Tracking Gene Expression Dynamics from Transcription to Degradation

跟踪从转录到降解的基因表达动态

• 批准号: 8912925
• 负责人: Klemens J Hertel
• 金额: $ 28.73万
• 依托单位: UNIVERSITY OF CALIFORNIA-IRVINE
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-03-01 至 2019-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8912925
• 关键词: 3' Untranslated Regions; Bioinformatics; Biological Models; Biology; Breast Epithelial Cells; Calculi; Cell Nucleus; Cells; Communities; Cues; Cytoplasm; Data; Defect; Dependency; Development; Early Diagnosis; Event; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Gene Expression Regulation; Generations; Genes; Genetic Transcription; Genetic Translation; Goals; Human; Investigation; Kinetics; Label; Laboratories; Lead; Length; Life; Location; Longevity; Messenger RNA; Metabolic; Methods; Molecular; Molecular Profiling; Monitor; Nature; Nuclear; Organ; Outcome; Physiologic pulse; Polyadenylation; Polyribosomes; Process; Protein Isoforms; Proteins; RNA; RNA Processing; RNA Splicing; RNA chemical synthesis; Regulation; Research; Research Proposals; Techniques; Testing; Time; Translations; anticancer research; base; cell transformation; cell type; computerized tools; daughter cell; genome-wide; human disease; improved; insight; mRNA Precursor; mRNA Stability; mRNA Transcript Degradation; malignant breast neoplasm; meetings; metaplastic cell transformation; novel; programs; public health relevance; research study; response; screening; tool; tumorigenesis; tumorigenic

 DESCRIPTION (provided by applicant): The regulation of gene expression dictates when, where, and to what degree protein isoforms are generated, thereby meeting the metabolic needs of various cell types that make up organs and living beings. Given the constantly changing microenvironment, this process is highly dynamic, capable of adjusting instantly to multiple external cues, or mounting gene expression responses within extended periods of time. To achieve diverse gene expression responses cells rely on multiple points of regulation that include modulating the origin and rate of transcription, altering pre-mRNA processing to induce the generation of alternatively spliced mRNA isoforms, changing the length or location of the 3' UTR through alternative polyadenylation, selective mRNA isoform translation, and altering the stability of mRNA pools. All of these gene expression steps are integrated and co-dependent. However, our understanding of the dynamic nature of gene expression is limited because most cell-based investigations analyze only steady-state levels of gene expression and because detailed analyses focus only on one of the multiple steps involved in representing a gene expression profile. This research application focuses on evaluating the dynamics of gene expression from pre-mRNA generation through RNA processing in the nucleus to translation and mRNA degradation in the cytoplasm with the long-term goal to chart the life span of all expressed mRNAs upon cellular transformation. We will test the hypothesis that alterations in the kinetics of gene expression steps set in stone unique gene expression programs that dictate cellular fate. Using novel metabolic labeling techniques we will track pre-mRNA dynamics in the nucleus (Aim 1) and mRNA dynamics in the cytoplasm (Aim 2) to develop a comprehensive understanding on the kinetic interplay that establishes steady-state gene expression patterns. Aim 3 will use this understanding and tools to determine to what degree alterations in the dynamics of gene expression steps contribute to the overall change in gene expression profiles that accompany Src-induced breast epithelial cell transformation. The experiments described will highlight how crucial the interplay between transcription, RNA processing and mRNA translation is for the development of altered gene expression programs. Furthermore, understanding the kinetics involved in establishing novel gene expression profiles may pave the way for novel therapies of human breast cancer. Throughout this project we will rely on our expertise in kinetics, RNA biology and bioinformatics to obtain complete kinetic profiles of gene expression unique to Src-induced breast epithelial cell transformation, thus producing a wealth of data useful to the gene expression and breast cancer research communities. The identification of breast cancer-specific gene expression events may be valuable for the development of novel early detection or prediction tools.

 描述（由申请人提供）： 基因表达的调控决定了蛋白质异构体产生的时间、地点和程度，从而满足了组成器官和生物的各种细胞类型的代谢需求。鉴于微环境的不断变化，这一过程是高度动态的，能够立即调整多种外部线索，或在较长的时间内安装基因表达反应。为了实现不同的基因表达反应，细胞依赖于多点调节，包括调节转录的起源和速率， 改变前体mRNA加工以诱导可变剪接的mRNA同种型的产生，通过可变聚腺苷酸化改变3'UTR的长度或位置，选择性mRNA同种型翻译，以及改变mRNA库的稳定性。所有这些基因表达步骤是整合的和相互依赖的。然而，我们对基因表达的动态性质的理解是有限的，因为大多数基于细胞的研究仅分析基因表达的稳态水平，并且因为详细的分析仅集中在代表基因表达谱的多个步骤中的一个。该研究应用程序的重点是评估基因表达的动态，从前体mRNA产生到细胞核中的RNA加工，再到细胞质中的翻译和mRNA降解，其长期目标是绘制细胞转化后所有表达mRNA的寿命。我们将检验这样一个假设，即基因表达动力学的改变是决定细胞命运的独特基因表达程序的一部分。使用新的代谢标记技术，我们将跟踪前mRNA在细胞核中的动态（目标1）和mRNA在细胞质中的动态（目标2），以建立稳态基因表达模式的动力学相互作用的全面理解。目的3将使用这种理解和工具，以确定在何种程度上改变的动态基因表达步骤有助于基因表达谱的整体变化，伴随Src诱导的乳腺上皮细胞转化。所描述的实验将强调转录，RNA加工和mRNA翻译之间的相互作用对于改变基因表达程序的发展是多么重要。此外，了解参与建立新的基因表达谱的动力学可能为人类乳腺癌的新疗法铺平道路。在整个项目中，我们将依靠我们在动力学，RNA生物学和生物信息学方面的专业知识，以获得完整的动力学特征的基因表达独特的Src诱导的乳腺上皮细胞转化，从而产生丰富的数据有用的基因表达和乳腺癌研究社区。乳腺癌特异性基因表达事件的鉴定可能对开发新的早期检测或预测工具有价值。