Tracking transcriptome diversity in real-time

实时跟踪转录组多样性

• 批准号: 10379741
• 负责人: Athma A Pai
• 金额: $ 6.39万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10379741
• 关键词: Address; Biogenesis; Cell physiology; Cells; Computer Analysis; Developmental Process; Disease; Drug Targeting; Equilibrium; Event; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genome; Genomics; Goals; Immune; Immune response; Individual; Kinetics; Knowledge; Logic; Malignant Neoplasms; Messenger RNA; Molecular; Nature; Neuronal Differentiation; Organism; Outcome; Phenotype; Play; Process; Production; RNA; RNA Processing; RNA Splicing; Regulator Genes; Research; Role; Speed; System; Techniques; Therapeutic; Time; Tissues; Transcription Elongation; Work; cell growth regulation; design; functional genomics; high dimensionality; improved; insight; response; spatiotemporal; transcriptome

SUMMARY Recent studies have provided unprecedented insights into how individual molecular mechanisms are correlated to changes in gene expression levels. It is now recognized that substantial transcriptome complexity arises from decisions involved in the processing of nascent mRNAs. However, by and large, the many studies of gene expression have focused on characterizing steady-state mRNA levels, even though living systems are inherently dynamic. Thus, a key open question in functional genomics is: how to the dynamics of individual molecular mechanisms combine to influence the cellular transcriptome? Our overarching hypothesis is that the fate of an mRNA is governed by kinetic interactions underlying molecular efficiency across disparate steps in the mRNA lifecycle – at the core, transcription elongation, mRNA splicing, and 3’ end cleavage. Current knowledge of spatiotemporal coordination across these processes likely represents the tip of the iceberg. In this proposal, we will combine genetic, molecular, and cellular genomic techniques with high-dimensional computational analyses to address two specific themes of mechanistic efficiency. First, we aim to dissect the kinetic basis for efficient mRNA biogenesis and maturation. Work from my research and others has suggested that there is substantial variability in kinetic actions and rate-limiting steps for mature mRNA production across genes. Determining the molecular logic underlying this variability will inform our understanding of the molecular basis for transcriptome complexity in both homeostatic and diseased cells. We will address this issue by answering three questions. 1) What are the kinetics of each individual step in mRNA processing?; 2) What are the factors that govern rate-limiting steps of mature mRNA production; and 3) How does the RNA processing machinery balance speed and accuracy? The goal of the second theme of our research is to determine how RNA processing kinetics underlie the regulation of cellular transitions. The kinetics of gene regulatory processes likely play a crucial role in cellular responses or transitions, by altering the order of molecular events or speed of processes to rapidly regulate gene expression dynamics. To dissect the kinetic plasticity underlying cellular response, we will answer related questions in two disparate systems: 4) How do immune cells rapidly change their transcriptome upon stimulation?; and 5) How is transcriptome complexity regulated upon neuronal differentiation? Our research will result in insights crucial to uncovering the cascade of molecular events that cumulatively establish steady- state gene expression levels, with implications for improved therapeutic designs or strategies that target the early progression of cellular shifts rather than only the final outcome.

概括 最近的研究为个体分子机制如何发挥作用提供了前所未有的见解 现在人们认识到与基因表达水平的变化相关。 转录组的复杂性源于新生 mRNA 加工过程中的决策。 然而，总的来说，许多基因表达研究都集中在表征 尽管生命系统本质上是动态的，但稳定状态的 mRNA 水平因此是一个打开的钥匙。 功能基因组学的问题是：如何研究个体分子机制的动态 结合起来影响细胞转录组？我们的首要假设是，一个人的命运 mRNA 受不同步骤分子效率背后的动力学相互作用控制 在 mRNA 生命周期中——核心是转录延伸、mRNA 剪接和 3' 端切割。 当前对这些过程的时空协调的了解可能代表了 在这个提案中，我们将结合遗传、分子和细胞基因组。 高维计算分析技术来解决两个特定主题 首先，我们的目标是剖析有效 mRNA 生物发生的动力学基础。 我和其他人的研究工作表明，存在大量的问题。 跨基因成熟 mRNA 产生的动力学作用和限速步骤的变异性。 确定这种变异性背后的分子逻辑将有助于我们理解 我们将研究稳态细胞和患病细胞转录组复杂性的分子基础。 通过回答三个问题来解决这个问题：1）每个步骤的动力学是什么。 mRNA 加工过程中？；2) 控制成熟 mRNA 限速步骤的因素有哪些？ 生产；以及 3) RNA 加工机器如何平衡速度和准确性？ 我们研究的第二个主题的目标是确定 RNA 加工动力学的基础 细胞转变的调控可能发挥着至关重要的作用。 通过改变分子事件的顺序或速度，在细胞反应或转变中发挥作用 快速调节基因表达动态的过程来剖析动力学可塑性。 潜在的细胞反应，我们将回答两个不同系统中的相关问题：4）如何 免疫细胞在受到刺激后会迅速改变其转录组吗？；5) 是怎样的？ 转录组复杂性受神经元分化调节？ 洞察力对于揭示分子事件的级联至关重要，这些分子事件累积地建立了稳定的 陈述基因表达水平，对改进的治疗设计或策略有影响 针对细胞转变的早期进展而不仅仅是最终结果。