疫代谢疾病和eRNA起始位点增强子变异的影响。 第二个重点是亚细胞区室，导致差异RNA运输，加工， 和腐烂无膜细胞器，如应激颗粒，被认为是新的机制， 通过相分离和螯合控制基因表达。我将探讨空间 区室化赋予时间基因表达的特异性。特别是，我将剖析 在免疫细胞激活和耗竭中，以高时间分辨率观察应激颗粒中的RNA加工， 探索它们与疾病相关基因失调的联系。这将导致新的发现 在相分离过程中的特异性因素的治疗目标。 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， 进一步调整它们。我们开发了新的RNA测序方法，如精确运行测序， 染色质连续测序、尾端置换测序和RNA颗粒测序。这些 方法阐明了高通量RNA机制的多个方面：新生转录，poly（A）尾 修饰和RNA螯合。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，并结合这些方法与亚细胞 以成本有效的方式以高空间和时间分辨率进行划分。这些创新将 导致改进遗传图谱和分析RNA时更高时空分辨率 表情我们的使命是发现RNA寿命的关键机制和检查点，重点是 eRNA和RNA颗粒。这将为高分辨率RNA的思路和方法的应用提供基础 在进一步的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.